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haskell-igraph 0.8.0 → 0.8.5

raw patch · 261 files changed

+8385/−5142 lines, 261 filesdep +singletons-basedep +singletons-thdep ~basedep ~singletonsnew-uploader

Dependencies added: singletons-base, singletons-th

Dependency ranges changed: base, singletons

Files

ChangeLog.md view
@@ -1,7 +1,13 @@ Revision history for haskell-igraph =================================== -v0.8.0 -- XXXX-XX-XX+v0.8.5 -- 2025-08-05+--------------------++* Ship igraph C sources v0.8.5+* Add more functions++v0.8.0 -- 2020-02-22 --------------------  * Ship igraph C sources v0.8.0
LICENSE view
@@ -1,4 +1,4 @@-Copyright (c) 2016-2020 Kai Zhang+Copyright (c) 2016-2021 Kai Zhang  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the
cbits/bytestring.c view
@@ -342,7 +342,7 @@   igraph_strvector_t *str;   size_t i;   igraph_strvector_init(str, from->len);-  for (i = 0; i++; i < from->len) {+  for (i = 0; i < from->len; i++) {     igraph_strvector_set(str, i, bytestring_to_char(from->data[i]));   }   return str;@@ -352,7 +352,7 @@   bsvector_t *str;   size_t i;   bsvector_init(str, from->len);-  for (i = 0; i++; i < from->len) {+  for (i = 0; i < from->len; i++) {     bsvector_set(str, i, char_to_bytestring(from->data[i]));   }   return str;
+ cbits/bytestring.h view
@@ -0,0 +1,115 @@+#ifndef HASKELL_IGRAPH_BYTESTRING+#define HASKELL_IGRAPH_BYTESTRING++#include "igraph.h"++__BEGIN_DECLS++typedef struct bytestring_t {+  unsigned long int len;+  char *value;+} bytestring_t;++typedef struct bsvector_t {+  bytestring_t **data;+  long int len;+} bsvector_t;++#define BSVECTOR_INIT_FINALLY(v, size) \+  do { IGRAPH_CHECK(bsvector_init(v, size)); \+  IGRAPH_FINALLY(bsvector_destroy, v); } while (0)++/**+ * \define STR+ * Indexing string vectors+ *+ * This is a macro which allows to query the elements of a string vector in+ * simpler way than \ref igraph_strvector_get(). Note this macro cannot be+ * used to set an element, for that use \ref igraph_strvector_set().+ * \param sv The string vector+ * \param i The the index of the element.+ * \return The element at position \p i.+ *+ * Time complexity: O(1).+ */+#define BS(sv,i) ((const bytestring_t *)((sv).data[(i)]))++int bsvector_init(bsvector_t *sv, long int len);++DECLDIR void bsvector_destroy(bsvector_t *sv);++DECLDIR void bsvector_get(const bsvector_t *sv, long int idx, bytestring_t **value);++DECLDIR int bsvector_set(bsvector_t *sv, long int idx, const bytestring_t *value);++DECLDIR void bsvector_remove_section(bsvector_t *v, long int from, long int to);++DECLDIR void bsvector_remove(bsvector_t *v, long int elem);++/*+void bsvector_move_interval(bsvector_t *v, long int begin,+				   long int end, long int to) {+  long int i;+  assert(v != 0);+  assert(v->data != 0);+  for (i=to; i<to+end-begin; i++) {+    if (v->data[i] != 0) {+      destroy_bytestring(v->data[i]);+    }+  }+  for (i=0; i<end-begin; i++) {+    if (v->data[begin+i] != 0) {+      size_t len=strlen(v->data[begin+i])+1;+      v->data[to+i]=igraph_Calloc(len, char);+      memcpy(v->data[to+i], v->data[begin+i], sizeof(char)*len);+    }+  }+}+*/++int bsvector_copy(bsvector_t *to, const bsvector_t *from);++int bsvector_append(bsvector_t *to, const bsvector_t *from);++void bsvector_clear(bsvector_t *sv);++int bsvector_resize(bsvector_t* v, long int newsize);++/**+ * \ingroup strvector+ * \function igraph_strvector_permdelete+ * \brief Removes elements from a string vector (for internal use)+ */++void bsvector_permdelete(bsvector_t *v, const igraph_vector_t *index,+				long int nremove);++/**+ * \ingroup strvector+ * \function igraph_strvector_remove_negidx+ * \brief Removes elements from a string vector (for internal use)+ */++void bsvector_remove_negidx(bsvector_t *v, const igraph_vector_t *neg,+				   long int nremove);++int bsvector_index(const bsvector_t *v, bsvector_t *newv,+                   const igraph_vector_t *idx);++long int bsvector_size(const bsvector_t *sv);++bytestring_t* new_bytestring(int n);++void destroy_bytestring(bytestring_t* str);++char* bytestring_to_char(bytestring_t* from);++bytestring_t* char_to_bytestring(char* from);++igraph_strvector_t* bsvector_to_strvector(bsvector_t* from);++bsvector_t* strvector_to_bsvector(igraph_strvector_t* from);++__END_DECLS++#endif
cbits/haskell_attributes.c view
@@ -466,8 +466,6 @@       }       if (oldrec->type == IGRAPH_ATTRIBUTE_STRING) { 				if (ne != bsvector_size(newstr)) {-					printf("number of edges: %d\n", ne);-					printf("number of attributes: %d\n", bsvector_size(newstr)); 					IGRAPH_ERROR("Invalid string attribute length", IGRAPH_EINVAL); 				} 				IGRAPH_CHECK(bsvector_append(oldstr, newstr));
+ cbits/haskell_attributes.h view
@@ -0,0 +1,218 @@+#ifndef HASKELL_IGRAPH_ATTRIBUTE+#define HASKELL_IGRAPH_ATTRIBUTE++#include "igraph.h"+#include "bytestring.h"++#include <string.h>++igraph_bool_t igraph_haskell_attribute_find(const igraph_vector_ptr_t *ptrvec,+				       const char *name, long int *idx);++typedef struct igraph_haskell_attributes_t {+  igraph_vector_ptr_t gal;+  igraph_vector_ptr_t val;+  igraph_vector_ptr_t eal;+} igraph_haskell_attributes_t;++int igraph_haskell_attributes_copy_attribute_record(igraph_attribute_record_t **newrec,+					       const igraph_attribute_record_t *rec);+++int igraph_haskell_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr);++void igraph_haskell_attribute_destroy(igraph_t *graph);++void igraph_haskell_attribute_copy_free(igraph_haskell_attributes_t *attr);++int igraph_haskell_attribute_copy(igraph_t *to, const igraph_t *from,+			     igraph_bool_t ga, igraph_bool_t va, igraph_bool_t ea);++int igraph_haskell_attribute_add_vertices(igraph_t *graph, long int nv,+				     igraph_vector_ptr_t *nattr);++void igraph_haskell_attribute_permute_free(igraph_vector_ptr_t *v);++int igraph_haskell_attribute_permute_vertices(const igraph_t *graph,+					 igraph_t *newgraph,+					 const igraph_vector_t *idx);++int igraph_haskell_attribute_combine_vertices(const igraph_t *graph,+			 igraph_t *newgraph,+			 const igraph_vector_ptr_t *merges,+			 const igraph_attribute_combination_t *comb);++int igraph_haskell_attribute_add_edges(igraph_t *graph, const igraph_vector_t *edges,+				 igraph_vector_ptr_t *nattr);++int igraph_haskell_attribute_permute_edges(const igraph_t *graph,+				      igraph_t *newgraph,+				      const igraph_vector_t *idx);++int igraph_haskell_attribute_combine_edges(const igraph_t *graph,+			 igraph_t *newgraph,+			 const igraph_vector_ptr_t *merges,+			 const igraph_attribute_combination_t *comb);++int igraph_haskell_attribute_get_info(const igraph_t *graph,+				 igraph_strvector_t *gnames,+				 igraph_vector_t *gtypes,+				 igraph_strvector_t *vnames,+				 igraph_vector_t *vtypes,+				 igraph_strvector_t *enames,+				 igraph_vector_t *etypes);++igraph_bool_t igraph_haskell_attribute_has_attr(const igraph_t *graph,+					 igraph_attribute_elemtype_t type,+					 const char *name);++int igraph_haskell_attribute_gettype(const igraph_t *graph,+			      igraph_attribute_type_t *type,+			      igraph_attribute_elemtype_t elemtype,+			      const char *name);++int igraph_haskell_attribute_get_numeric_graph_attr(const igraph_t *graph,+					      const char *name,+					      igraph_vector_t *value);++int igraph_haskell_attribute_get_bool_graph_attr(const igraph_t *graph,+					    const char *name,+					    igraph_vector_bool_t *value);++int igraph_haskell_attribute_get_string_graph_attr(const igraph_t *graph,+					     const char *name,+					     igraph_strvector_t *value_);++int igraph_haskell_attribute_get_numeric_vertex_attr(const igraph_t *graph,+					      const char *name,+					      igraph_vs_t vs,+					      igraph_vector_t *value);++int igraph_haskell_attribute_get_bool_vertex_attr(const igraph_t *graph,+					     const char *name,+					     igraph_vs_t vs,+					     igraph_vector_bool_t *value);++int igraph_haskell_attribute_get_string_vertex_attr(const igraph_t *graph,+					     const char *name,+					     igraph_vs_t vs,+					     igraph_strvector_t *value_);++int igraph_haskell_attribute_get_numeric_edge_attr(const igraph_t *graph,+					    const char *name,+					    igraph_es_t es,+					    igraph_vector_t *value);++int igraph_haskell_attribute_get_string_edge_attr(const igraph_t *graph,+					   const char *name,+					   igraph_es_t es,+					   igraph_strvector_t *value_);++int igraph_haskell_attribute_get_bool_edge_attr(const igraph_t *graph,+					   const char *name,+					   igraph_es_t es,+					   igraph_vector_bool_t *value);++igraph_real_t igraph_haskell_attribute_GAN(const igraph_t *graph, const char *name);++igraph_bool_t igraph_haskell_attribute_GAB(const igraph_t *graph, const char *name);++const bytestring_t* igraph_haskell_attribute_GAS(const igraph_t *graph, const char *name);++igraph_real_t igraph_haskell_attribute_VAN(const igraph_t *graph, const char *name,+				      igraph_integer_t vid);++igraph_bool_t igraph_haskell_attribute_VAB(const igraph_t *graph, const char *name,+				    igraph_integer_t vid);++const bytestring_t* igraph_haskell_attribute_VAS(const igraph_t *graph, const char *name,+				    igraph_integer_t vid);++igraph_real_t igraph_haskell_attribute_EAN(const igraph_t *graph, const char *name,+				      igraph_integer_t eid);++igraph_bool_t igraph_haskell_attribute_EAB(const igraph_t *graph, const char *name,+				    igraph_integer_t eid);++const bytestring_t* igraph_haskell_attribute_EAS(const igraph_t *graph, const char *name,+				    igraph_integer_t eid);++int igraph_haskell_attribute_VANV(const igraph_t *graph, const char *name,+			   igraph_vs_t vids, igraph_vector_t *result);++int igraph_haskell_attribute_VABV(const igraph_t *graph, const char *name,+			   igraph_vs_t vids, igraph_vector_bool_t *result);++int igraph_haskell_attribute_EANV(const igraph_t *graph, const char *name,+			   igraph_es_t eids, igraph_vector_t *result);++int igraph_haskell_attribute_EABV(const igraph_t *graph, const char *name,+			   igraph_es_t eids, igraph_vector_bool_t *result);++int igraph_haskell_attribute_VASV(const igraph_t *graph, const char *name,+			   igraph_vs_t vids, igraph_strvector_t *result);++int igraph_haskell_attribute_EASV(const igraph_t *graph, const char *name,+			   igraph_es_t eids, igraph_strvector_t *result);++int igraph_haskell_attribute_list(const igraph_t *graph,+			   igraph_strvector_t *gnames, igraph_vector_t *gtypes,+			   igraph_strvector_t *vnames, igraph_vector_t *vtypes,+			   igraph_strvector_t *enames, igraph_vector_t *etypes);++int igraph_haskell_attribute_GAN_set(igraph_t *graph, const char *name,+			      igraph_real_t value);++int igraph_haskell_attribute_GAB_set(igraph_t *graph, const char *name,+			      igraph_bool_t value);++int igraph_haskell_attribute_GAS_set(igraph_t *graph, const char *name,+			      const bytestring_t *value);++int igraph_haskell_attribute_VAN_set(igraph_t *graph, const char *name,+			      igraph_integer_t vid, igraph_real_t value);++int igraph_haskell_attribute_VAB_set(igraph_t *graph, const char *name,+			      igraph_integer_t vid, igraph_bool_t value);++int igraph_haskell_attribute_VAS_set(igraph_t *graph, const char *name,+			      igraph_integer_t vid, const bytestring_t *value);++int igraph_haskell_attribute_EAN_set(igraph_t *graph, const char *name,+			      igraph_integer_t eid, igraph_real_t value);++int igraph_haskell_attribute_EAB_set(igraph_t *graph, const char *name,+			      igraph_integer_t eid, igraph_bool_t value);++int igraph_haskell_attribute_EAS_set(igraph_t *graph, const char *name,+			      igraph_integer_t eid, const bytestring_t *value);++int igraph_haskell_attribute_VAN_setv(igraph_t *graph, const char *name,+			       const igraph_vector_t *v);++int igraph_haskell_attribute_VAB_setv(igraph_t *graph, const char *name,+			       const igraph_vector_bool_t *v);++int igraph_haskell_attribute_VAS_setv(igraph_t *graph, const char *name,+			       const bsvector_t *sv);++int igraph_haskell_attribute_EAN_setv(igraph_t *graph, const char *name,+			       const igraph_vector_t *v);++int igraph_haskell_attribute_EAB_setv(igraph_t *graph, const char *name,+			       const igraph_vector_bool_t *v);++int igraph_haskell_attribute_EAS_setv(igraph_t *graph, const char *name,+			       const bsvector_t *sv);++void igraph_haskell_attribute_free_rec(igraph_attribute_record_t *rec);++void igraph_haskell_attribute_remove_g(igraph_t *graph, const char *name);++void igraph_haskell_attribute_remove_v(igraph_t *graph, const char *name);++void igraph_haskell_attribute_remove_e(igraph_t *graph, const char *name);++void igraph_haskell_attribute_remove_all(igraph_t *graph, igraph_bool_t g,+				  igraph_bool_t v, igraph_bool_t e);+#endif
+ cbits/haskell_igraph.h view
@@ -0,0 +1,8 @@+#ifndef HASKELL_IGRAPH+#define HASKELL_IGRAPH++#include "igraph.h"++void haskelligraph_init();++#endif
haskell-igraph.cabal view
@@ -1,653 +1,860 @@-cabal-version:       2.2-name:                haskell-igraph-version:             0.8.0-synopsis:            Bindings to the igraph C library (v0.8.0).-description:         igraph<"http://igraph.org/c/"> is a library for creating-                     and manipulating large graphs. This package provides the Haskell-                     interface of igraph.-license:             MIT-license-file:        LICENSE-author:              Kai Zhang-maintainer:          kai@kzhang.org-copyright:           (c) 2016-2020 Kai Zhang-category:            Math-build-type:          Simple-extra-source-files:-  include/*.h-  igraph/include/*.h-  igraph/include/*.pmt-  igraph/include/f2c/*.h-  igraph/include/prpack/*.h-  igraph/include/cs/*.h-  igraph/include/cliquer/*.h-  igraph/include/bliss/*.hh-  igraph/include/plfit/*.h-  igraph/AUTHORS-  igraph/COPYING-  stack.yaml-  README.md-  ChangeLog.md--library-  exposed-modules:-    IGraph.Internal.Initialization-    IGraph.Internal.Constants-    IGraph.Internal-    IGraph-    IGraph.Mutable-    IGraph.Random-    IGraph.Types-    IGraph.Algorithms-    IGraph.Algorithms.Structure-    IGraph.Algorithms.Community-    IGraph.Algorithms.Clique-    --IGraph.Algorithms.Layout-    IGraph.Algorithms.Motif-    IGraph.Algorithms.Generators-    IGraph.Algorithms.Isomorphism-    IGraph.Algorithms.Centrality--  other-modules:-    IGraph.Internal.C2HS--  build-depends:-      base >= 4.0 && < 5.0-    , bytestring >= 0.9-    , cereal-    , conduit >= 1.3.0-    , containers-    , data-ordlist-    , primitive-    , singletons--  extra-libraries:     stdc++-  hs-source-dirs:      src-  default-language:    Haskell2010-  ghc-options:         -Wall-  build-tool-depends: c2hs:c2hs >=0.25.0-  c-sources:-    cbits/haskell_igraph.c-    cbits/haskell_attributes.c-    cbits/bytestring.c--    -- igraph-    igraph/src/abort_.c-    igraph/src/adjlist.c-    igraph/src/arithchk.c-    igraph/src/arpack.c-    igraph/src/array.c-    igraph/src/atlas.c-    igraph/src/attributes.c-    igraph/src/backspac.c-    igraph/src/basic_query.c-    igraph/src/bfgs.c-    igraph/src/bigint.c-    igraph/src/bignum.c-    igraph/src/bipartite.c-    igraph/src/blas.c-    igraph/src/c_abs.c-    igraph/src/cabs.c-    igraph/src/cattributes.c-    igraph/src/c_cos.c-    igraph/src/c_div.c-    igraph/src/centrality.c-    igraph/src/c_exp.c-    igraph/src/cliquer.c-    igraph/src/cliquer_graph.c-    igraph/src/cliques.c-    igraph/src/c_log.c-    igraph/src/close.c-    igraph/src/cocitation.c-    igraph/src/cohesive_blocks.c-    igraph/src/coloring.c-    igraph/src/community.c-    igraph/src/community_leiden.c-    igraph/src/complex.c-    igraph/src/components.c-    igraph/src/conversion.c-    igraph/src/cores.c-    igraph/src/cs_add.c-    igraph/src/cs_amd.c-    igraph/src/cs_chol.c-    igraph/src/cs_cholsol.c-    igraph/src/cs_compress.c-    igraph/src/cs_counts.c-    igraph/src/cs_cumsum.c-    igraph/src/cs_dfs.c-    igraph/src/cs_dmperm.c-    igraph/src/cs_droptol.c-    igraph/src/cs_dropzeros.c-    igraph/src/cs_dupl.c-    igraph/src/cs_entry.c-    igraph/src/cs_ereach.c-    igraph/src/cs_etree.c-    igraph/src/cs_fkeep.c-    igraph/src/cs_gaxpy.c-    igraph/src/cs_happly.c-    igraph/src/cs_house.c-    igraph/src/c_sin.c-    igraph/src/cs_ipvec.c-    igraph/src/cs_leaf.c-    igraph/src/cs_load.c-    igraph/src/cs_lsolve.c-    igraph/src/cs_ltsolve.c-    igraph/src/cs_lu.c-    igraph/src/cs_lusol.c-    igraph/src/cs_malloc.c-    igraph/src/cs_maxtrans.c-    igraph/src/cs_multiply.c-    igraph/src/cs_norm.c-    igraph/src/cs_permute.c-    igraph/src/cs_pinv.c-    igraph/src/cs_post.c-    igraph/src/cs_print.c-    igraph/src/cs_pvec.c-    igraph/src/cs_qr.c-    igraph/src/cs_qrsol.c-    igraph/src/c_sqrt.c-    igraph/src/cs_randperm.c-    igraph/src/cs_reach.c-    igraph/src/cs_scatter.c-    igraph/src/cs_scc.c-    igraph/src/cs_schol.c-    igraph/src/cs_spsolve.c-    igraph/src/cs_sqr.c-    igraph/src/cs_symperm.c-    igraph/src/cs_tdfs.c-    igraph/src/cs_transpose.c-    igraph/src/cs_updown.c-    igraph/src/cs_usolve.c-    igraph/src/cs_util.c-    igraph/src/cs_utsolve.c-    igraph/src/ctype.c-    igraph/src/d_abs.c-    igraph/src/d_acos.c-    igraph/src/d_asin.c-    igraph/src/dasum.c-    igraph/src/d_atan.c-    igraph/src/d_atn2.c-    igraph/src/daxpy.c-    igraph/src/d_cnjg.c-    igraph/src/dcopy.c-    igraph/src/d_cos.c-    igraph/src/d_cosh.c-    igraph/src/d_dim.c-    igraph/src/ddot.c-    igraph/src/decomposition.c-    igraph/src/derf_.c-    igraph/src/derfc_.c-    igraph/src/d_exp.c-    igraph/src/dfe.c-    igraph/src/dgebak.c-    igraph/src/dgebal.c-    igraph/src/dgeev.c-    igraph/src/dgeevx.c-    igraph/src/dgehd2.c-    igraph/src/dgehrd.c-    igraph/src/dgemm.c-    igraph/src/dgemv.c-    igraph/src/dgeqr2.c-    igraph/src/dger.c-    igraph/src/dgesv.c-    igraph/src/dgetf2.c-    igraph/src/dgetrf.c-    igraph/src/dgetrs.c-    igraph/src/dgetv0.c-    igraph/src/dhseqr.c-    igraph/src/d_imag.c-    igraph/src/d_int.c-    igraph/src/disnan.c-    igraph/src/distances.c-    igraph/src/dlabad.c-    igraph/src/dlacn2.c-    igraph/src/dlacpy.c-    igraph/src/dladiv.c-    igraph/src/dlae2.c-    igraph/src/dlaebz.c-    igraph/src/dlaev2.c-    igraph/src/dlaexc.c-    igraph/src/dlagtf.c-    igraph/src/dlagts.c-    igraph/src/dlahqr.c-    igraph/src/dlahr2.c-    igraph/src/dlaisnan.c-    igraph/src/dlaln2.c-    igraph/src/dlamch.c-    igraph/src/dlaneg.c-    igraph/src/dlange.c-    igraph/src/dlanhs.c-    igraph/src/dlanst.c-    igraph/src/dlansy.c-    igraph/src/dlanv2.c-    igraph/src/dlapy2.c-    igraph/src/dlaqr0.c-    igraph/src/dlaqr1.c-    igraph/src/dlaqr2.c-    igraph/src/dlaqr3.c-    igraph/src/dlaqr4.c-    igraph/src/dlaqr5.c-    igraph/src/dlaqrb.c-    igraph/src/dlaqtr.c-    igraph/src/dlar1v.c-    igraph/src/dlarfb.c-    igraph/src/dlarf.c-    igraph/src/dlarfg.c-    igraph/src/dlarft.c-    igraph/src/dlarfx.c-    igraph/src/dlarnv.c-    igraph/src/dlarra.c-    igraph/src/dlarrb.c-    igraph/src/dlarrc.c-    igraph/src/dlarrd.c-    igraph/src/dlarre.c-    igraph/src/dlarrf.c-    igraph/src/dlarrj.c-    igraph/src/dlarrk.c-    igraph/src/dlarrr.c-    igraph/src/dlarrv.c-    igraph/src/dlartg.c-    igraph/src/dlaruv.c-    igraph/src/dlascl.c-    igraph/src/dlaset.c-    igraph/src/dlasq2.c-    igraph/src/dlasq3.c-    igraph/src/dlasq4.c-    igraph/src/dlasq5.c-    igraph/src/dlasq6.c-    igraph/src/dlasr.c-    igraph/src/dlasrt.c-    igraph/src/dlassq.c-    igraph/src/dlaswp.c-    igraph/src/dlasy2.c-    igraph/src/dlatrd.c-    igraph/src/d_lg10.c-    igraph/src/d_log.c-    igraph/src/d_mod.c-    igraph/src/dmout.c-    igraph/src/dnaitr.c-    igraph/src/dnapps.c-    igraph/src/dnaup2.c-    igraph/src/dnaupd.c-    igraph/src/dnconv.c-    igraph/src/dneigh.c-    igraph/src/dneupd.c-    igraph/src/dngets.c-    igraph/src/d_nint.c-    igraph/src/dnrm2.c-    igraph/src/dolio.c-    igraph/src/dorg2r.c-    igraph/src/dorghr.c-    igraph/src/dorgqr.c-    igraph/src/dorm2l.c-    igraph/src/dorm2r.c-    igraph/src/dormhr.c-    igraph/src/dormql.c-    igraph/src/dormqr.c-    igraph/src/dormtr.c-    igraph/src/dotproduct.c-    igraph/src/dpotf2.c-    igraph/src/dpotrf.c-    igraph/src/d_prod.c-    igraph/src/dqueue.c-    igraph/src/drot.c-    igraph/src/dsaitr.c-    igraph/src/dsapps.c-    igraph/src/dsaup2.c-    igraph/src/dsaupd.c-    igraph/src/dscal.c-    igraph/src/dsconv.c-    igraph/src/dseigt.c-    igraph/src/dsesrt.c-    igraph/src/dseupd.c-    igraph/src/dsgets.c-    igraph/src/d_sign.c-    igraph/src/d_sin.c-    igraph/src/d_sinh.c-    igraph/src/dsortc.c-    igraph/src/dsortr.c-    igraph/src/d_sqrt.c-    igraph/src/dstatn.c-    igraph/src/dstats.c-    igraph/src/dstebz.c-    igraph/src/dstein.c-    igraph/src/dstemr.c-    igraph/src/dsteqr.c-    igraph/src/dsterf.c-    igraph/src/dstqrb.c-    igraph/src/dswap.c-    igraph/src/dsyevr.c-    igraph/src/dsymv.c-    igraph/src/dsyr2.c-    igraph/src/dsyr2k.c-    igraph/src/dsyrk.c-    igraph/src/dsytd2.c-    igraph/src/dsytrd.c-    igraph/src/d_tan.c-    igraph/src/d_tanh.c-    igraph/src/dtime_.c-    igraph/src/dtrevc.c-    igraph/src/dtrexc.c-    igraph/src/dtrmm.c-    igraph/src/dtrmv.c-    igraph/src/dtrsen.c-    igraph/src/dtrsm.c-    igraph/src/dtrsna.c-    igraph/src/dtrsv.c-    igraph/src/dtrsyl.c-    igraph/src/due.c-    igraph/src/dummy.c-    igraph/src/dvout.c-    igraph/src/ef1asc_.c-    igraph/src/ef1cmc_.c-    igraph/src/eigen.c-    igraph/src/embedding.c-    igraph/src/endfile.c-    igraph/src/erf_.c-    igraph/src/erfc_.c-    igraph/src/err.c-    igraph/src/error.c-    igraph/src/etime_.c-    igraph/src/exit_.c-    igraph/src/f77_aloc.c-    igraph/src/f77vers.c-    igraph/src/fast_community.c-    igraph/src/feedback_arc_set.c-    igraph/src/flow.c-    igraph/src/fmt.c-    igraph/src/fmtlib.c-    igraph/src/foreign.c-    igraph/src/foreign-dl-lexer.c-    igraph/src/foreign-dl-parser.c-    igraph/src/foreign-gml-lexer.c-    igraph/src/foreign-gml-parser.c-    igraph/src/foreign-graphml.c-    igraph/src/foreign-lgl-lexer.c-    igraph/src/foreign-lgl-parser.c-    igraph/src/foreign-ncol-lexer.c-    igraph/src/foreign-ncol-parser.c-    igraph/src/foreign-pajek-lexer.c-    igraph/src/foreign-pajek-parser.c-    igraph/src/forestfire.c-    igraph/src/fortran_intrinsics.c-    igraph/src/ftell_.c-    igraph/src/games.c-    igraph/src/getenv_.c-    igraph/src/glet.c-    igraph/src/glpk_support.c-    igraph/src/gml_tree.c-    igraph/src/gss.c-    igraph/src/h_abs.c-    igraph/src/hacks.c-    igraph/src/h_dim.c-    igraph/src/h_dnnt.c-    igraph/src/heap.c-    igraph/src/h_indx.c-    igraph/src/h_len.c-    igraph/src/hl_ge.c-    igraph/src/hl_gt.c-    igraph/src/hl_le.c-    igraph/src/hl_lt.c-    igraph/src/h_mod.c-    igraph/src/h_nint.c-    igraph/src/h_sign.c-    igraph/src/i77vers.c-    igraph/src/i_abs.c-    igraph/src/idamax.c-    igraph/src/i_dim.c-    igraph/src/i_dnnt.c-    igraph/src/ieeeck.c-    igraph/src/igraph_buckets.c-    igraph/src/igraph_cliquer.c-    igraph/src/igraph_error.c-    igraph/src/igraph_estack.c-    igraph/src/igraph_fixed_vectorlist.c-    igraph/src/igraph_grid.c-    igraph/src/igraph_hashtable.c-    igraph/src/igraph_heap.c-    igraph/src/igraph_marked_queue.c-    igraph/src/igraph_psumtree.c-    igraph/src/igraph_set.c-    igraph/src/igraph_stack.c-    igraph/src/igraph_strvector.c-    igraph/src/igraph_trie.c-    igraph/src/i_indx.c-    igraph/src/iio.c-    igraph/src/iladlc.c-    igraph/src/iladlr.c-    igraph/src/ilaenv.c-    igraph/src/i_len.c-    igraph/src/ilnw.c-    igraph/src/i_mod.c-    igraph/src/i_nint.c-    igraph/src/inquire.c-    igraph/src/interrupt.c-    igraph/src/iparmq.c-    igraph/src/i_sign.c-    igraph/src/iterators.c-    igraph/src/ivout.c-    igraph/src/kolmogorov.c-    igraph/src/lad.c-    igraph/src/lapack.c-    igraph/src/layout.c-    igraph/src/layout_dh.c-    igraph/src/layout_fr.c-    igraph/src/layout_gem.c-    igraph/src/layout_kk.c-    igraph/src/lbfgs.c-    igraph/src/lbitbits.c-    igraph/src/lbitshft.c-    igraph/src/len_trim.c-    igraph/src/l_ge.c-    igraph/src/l_gt.c-    igraph/src/l_le.c-    igraph/src/l_lt.c-    igraph/src/lread.c-    igraph/src/lsame.c-    igraph/src/lsap.c-    igraph/src/lwrite.c-    igraph/src/matching.c-    igraph/src/math.c-    igraph/src/matrix.c-    igraph/src/maximal_cliques.c-    igraph/src/memory.c-    igraph/src/microscopic_update.c-    igraph/src/mixing.c-    igraph/src/motifs.c-    igraph/src/open.c-    igraph/src/operators.c-    igraph/src/optimal_modularity.c-    igraph/src/options.c-    igraph/src/other.c-    igraph/src/paths.c-    igraph/src/plfit.c-    igraph/src/pow_ci.c-    igraph/src/pow_dd.c-    igraph/src/pow_di.c-    igraph/src/pow_hh.c-    igraph/src/pow_ii.c-    igraph/src/pow_ri.c-    igraph/src/pow_zi.c-    igraph/src/pow_zz.c-    igraph/src/progress.c-    igraph/src/qsort.c-    igraph/src/qsort_r.c-    igraph/src/r_abs.c-    igraph/src/r_acos.c-    igraph/src/random.c-    igraph/src/random_walk.c-    igraph/src/r_asin.c-    igraph/src/r_atan.c-    igraph/src/r_atn2.c-    igraph/src/r_cnjg.c-    igraph/src/r_cos.c-    igraph/src/r_cosh.c-    igraph/src/rdfmt.c-    igraph/src/r_dim.c-    igraph/src/reorder.c-    igraph/src/rewind.c-    igraph/src/r_exp.c-    igraph/src/r_imag.c-    igraph/src/r_int.c-    igraph/src/r_lg10.c-    igraph/src/r_log.c-    igraph/src/r_mod.c-    igraph/src/r_nint.c-    igraph/src/rsfe.c-    igraph/src/r_sign.c-    igraph/src/r_sin.c-    igraph/src/r_sinh.c-    igraph/src/rsli.c-    igraph/src/rsne.c-    igraph/src/r_sqrt.c-    igraph/src/r_tan.c-    igraph/src/r_tanh.c-    igraph/src/sbm.c-    igraph/src/scan.c-    igraph/src/s_cat.c-    igraph/src/scg_approximate_methods.c-    igraph/src/scg.c-    igraph/src/scg_exact_scg.c-    igraph/src/scg_kmeans.c-    igraph/src/scg_optimal_method.c-    igraph/src/scg_utils.c-    igraph/src/s_cmp.c-    igraph/src/s_copy.c-    igraph/src/second.c-    igraph/src/separators.c-    igraph/src/sfe.c-    igraph/src/sig_die.c-    igraph/src/signal_.c-    igraph/src/signbit.c-    igraph/src/sir.c-    igraph/src/spanning_trees.c-    igraph/src/sparsemat.c-    igraph/src/s_paus.c-    igraph/src/spectral_properties.c-    igraph/src/spmatrix.c-    igraph/src/s_rnge.c-    igraph/src/s_stop.c-    igraph/src/statusbar.c-    igraph/src/st-cuts.c-    igraph/src/structural_properties.c-    igraph/src/structure_generators.c-    igraph/src/sue.c-    igraph/src/sugiyama.c-    igraph/src/system_.c-    igraph/src/topology.c-    igraph/src/triangles.c-    igraph/src/type_indexededgelist.c-    igraph/src/types.c-    igraph/src/typesize.c-    igraph/src/uio.c-    igraph/src/uninit.c-    igraph/src/util.c-    igraph/src/vector.c-    igraph/src/vector_ptr.c-    igraph/src/version.c-    igraph/src/visitors.c-    igraph/src/wref.c-    igraph/src/wrtfmt.c-    igraph/src/wsfe.c-    igraph/src/wsle.c-    igraph/src/wsne.c-    igraph/src/xerbla.c-    igraph/src/xwsne.c-    igraph/src/z_abs.c-    igraph/src/z_cos.c-    igraph/src/z_div.c-    igraph/src/zeroin.c-    igraph/src/zeta.c-    igraph/src/z_exp.c-    igraph/src/z_log.c-    igraph/src/z_sin.c-    igraph/src/z_sqrt.c--  cxx-sources:-    igraph/src/clustertool.cpp-    igraph/src/degree_sequence.cpp-    igraph/src/DensityGrid_3d.cpp-    igraph/src/DensityGrid.cpp-    igraph/src/drl_graph_3d.cpp-    igraph/src/drl_graph.cpp-    igraph/src/drl_layout_3d.cpp-    igraph/src/drl_layout.cpp-    igraph/src/drl_parse.cpp-    igraph/src/gengraph_box_list.cpp-    igraph/src/gengraph_degree_sequence.cpp-    igraph/src/gengraph_graph_molloy_hash.cpp-    igraph/src/gengraph_graph_molloy_optimized.cpp-    igraph/src/gengraph_mr-connected.cpp-    igraph/src/gengraph_powerlaw.cpp-    igraph/src/gengraph_random.cpp-    igraph/src/NetDataTypes.cpp-    igraph/src/NetRoutines.cpp-    igraph/src/pottsmodel_2.cpp-    igraph/src/prpack_base_graph.cpp-    igraph/src/prpack.cpp-    igraph/src/prpack_igraph_graph.cpp-    igraph/src/prpack_preprocessed_ge_graph.cpp-    igraph/src/prpack_preprocessed_gs_graph.cpp-    igraph/src/prpack_preprocessed_scc_graph.cpp-    igraph/src/prpack_preprocessed_schur_graph.cpp-    igraph/src/prpack_result.cpp-    igraph/src/prpack_solver.cpp-    igraph/src/prpack_utils.cpp-    igraph/src/walktrap_communities.cpp-    igraph/src/walktrap.cpp-    igraph/src/walktrap_graph.cpp-    igraph/src/walktrap_heap.cpp-    igraph/src/bliss.cc-    igraph/src/bliss_heap.cc-    igraph/src/defs.cc-    igraph/src/graph.cc-    igraph/src/igraph_hrg.cc-    igraph/src/igraph_hrg_types.cc-    igraph/src/infomap.cc-    igraph/src/infomap_FlowGraph.cc-    igraph/src/infomap_Greedy.cc-    igraph/src/infomap_Node.cc-    igraph/src/orbit.cc-    igraph/src/partition.cc-    igraph/src/uintseqhash.cc-    igraph/src/utils.cc--  include-dirs:-    include-    igraph/include-    igraph/include/f2c-    igraph/include/prpack-    igraph/include/cs-    igraph/include/cliquer-    igraph/include/bliss-    igraph/include/plfit-  -  cxx-options: -DPRPACK_IGRAPH_SUPPORT--test-suite tests-  type: exitcode-stdio-1.0-  hs-source-dirs: tests-  ghc-options:         -Wall-  main-is: test.hs-  other-modules:-    Test.Basic-    Test.Attributes-    Test.Algorithms-    Test.Utils--  default-language:    Haskell2010-  build-depends:-      base-    , haskell-igraph-    , cereal-    , conduit >= 1.3.0-    , data-ordlist-    , matrices-    , tasty-    , tasty-golden-    , tasty-hunit-    , random--source-repository  head-  type: git-  location: https://github.com/kaizhang/haskell-igraph.git-+cabal-version: 2.2++-- This file has been generated from package.yaml by hpack version 0.33.0.+--+-- see: https://github.com/sol/hpack+--+-- hash: eec35679c2bc2e9790d121f0e5e57bf25eb87dcf0776ae132bba4f4ff0d168b1++name:           haskell-igraph+version:        0.8.5+synopsis:       Bindings to the igraph C library (v0.8.5).+description:    igraph<"http://igraph.org/c/"> is a library for creating and manipulating large graphs. This package provides the Haskell interface of igraph.+category:       Math+homepage:       https://github.com/jmazon/haskell-igraph#readme+bug-reports:    https://github.com/jmazon/haskell-igraph/issues+author:         Kai Zhang+maintainer:     Jean-Baptiste Mazon+copyright:      (c) 2016-2021 Kai Zhang+license:        MIT+license-file:   LICENSE+build-type:     Simple+extra-source-files:+    cbits/bytestring.h+    cbits/haskell_attributes.h+    cbits/haskell_igraph.h+    igraph/include/arith.h+    igraph/include/atlas-edges.h+    igraph/include/bigint.h+    igraph/include/bignum.h+    igraph/include/config.h+    igraph/include/DensityGrid.h+    igraph/include/DensityGrid_3d.h+    igraph/include/drl_graph.h+    igraph/include/drl_graph_3d.h+    igraph/include/drl_layout.h+    igraph/include/drl_layout_3d.h+    igraph/include/drl_Node.h+    igraph/include/drl_Node_3d.h+    igraph/include/drl_parse.h+    igraph/include/f2c.h+    igraph/include/foreign-dl-header.h+    igraph/include/foreign-dl-parser.h+    igraph/include/foreign-gml-header.h+    igraph/include/foreign-gml-parser.h+    igraph/include/foreign-lgl-header.h+    igraph/include/foreign-lgl-parser.h+    igraph/include/foreign-ncol-header.h+    igraph/include/foreign-ncol-parser.h+    igraph/include/foreign-pajek-header.h+    igraph/include/foreign-pajek-parser.h+    igraph/include/gengraph_box_list.h+    igraph/include/gengraph_definitions.h+    igraph/include/gengraph_degree_sequence.h+    igraph/include/gengraph_graph_molloy_hash.h+    igraph/include/gengraph_graph_molloy_optimized.h+    igraph/include/gengraph_hash.h+    igraph/include/gengraph_header.h+    igraph/include/gengraph_powerlaw.h+    igraph/include/gengraph_qsort.h+    igraph/include/gengraph_random.h+    igraph/include/gengraph_vertex_cover.h+    igraph/include/hrg_dendro.h+    igraph/include/hrg_graph.h+    igraph/include/hrg_graph_simp.h+    igraph/include/hrg_rbtree.h+    igraph/include/hrg_splittree_eq.h+    igraph/include/igraph.h+    igraph/include/igraph_adjlist.h+    igraph/include/igraph_arpack.h+    igraph/include/igraph_arpack_internal.h+    igraph/include/igraph_array.h+    igraph/include/igraph_array_pmt.h+    igraph/include/igraph_attributes.h+    igraph/include/igraph_bipartite.h+    igraph/include/igraph_blas.h+    igraph/include/igraph_blas_internal.h+    igraph/include/igraph_centrality.h+    igraph/include/igraph_cliquer.h+    igraph/include/igraph_cliques.h+    igraph/include/igraph_cocitation.h+    igraph/include/igraph_cohesive_blocks.h+    igraph/include/igraph_coloring.h+    igraph/include/igraph_community.h+    igraph/include/igraph_complex.h+    igraph/include/igraph_components.h+    igraph/include/igraph_constants.h+    igraph/include/igraph_constructors.h+    igraph/include/igraph_conversion.h+    igraph/include/igraph_datatype.h+    igraph/include/igraph_decls.h+    igraph/include/igraph_dqueue.h+    igraph/include/igraph_dqueue_pmt.h+    igraph/include/igraph_eigen.h+    igraph/include/igraph_embedding.h+    igraph/include/igraph_epidemics.h+    igraph/include/igraph_error.h+    igraph/include/igraph_estack.h+    igraph/include/igraph_flow.h+    igraph/include/igraph_flow_internal.h+    igraph/include/igraph_foreign.h+    igraph/include/igraph_games.h+    igraph/include/igraph_glpk_support.h+    igraph/include/igraph_gml_tree.h+    igraph/include/igraph_graphlets.h+    igraph/include/igraph_hacks_internal.h+    igraph/include/igraph_handle_exceptions.h+    igraph/include/igraph_heap.h+    igraph/include/igraph_heap_pmt.h+    igraph/include/igraph_hrg.h+    igraph/include/igraph_interface.h+    igraph/include/igraph_interrupt.h+    igraph/include/igraph_interrupt_internal.h+    igraph/include/igraph_isoclasses.h+    igraph/include/igraph_iterators.h+    igraph/include/igraph_lapack.h+    igraph/include/igraph_lapack_internal.h+    igraph/include/igraph_layout.h+    igraph/include/igraph_lsap.h+    igraph/include/igraph_marked_queue.h+    igraph/include/igraph_matching.h+    igraph/include/igraph_math.h+    igraph/include/igraph_matrix.h+    igraph/include/igraph_matrix_pmt.h+    igraph/include/igraph_memory.h+    igraph/include/igraph_microscopic_update.h+    igraph/include/igraph_mixing.h+    igraph/include/igraph_motifs.h+    igraph/include/igraph_neighborhood.h+    igraph/include/igraph_nongraph.h+    igraph/include/igraph_operators.h+    igraph/include/igraph_paths.h+    igraph/include/igraph_pmt.h+    igraph/include/igraph_pmt_off.h+    igraph/include/igraph_progress.h+    igraph/include/igraph_psumtree.h+    igraph/include/igraph_qsort.h+    igraph/include/igraph_random.h+    igraph/include/igraph_scan.h+    igraph/include/igraph_scg.h+    igraph/include/igraph_separators.h+    igraph/include/igraph_sparsemat.h+    igraph/include/igraph_spmatrix.h+    igraph/include/igraph_stack.h+    igraph/include/igraph_stack_pmt.h+    igraph/include/igraph_statusbar.h+    igraph/include/igraph_structural.h+    igraph/include/igraph_strvector.h+    igraph/include/igraph_threading.h+    igraph/include/igraph_topology.h+    igraph/include/igraph_transitivity.h+    igraph/include/igraph_types.h+    igraph/include/igraph_types_internal.h+    igraph/include/igraph_vector.h+    igraph/include/igraph_vector_pmt.h+    igraph/include/igraph_vector_ptr.h+    igraph/include/igraph_vector_type.h+    igraph/include/igraph_version.h+    igraph/include/igraph_visitor.h+    igraph/include/infomap_FlowGraph.h+    igraph/include/infomap_Greedy.h+    igraph/include/infomap_Node.h+    igraph/include/maximal_cliques_template.h+    igraph/include/NetDataTypes.h+    igraph/include/NetRoutines.h+    igraph/include/pottsmodel_2.h+    igraph/include/prpack.h+    igraph/include/scg_headers.h+    igraph/include/structural_properties_internal.h+    igraph/include/triangles_template.h+    igraph/include/triangles_template1.h+    igraph/include/walktrap_communities.h+    igraph/include/walktrap_graph.h+    igraph/include/walktrap_heap.h+    igraph/include/array.pmt+    igraph/include/dqueue.pmt+    igraph/include/heap.pmt+    igraph/include/matrix.pmt+    igraph/include/stack.pmt+    igraph/include/vector.pmt+    igraph/include/f2c/fio.h+    igraph/include/f2c/fmt.h+    igraph/include/f2c/fp.h+    igraph/include/f2c/lio.h+    igraph/include/f2c/signal1.h+    igraph/include/f2c/sysdep1.h+    igraph/include/prpack/prpack.h+    igraph/include/prpack/prpack_base_graph.h+    igraph/include/prpack/prpack_csc.h+    igraph/include/prpack/prpack_csr.h+    igraph/include/prpack/prpack_edge_list.h+    igraph/include/prpack/prpack_igraph_graph.h+    igraph/include/prpack/prpack_preprocessed_ge_graph.h+    igraph/include/prpack/prpack_preprocessed_graph.h+    igraph/include/prpack/prpack_preprocessed_gs_graph.h+    igraph/include/prpack/prpack_preprocessed_scc_graph.h+    igraph/include/prpack/prpack_preprocessed_schur_graph.h+    igraph/include/prpack/prpack_result.h+    igraph/include/prpack/prpack_solver.h+    igraph/include/prpack/prpack_utils.h+    igraph/include/cs/cs.h+    igraph/include/cs/UFconfig.h+    igraph/include/cliquer/cliquer.h+    igraph/include/cliquer/cliquerconf.h+    igraph/include/cliquer/graph.h+    igraph/include/cliquer/misc.h+    igraph/include/cliquer/reorder.h+    igraph/include/cliquer/set.h+    igraph/include/bliss/bignum.hh+    igraph/include/bliss/defs.hh+    igraph/include/bliss/graph.hh+    igraph/include/bliss/heap.hh+    igraph/include/bliss/kqueue.hh+    igraph/include/bliss/kstack.hh+    igraph/include/bliss/orbit.hh+    igraph/include/bliss/partition.hh+    igraph/include/bliss/uintseqhash.hh+    igraph/include/bliss/utils.hh+    igraph/include/plfit/arithmetic_ansi.h+    igraph/include/plfit/arithmetic_sse_double.h+    igraph/include/plfit/arithmetic_sse_float.h+    igraph/include/plfit/error.h+    igraph/include/plfit/gss.h+    igraph/include/plfit/hzeta.h+    igraph/include/plfit/kolmogorov.h+    igraph/include/plfit/lbfgs.h+    igraph/include/plfit/mt.h+    igraph/include/plfit/platform.h+    igraph/include/plfit/plfit.h+    igraph/include/plfit/sampling.h+    igraph/AUTHORS+    igraph/COPYING+    stack.yaml++extra-doc-files:+    README.md+    ChangeLog.md++source-repository head+  type: git+  location: https://github.com/jmazon/haskell-igraph++library+  exposed-modules:+      IGraph.Internal.Initialization+      IGraph.Internal.Constants+      IGraph.Internal+      IGraph+      IGraph.Mutable+      IGraph.Random+      IGraph.Types+      IGraph.Algorithms+      IGraph.Algorithms.Structure+      IGraph.Algorithms.Community+      IGraph.Algorithms.Clique+      IGraph.Algorithms.Layout+      IGraph.Algorithms.Motif+      IGraph.Algorithms.Generators+      IGraph.Algorithms.Isomorphism+      IGraph.Algorithms.Centrality+  other-modules:+      IGraph.Internal.C2HS+  hs-source-dirs:+      src+  ghc-options: -Wall -fno-warn-unused-matches+  cxx-options: -std=c++11 -DPRPACK_IGRAPH_SUPPORT+  include-dirs:+      cbits+      igraph/include+      igraph/include/f2c+      igraph/include/prpack+      igraph/include/cs+      igraph/include/cliquer+      igraph/include/bliss+      igraph/include/plfit+  c-sources:+      cbits/bytestring.c+      cbits/haskell_attributes.c+      cbits/haskell_igraph.c+      igraph/src/abort_.c+      igraph/src/adjlist.c+      igraph/src/arithchk.c+      igraph/src/arpack.c+      igraph/src/array.c+      igraph/src/atlas.c+      igraph/src/attributes.c+      igraph/src/backspac.c+      igraph/src/basic_query.c+      igraph/src/bfgs.c+      igraph/src/bigint.c+      igraph/src/bignum.c+      igraph/src/bipartite.c+      igraph/src/blas.c+      igraph/src/c_abs.c+      igraph/src/c_cos.c+      igraph/src/c_div.c+      igraph/src/c_exp.c+      igraph/src/c_log.c+      igraph/src/c_sin.c+      igraph/src/c_sqrt.c+      igraph/src/cabs.c+      igraph/src/cattributes.c+      igraph/src/centrality.c+      igraph/src/cliquer.c+      igraph/src/cliquer_graph.c+      igraph/src/cliques.c+      igraph/src/close.c+      igraph/src/cocitation.c+      igraph/src/cohesive_blocks.c+      igraph/src/coloring.c+      igraph/src/community.c+      igraph/src/community_leiden.c+      igraph/src/complex.c+      igraph/src/components.c+      igraph/src/conversion.c+      igraph/src/cores.c+      igraph/src/cs_add.c+      igraph/src/cs_amd.c+      igraph/src/cs_chol.c+      igraph/src/cs_cholsol.c+      igraph/src/cs_compress.c+      igraph/src/cs_counts.c+      igraph/src/cs_cumsum.c+      igraph/src/cs_dfs.c+      igraph/src/cs_dmperm.c+      igraph/src/cs_droptol.c+      igraph/src/cs_dropzeros.c+      igraph/src/cs_dupl.c+      igraph/src/cs_entry.c+      igraph/src/cs_ereach.c+      igraph/src/cs_etree.c+      igraph/src/cs_fkeep.c+      igraph/src/cs_gaxpy.c+      igraph/src/cs_happly.c+      igraph/src/cs_house.c+      igraph/src/cs_ipvec.c+      igraph/src/cs_leaf.c+      igraph/src/cs_load.c+      igraph/src/cs_lsolve.c+      igraph/src/cs_ltsolve.c+      igraph/src/cs_lu.c+      igraph/src/cs_lusol.c+      igraph/src/cs_malloc.c+      igraph/src/cs_maxtrans.c+      igraph/src/cs_multiply.c+      igraph/src/cs_norm.c+      igraph/src/cs_permute.c+      igraph/src/cs_pinv.c+      igraph/src/cs_post.c+      igraph/src/cs_print.c+      igraph/src/cs_pvec.c+      igraph/src/cs_qr.c+      igraph/src/cs_qrsol.c+      igraph/src/cs_randperm.c+      igraph/src/cs_reach.c+      igraph/src/cs_scatter.c+      igraph/src/cs_scc.c+      igraph/src/cs_schol.c+      igraph/src/cs_spsolve.c+      igraph/src/cs_sqr.c+      igraph/src/cs_symperm.c+      igraph/src/cs_tdfs.c+      igraph/src/cs_transpose.c+      igraph/src/cs_updown.c+      igraph/src/cs_usolve.c+      igraph/src/cs_util.c+      igraph/src/cs_utsolve.c+      igraph/src/ctype.c+      igraph/src/d_abs.c+      igraph/src/d_acos.c+      igraph/src/d_asin.c+      igraph/src/d_atan.c+      igraph/src/d_atn2.c+      igraph/src/d_cnjg.c+      igraph/src/d_cos.c+      igraph/src/d_cosh.c+      igraph/src/d_dim.c+      igraph/src/d_exp.c+      igraph/src/d_imag.c+      igraph/src/d_int.c+      igraph/src/d_lg10.c+      igraph/src/d_log.c+      igraph/src/d_mod.c+      igraph/src/d_nint.c+      igraph/src/d_prod.c+      igraph/src/d_sign.c+      igraph/src/d_sin.c+      igraph/src/d_sinh.c+      igraph/src/d_sqrt.c+      igraph/src/d_tan.c+      igraph/src/d_tanh.c+      igraph/src/dasum.c+      igraph/src/daxpy.c+      igraph/src/dcopy.c+      igraph/src/ddot.c+      igraph/src/decomposition.c+      igraph/src/derf_.c+      igraph/src/derfc_.c+      igraph/src/dfe.c+      igraph/src/dgebak.c+      igraph/src/dgebal.c+      igraph/src/dgeev.c+      igraph/src/dgeevx.c+      igraph/src/dgehd2.c+      igraph/src/dgehrd.c+      igraph/src/dgemm.c+      igraph/src/dgemv.c+      igraph/src/dgeqr2.c+      igraph/src/dger.c+      igraph/src/dgesv.c+      igraph/src/dgetf2.c+      igraph/src/dgetrf.c+      igraph/src/dgetrs.c+      igraph/src/dgetv0.c+      igraph/src/dhseqr.c+      igraph/src/disnan.c+      igraph/src/distances.c+      igraph/src/dlabad.c+      igraph/src/dlacn2.c+      igraph/src/dlacpy.c+      igraph/src/dladiv.c+      igraph/src/dlae2.c+      igraph/src/dlaebz.c+      igraph/src/dlaev2.c+      igraph/src/dlaexc.c+      igraph/src/dlagtf.c+      igraph/src/dlagts.c+      igraph/src/dlahqr.c+      igraph/src/dlahr2.c+      igraph/src/dlaisnan.c+      igraph/src/dlaln2.c+      igraph/src/dlamch.c+      igraph/src/dlaneg.c+      igraph/src/dlange.c+      igraph/src/dlanhs.c+      igraph/src/dlanst.c+      igraph/src/dlansy.c+      igraph/src/dlanv2.c+      igraph/src/dlapy2.c+      igraph/src/dlaqr0.c+      igraph/src/dlaqr1.c+      igraph/src/dlaqr2.c+      igraph/src/dlaqr3.c+      igraph/src/dlaqr4.c+      igraph/src/dlaqr5.c+      igraph/src/dlaqrb.c+      igraph/src/dlaqtr.c+      igraph/src/dlar1v.c+      igraph/src/dlarf.c+      igraph/src/dlarfb.c+      igraph/src/dlarfg.c+      igraph/src/dlarft.c+      igraph/src/dlarfx.c+      igraph/src/dlarnv.c+      igraph/src/dlarra.c+      igraph/src/dlarrb.c+      igraph/src/dlarrc.c+      igraph/src/dlarrd.c+      igraph/src/dlarre.c+      igraph/src/dlarrf.c+      igraph/src/dlarrj.c+      igraph/src/dlarrk.c+      igraph/src/dlarrr.c+      igraph/src/dlarrv.c+      igraph/src/dlartg.c+      igraph/src/dlaruv.c+      igraph/src/dlascl.c+      igraph/src/dlaset.c+      igraph/src/dlasq2.c+      igraph/src/dlasq3.c+      igraph/src/dlasq4.c+      igraph/src/dlasq5.c+      igraph/src/dlasq6.c+      igraph/src/dlasr.c+      igraph/src/dlasrt.c+      igraph/src/dlassq.c+      igraph/src/dlaswp.c+      igraph/src/dlasy2.c+      igraph/src/dlatrd.c+      igraph/src/dmout.c+      igraph/src/dnaitr.c+      igraph/src/dnapps.c+      igraph/src/dnaup2.c+      igraph/src/dnaupd.c+      igraph/src/dnconv.c+      igraph/src/dneigh.c+      igraph/src/dneupd.c+      igraph/src/dngets.c+      igraph/src/dnrm2.c+      igraph/src/dolio.c+      igraph/src/dorg2r.c+      igraph/src/dorghr.c+      igraph/src/dorgqr.c+      igraph/src/dorm2l.c+      igraph/src/dorm2r.c+      igraph/src/dormhr.c+      igraph/src/dormql.c+      igraph/src/dormqr.c+      igraph/src/dormtr.c+      igraph/src/dotproduct.c+      igraph/src/dpotf2.c+      igraph/src/dpotrf.c+      igraph/src/dqueue.c+      igraph/src/drot.c+      igraph/src/dsaitr.c+      igraph/src/dsapps.c+      igraph/src/dsaup2.c+      igraph/src/dsaupd.c+      igraph/src/dscal.c+      igraph/src/dsconv.c+      igraph/src/dseigt.c+      igraph/src/dsesrt.c+      igraph/src/dseupd.c+      igraph/src/dsgets.c+      igraph/src/dsortc.c+      igraph/src/dsortr.c+      igraph/src/dstatn.c+      igraph/src/dstats.c+      igraph/src/dstebz.c+      igraph/src/dstein.c+      igraph/src/dstemr.c+      igraph/src/dsteqr.c+      igraph/src/dsterf.c+      igraph/src/dstqrb.c+      igraph/src/dswap.c+      igraph/src/dsyevr.c+      igraph/src/dsymv.c+      igraph/src/dsyr2.c+      igraph/src/dsyr2k.c+      igraph/src/dsyrk.c+      igraph/src/dsytd2.c+      igraph/src/dsytrd.c+      igraph/src/dtime_.c+      igraph/src/dtrevc.c+      igraph/src/dtrexc.c+      igraph/src/dtrmm.c+      igraph/src/dtrmv.c+      igraph/src/dtrsen.c+      igraph/src/dtrsm.c+      igraph/src/dtrsna.c+      igraph/src/dtrsv.c+      igraph/src/dtrsyl.c+      igraph/src/due.c+      igraph/src/dummy.c+      igraph/src/dvout.c+      igraph/src/ef1asc_.c+      igraph/src/ef1cmc_.c+      igraph/src/eigen.c+      igraph/src/embedding.c+      igraph/src/endfile.c+      igraph/src/erf_.c+      igraph/src/erfc_.c+      igraph/src/err.c+      igraph/src/error.c+      igraph/src/etime_.c+      igraph/src/exit_.c+      igraph/src/f77_aloc.c+      igraph/src/f77vers.c+      igraph/src/fast_community.c+      igraph/src/feedback_arc_set.c+      igraph/src/flow.c+      igraph/src/fmt.c+      igraph/src/fmtlib.c+      igraph/src/foreign-dl-lexer.c+      igraph/src/foreign-dl-parser.c+      igraph/src/foreign-gml-lexer.c+      igraph/src/foreign-gml-parser.c+      igraph/src/foreign-graphml.c+      igraph/src/foreign-lgl-lexer.c+      igraph/src/foreign-lgl-parser.c+      igraph/src/foreign-ncol-lexer.c+      igraph/src/foreign-ncol-parser.c+      igraph/src/foreign-pajek-lexer.c+      igraph/src/foreign-pajek-parser.c+      igraph/src/foreign.c+      igraph/src/forestfire.c+      igraph/src/fortran_intrinsics.c+      igraph/src/ftell_.c+      igraph/src/games.c+      igraph/src/getenv_.c+      igraph/src/glet.c+      igraph/src/glpk_support.c+      igraph/src/gml_tree.c+      igraph/src/gss.c+      igraph/src/h_abs.c+      igraph/src/h_dim.c+      igraph/src/h_dnnt.c+      igraph/src/h_indx.c+      igraph/src/h_len.c+      igraph/src/h_mod.c+      igraph/src/h_nint.c+      igraph/src/h_sign.c+      igraph/src/hacks.c+      igraph/src/heap.c+      igraph/src/hl_ge.c+      igraph/src/hl_gt.c+      igraph/src/hl_le.c+      igraph/src/hl_lt.c+      igraph/src/hzeta.c+      igraph/src/i77vers.c+      igraph/src/i_abs.c+      igraph/src/i_dim.c+      igraph/src/i_dnnt.c+      igraph/src/i_indx.c+      igraph/src/i_len.c+      igraph/src/i_mod.c+      igraph/src/i_nint.c+      igraph/src/i_sign.c+      igraph/src/idamax.c+      igraph/src/ieeeck.c+      igraph/src/igraph_buckets.c+      igraph/src/igraph_cliquer.c+      igraph/src/igraph_error.c+      igraph/src/igraph_estack.c+      igraph/src/igraph_fixed_vectorlist.c+      igraph/src/igraph_grid.c+      igraph/src/igraph_hashtable.c+      igraph/src/igraph_heap.c+      igraph/src/igraph_marked_queue.c+      igraph/src/igraph_psumtree.c+      igraph/src/igraph_set.c+      igraph/src/igraph_stack.c+      igraph/src/igraph_strvector.c+      igraph/src/igraph_trie.c+      igraph/src/iio.c+      igraph/src/iladlc.c+      igraph/src/iladlr.c+      igraph/src/ilaenv.c+      igraph/src/ilnw.c+      igraph/src/inquire.c+      igraph/src/interrupt.c+      igraph/src/iparmq.c+      igraph/src/iterators.c+      igraph/src/ivout.c+      igraph/src/kolmogorov.c+      igraph/src/l_ge.c+      igraph/src/l_gt.c+      igraph/src/l_le.c+      igraph/src/l_lt.c+      igraph/src/lad.c+      igraph/src/lapack.c+      igraph/src/layout.c+      igraph/src/layout_dh.c+      igraph/src/layout_fr.c+      igraph/src/layout_gem.c+      igraph/src/layout_kk.c+      igraph/src/lbfgs.c+      igraph/src/lbitbits.c+      igraph/src/lbitshft.c+      igraph/src/len_trim.c+      igraph/src/lread.c+      igraph/src/lsame.c+      igraph/src/lsap.c+      igraph/src/lwrite.c+      igraph/src/matching.c+      igraph/src/math.c+      igraph/src/matrix.c+      igraph/src/maximal_cliques.c+      igraph/src/memory.c+      igraph/src/microscopic_update.c+      igraph/src/mixing.c+      igraph/src/motifs.c+      igraph/src/mt.c+      igraph/src/open.c+      igraph/src/operators.c+      igraph/src/optimal_modularity.c+      igraph/src/options.c+      igraph/src/other.c+      igraph/src/paths.c+      igraph/src/platform.c+      igraph/src/plfit.c+      igraph/src/pow_ci.c+      igraph/src/pow_dd.c+      igraph/src/pow_di.c+      igraph/src/pow_hh.c+      igraph/src/pow_ii.c+      igraph/src/pow_ri.c+      igraph/src/pow_zi.c+      igraph/src/pow_zz.c+      igraph/src/progress.c+      igraph/src/qsort.c+      igraph/src/qsort_r.c+      igraph/src/r_abs.c+      igraph/src/r_acos.c+      igraph/src/r_asin.c+      igraph/src/r_atan.c+      igraph/src/r_atn2.c+      igraph/src/r_cnjg.c+      igraph/src/r_cos.c+      igraph/src/r_cosh.c+      igraph/src/r_dim.c+      igraph/src/r_exp.c+      igraph/src/r_imag.c+      igraph/src/r_int.c+      igraph/src/r_lg10.c+      igraph/src/r_log.c+      igraph/src/r_mod.c+      igraph/src/r_nint.c+      igraph/src/r_sign.c+      igraph/src/r_sin.c+      igraph/src/r_sinh.c+      igraph/src/r_sqrt.c+      igraph/src/r_tan.c+      igraph/src/r_tanh.c+      igraph/src/random.c+      igraph/src/random_walk.c+      igraph/src/rbinom.c+      igraph/src/rdfmt.c+      igraph/src/reorder.c+      igraph/src/rewind.c+      igraph/src/rsfe.c+      igraph/src/rsli.c+      igraph/src/rsne.c+      igraph/src/s_cat.c+      igraph/src/s_cmp.c+      igraph/src/s_copy.c+      igraph/src/s_paus.c+      igraph/src/s_rnge.c+      igraph/src/s_stop.c+      igraph/src/sampling.c+      igraph/src/sbm.c+      igraph/src/scan.c+      igraph/src/scg.c+      igraph/src/scg_approximate_methods.c+      igraph/src/scg_exact_scg.c+      igraph/src/scg_kmeans.c+      igraph/src/scg_optimal_method.c+      igraph/src/scg_utils.c+      igraph/src/second.c+      igraph/src/separators.c+      igraph/src/sfe.c+      igraph/src/sig_die.c+      igraph/src/signal_.c+      igraph/src/signbit.c+      igraph/src/sir.c+      igraph/src/spanning_trees.c+      igraph/src/sparsemat.c+      igraph/src/spectral_properties.c+      igraph/src/spmatrix.c+      igraph/src/st-cuts.c+      igraph/src/statusbar.c+      igraph/src/structural_properties.c+      igraph/src/structure_generators.c+      igraph/src/sue.c+      igraph/src/sugiyama.c+      igraph/src/system_.c+      igraph/src/topology.c+      igraph/src/triangles.c+      igraph/src/type_indexededgelist.c+      igraph/src/types.c+      igraph/src/typesize.c+      igraph/src/uio.c+      igraph/src/uninit.c+      igraph/src/util.c+      igraph/src/vector.c+      igraph/src/vector_ptr.c+      igraph/src/version.c+      igraph/src/visitors.c+      igraph/src/wref.c+      igraph/src/wrtfmt.c+      igraph/src/wsfe.c+      igraph/src/wsle.c+      igraph/src/wsne.c+      igraph/src/xerbla.c+      igraph/src/xwsne.c+      igraph/src/z_abs.c+      igraph/src/z_cos.c+      igraph/src/z_div.c+      igraph/src/z_exp.c+      igraph/src/z_log.c+      igraph/src/z_sin.c+      igraph/src/z_sqrt.c+      igraph/src/zeroin.c+  cxx-sources:+      igraph/src/clustertool.cpp+      igraph/src/degree_sequence.cpp+      igraph/src/DensityGrid.cpp+      igraph/src/DensityGrid_3d.cpp+      igraph/src/drl_graph.cpp+      igraph/src/drl_graph_3d.cpp+      igraph/src/drl_layout.cpp+      igraph/src/drl_layout_3d.cpp+      igraph/src/drl_parse.cpp+      igraph/src/gengraph_box_list.cpp+      igraph/src/gengraph_degree_sequence.cpp+      igraph/src/gengraph_graph_molloy_hash.cpp+      igraph/src/gengraph_graph_molloy_optimized.cpp+      igraph/src/gengraph_mr-connected.cpp+      igraph/src/gengraph_powerlaw.cpp+      igraph/src/gengraph_random.cpp+      igraph/src/NetDataTypes.cpp+      igraph/src/NetRoutines.cpp+      igraph/src/pottsmodel_2.cpp+      igraph/src/prpack.cpp+      igraph/src/prpack_base_graph.cpp+      igraph/src/prpack_igraph_graph.cpp+      igraph/src/prpack_preprocessed_ge_graph.cpp+      igraph/src/prpack_preprocessed_gs_graph.cpp+      igraph/src/prpack_preprocessed_scc_graph.cpp+      igraph/src/prpack_preprocessed_schur_graph.cpp+      igraph/src/prpack_result.cpp+      igraph/src/prpack_solver.cpp+      igraph/src/prpack_utils.cpp+      igraph/src/walktrap.cpp+      igraph/src/walktrap_communities.cpp+      igraph/src/walktrap_graph.cpp+      igraph/src/walktrap_heap.cpp+      igraph/src/bliss.cc+      igraph/src/bliss_heap.cc+      igraph/src/defs.cc+      igraph/src/graph.cc+      igraph/src/igraph_hrg.cc+      igraph/src/igraph_hrg_types.cc+      igraph/src/infomap.cc+      igraph/src/infomap_FlowGraph.cc+      igraph/src/infomap_Greedy.cc+      igraph/src/infomap_Node.cc+      igraph/src/orbit.cc+      igraph/src/partition.cc+      igraph/src/uintseqhash.cc+      igraph/src/utils.cc+  extra-libraries:+      stdc+++  build-tool-depends:+      c2hs:c2hs >=0.25.0+  build-depends:+      base >=4.10 && <5.0+    , bytestring >=0.9+    , cereal+    , conduit >=1.3.0+    , containers+    , data-ordlist+    , primitive+    , singletons >=3.0+    , singletons-base+    , singletons-th+  default-language: Haskell2010++test-suite test+  type: exitcode-stdio-1.0+  main-is: test.hs+  other-modules:+      Test.Basic+      Test.Attributes+      Test.Algorithms+      Test.Utils+  hs-source-dirs:+      tests+  ghc-options: -threaded+  build-depends:+      base+    , cereal+    , conduit >=1.3.0+    , data-ordlist+    , haskell-igraph+    , matrices+    , random+    , tasty+    , tasty-golden+    , tasty-hunit+  default-language: Haskell2010
igraph/AUTHORS view
@@ -2,3 +2,5 @@ Tamas Nepusz <ntamas@gmail.com> Szabolcs Horvat <szhorvat@gmail.com> Vincent Traag <v.a.traag@cwts.leidenuniv.nl>+Fabio Zanini <fabio.zanini@unsw.edu.au>+
igraph/include/DensityGrid.h view
@@ -36,17 +36,14 @@  // Compile time adjustable parameters --#include <deque>--using namespace std;- #include "drl_layout.h" #include "drl_Node.h" #ifdef MUSE_MPI     #include <mpi.h> #endif +#include <deque>+ namespace drl {  class DensityGrid {@@ -74,7 +71,7 @@     // new dynamic variables -- SBM     float (*fall_off)[RADIUS * 2 + 1];     float (*Density)[GRID_SIZE];-    deque<Node>* Bins;+    std::deque<Node>* Bins;      // old static variables     //float fall_off[RADIUS*2+1][RADIUS*2+1];
igraph/include/DensityGrid_3d.h view
@@ -36,17 +36,14 @@  // Compile time adjustable parameters --#include <deque>--using namespace std;- #include "drl_layout_3d.h" #include "drl_Node_3d.h" #ifdef MUSE_MPI     #include <mpi.h> #endif +#include <deque>+ namespace drl3d {  class DensityGrid {@@ -74,7 +71,7 @@     // new dynamic variables -- SBM     float (*fall_off)[RADIUS * 2 + 1][RADIUS * 2 + 1];     float (*Density)[GRID_SIZE][GRID_SIZE];-    deque<Node>* Bins;+    std::deque<Node>* Bins;      // old static variables     //float fall_off[RADIUS*2+1][RADIUS*2+1];
igraph/include/NetDataTypes.h view
@@ -43,7 +43,7 @@ #ifndef NETDATATYPES_H #define NETDATATYPES_H -#include <string.h>+#include <cstring>  //########################################################################################### @@ -449,7 +449,7 @@  template <class DATA> HugeArray<DATA>::HugeArray(void) {-    max_bit_left = 1 << 31; //wir setzen das 31. Bit auf 1+    max_bit_left = 1UL << 31; //wir setzen das 31. Bit auf 1     size = 2;     max_index = 0;     highest_field_index = 0;@@ -486,7 +486,7 @@         shift_index++;     }     h_index.field_index = 31 - shift_index;   // das hoechste  besetzte Bit im Index-    help_index = 1 << h_index.field_index;  // in help_index wird das hoechste besetzte Bit von Index gesetzt+    help_index = 1UL << h_index.field_index;  // in help_index wird das hoechste besetzte Bit von Index gesetzt     h_index.in_field_index = (index ^ help_index); // index XOR help_index, womit alle bits unter dem hoechsten erhalten bleiben     return h_index; }@@ -497,7 +497,7 @@     unsigned long data_size;     while (size < index + 1) {         highest_field_index++;-        data_size = 1 << highest_field_index;+        data_size = 1UL << highest_field_index;         data = new DATA[data_size];         for (unsigned long i = 0; i < data_size; i++) {             data[i] = 0;
igraph/include/bliss/bignum.hh view
@@ -21,7 +21,7 @@ */  #include <cstdlib>-#include <cstdio>+// #include <cstdio> #include <cmath> #include <cstring> #include <sstream>@@ -111,7 +111,7 @@   /**    * Print the number in the file stream \a fp.    */-  size_t print(FILE* const fp) const {return fprintf(fp, "%Lg", v); }+  // size_t print(FILE* const fp) const {return fprintf(fp, "%Lg", v); }    int tostring(char **str) const {     int size=static_cast<int>( (std::log(std::abs(v))/std::log(10.0))+4 );
igraph/include/bliss/defs.hh view
@@ -29,11 +29,6 @@ #  define BLISS_USE_GMP #endif -#ifdef USING_R-#include <R.h>-#define fatal_error(...) (error(__VA_ARGS__))-#endif- namespace bliss {  /**@@ -47,9 +42,7 @@  * There should not be a return from this function but exit or  * a jump to code that deallocates the AbstractGraph instance that called this.  */-#ifndef USING_R void fatal_error(const char* fmt, ...);-#endif   #if defined(BLISS_DEBUG)
igraph/include/bliss/graph.hh view
@@ -29,7 +29,7 @@   class AbstractGraph; } -#include <cstdio>+// #include <cstdio> #include <vector> #include "kstack.hh" #include "kqueue.hh"@@ -81,6 +81,7 @@ public:   Stats() { reset(); }   /** Print the statistics. */+  /*   size_t print(FILE* const fp) const   {     size_t r = 0;@@ -94,6 +95,7 @@     fflush(fp);     return r;   }+  */   /** An approximation (due to possible overflows/rounding errors) of    * the size of the automorphism group. */   long double get_group_size_approx() const {return group_size_approx;}@@ -241,6 +243,7 @@ 						  const unsigned int* aut), 				     void* hook_user_param); +#if 0   /**    * Write the graph to a file in a variant of the DIMACS format.    * See the <A href="http://www.tcs.hut.fi/Software/bliss/">bliss website</A>@@ -264,6 +267,7 @@    * \param file_name  the name of the file to which the graph is written    */   virtual void write_dot(const char * const file_name) = 0;+#endif    /**    * Get a hash value for the graph.@@ -294,7 +298,7 @@   unsigned int verbose_level;   /** \internal    * The output stream for verbose output. */-  FILE *verbstr;+  // FILE *verbstr; protected:    /** \internal@@ -391,7 +395,7 @@    * Data structures and routines for refining the partition p into equitable    */   Heap neighbour_heap;-  virtual bool split_neighbourhood_of_unit_cell(Partition::Cell *) = 0;+  virtual bool split_neighbourhood_of_unit_cell(Partition::Cell * const) = 0;   virtual bool split_neighbourhood_of_cell(Partition::Cell * const) = 0;   void refine_to_equitable();   void refine_to_equitable(Partition::Cell * const unit_cell);@@ -658,6 +662,7 @@    */   ~Graph(); +#if 0   /**    * Read the graph from the file \a fp in a variant of the DIMACS format.    * See the <A href="http://www.tcs.hut.fi/Software/bliss/">bliss website</A>@@ -690,6 +695,7 @@    * \copydoc AbstractGraph::write_dot(const char * const file_name)    */   void write_dot(const char* const file_name);+#endif    /**    * \copydoc AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const@@ -898,6 +904,7 @@    */   ~Digraph(); +#if 0   /**    * Read the graph from the file \a fp in a variant of the DIMACS format.    * See the <A href="http://www.tcs.hut.fi/Software/bliss/">bliss website</A>@@ -928,6 +935,7 @@    * \copydoc AbstractGraph::write_dot(const char * const file_name)    */   void write_dot(const char * const file_name);+#endif    /**    * \copydoc AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const
igraph/include/bliss/partition.hh view
@@ -25,7 +25,7 @@ }  #include <cstdlib>-#include <cstdio>+//#include <cstdio> #include <climits> #include "kstack.hh" #include "kqueue.hh"@@ -186,12 +186,12 @@   /**    * Print the partition into the file stream \a fp.    */-  size_t print(FILE* const fp, const bool add_newline = true) const;+  // size_t print(FILE* const fp, const bool add_newline = true) const;    /**    * Print the partition cell sizes into the file stream \a fp.    */-  size_t print_signature(FILE* const fp, const bool add_newline = true) const;+  // size_t print_signature(FILE* const fp, const bool add_newline = true) const;    /*    * Splits the Cell \a cell into [cell_1,...,cell_n]
igraph/include/bliss/uintseqhash.hh view
@@ -1,7 +1,7 @@ #ifndef BLISS_UINTSEQHASH_HH #define BLISS_UINTSEQHASH_HH -#include <cstdio>+// #include <cstdio>  /*   Copyright (c) 2003-2015 Tommi Junttila
igraph/include/bliss/utils.hh view
@@ -26,11 +26,12 @@  *  */ -#include <cstdio>-using namespace std;+//#include <cstdio>+#include <vector>  namespace bliss { +#if 0 /**  * Print the permutation \a perm of {0,...,N-1} in the cycle format  * in the file stream \a fp.@@ -51,6 +52,7 @@ void print_permutation(FILE* fp, 		       const std::vector<unsigned int>& perm, 		       const unsigned int offset = 0);+#endif  /**  * Check whether \a perm is a valid permutation on {0,...,N-1}.
igraph/include/cliquer/set.h view
igraph/include/config.h view
@@ -11,6 +11,7 @@ #define HAVE_RINTF 1 #define HAVE_ROUND 1 #define HAVE_SNPRINTF 1+#undef HAVE_ISFINITE  /* libraries */ #define HAVE_MEMORY_H 1@@ -18,8 +19,10 @@ #define HAVE_STRINGS_H 1 #define HAVE_STRING_H 1 +#define HAVE_TLS 1 #define IGRAPH_F77_SAVE static IGRAPH_THREAD_LOCAL-#define IGRAPH_THREAD_LOCAL +#define IGRAPH_THREAD_LOCAL __thread+#define TLS __thread  #define INTERNAL_ARPACK 1 #define INTERNAL_BLAS 1@@ -27,13 +30,15 @@ #define INTERNAL_GLPK 1 #define INTERNAL_LAPACK 1 + #define LT_OBJDIR ".libs/" #define PACKAGE "igraph" #define PACKAGE_BUGREPORT "igraph@igraph.org" #define PACKAGE_NAME "igraph"-#define PACKAGE_STRING "igraph 0.8.0"+#define PACKAGE_STRING "igraph 0.8.5" #define PACKAGE_TARNAME "igraph" #define PACKAGE_URL ""-#define PACKAGE_VERSION "0.8.0"+#define PACKAGE_VERSION "0.8.5" #define STDC_HEADERS 1-#define VERSION "0.8.0"+#define VERSION "0.8.5"+#undef YYTEXT_POINTER
igraph/include/drl_graph.h view
@@ -37,6 +37,10 @@ #include "DensityGrid.h" #include "igraph_layout.h" +#include <map>+#include <vector>+#include <ctime>+ namespace drl {  // layout schedule information@@ -81,8 +85,8 @@     void update_nodes ( );     float Compute_Node_Energy ( int node_ind );     void Solve_Analytic ( int node_ind, float &pos_x, float &pos_y );-    void get_positions ( vector<int> &node_indices, float return_positions[2 * MAX_PROCS] );-    void update_density ( vector<int> &node_indices,+    void get_positions ( std::vector<int> &node_indices, float return_positions[2 * MAX_PROCS] );+    void update_density ( std::vector<int> &node_indices,                           float old_positions[2 * MAX_PROCS],                           float new_positions[2 * MAX_PROCS] );     void update_node_pos ( int node_ind,@@ -95,11 +99,11 @@     // graph decomposition information     int num_nodes;                  // number of nodes in graph     float highest_sim;              // highest sim for normalization-    map <int, int> id_catalog;      // id_catalog[file id] = internal id-    map <int, map <int, float> > neighbors;     // neighbors of nodes on this proc.+    std::map <int, int> id_catalog;      // id_catalog[file id] = internal id+    std::map <int, std::map <int, float> > neighbors;     // neighbors of nodes on this proc.      // graph layout information-    vector<Node> positions;+    std::vector<Node> positions;     DensityGrid density_server;      // original VxOrd information
igraph/include/drl_graph_3d.h view
@@ -37,6 +37,10 @@ #include "DensityGrid_3d.h" #include "igraph_layout.h" +#include <map>+#include <vector>+#include <ctime>+ namespace drl3d {  // layout schedule information@@ -73,8 +77,8 @@     void update_nodes ( );     float Compute_Node_Energy ( int node_ind );     void Solve_Analytic ( int node_ind, float &pos_x, float &pos_y, float &pos_z );-    void get_positions ( vector<int> &node_indices, float return_positions[3 * MAX_PROCS] );-    void update_density ( vector<int> &node_indices,+    void get_positions ( std::vector<int> &node_indices, float return_positions[3 * MAX_PROCS] );+    void update_density ( std::vector<int> &node_indices,                           float old_positions[3 * MAX_PROCS],                           float new_positions[3 * MAX_PROCS] );     void update_node_pos ( int node_ind,@@ -87,11 +91,11 @@     // graph decomposition information     int num_nodes;                  // number of nodes in graph     float highest_sim;              // highest sim for normalization-    map <int, int> id_catalog;      // id_catalog[file id] = internal id-    map <int, map <int, float> > neighbors;     // neighbors of nodes on this proc.+    std::map <int, int> id_catalog;      // id_catalog[file id] = internal id+    std::map <int, std::map <int, float> > neighbors;     // neighbors of nodes on this proc.      // graph layout information-    vector<Node> positions;+    std::vector<Node> positions;     DensityGrid density_server;      // original VxOrd information
igraph/include/drl_parse.h view
@@ -37,6 +37,8 @@     #include <mpi.h> #endif +#include <string>+ namespace drl {  class parse {@@ -49,10 +51,10 @@     ~parse () {}      // user parameters-    string sim_file;        // .sim file-    string coord_file;      // .coord file-    string parms_file;      // .parms file-    string real_file;       // .real file+    std::string sim_file;        // .sim file+    std::string coord_file;      // .coord file+    std::string parms_file;      // .parms file+    std::string real_file;       // .real file      int rand_seed;      // random seed int >= 0     float edge_cut;         // edge cutting real [0,1]
igraph/include/gengraph_box_list.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -27,12 +27,6 @@  #ifndef _BOX_LIST_H #define _BOX_LIST_H--#ifndef _MSC_VER-    #ifndef register-        #define register-    #endif-#endif  namespace gengraph { 
igraph/include/gengraph_definitions.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -21,12 +21,6 @@ #ifndef DEFINITIONS_H #define DEFINITIONS_H -#ifndef _MSC_VER-    #ifndef register-        #define register-    #endif-#endif- #include <stdio.h> #include <math.h> #include <string.h>@@ -124,7 +118,7 @@   if(fabs(x)<1e-6) return x+0.5*x*x+0.333333333333333*x*x*x;   else return log(1.0+x); }-//*/+*/   //Fast search or replace@@ -197,7 +191,7 @@ static int _random_bits = 0;  inline int random_bit() {-    register int a = _random_bits;+    int a = _random_bits;     _random_bits = a >> 1;     if (_random_bits_stored--) {         return a & 0x1;
igraph/include/gengraph_degree_sequence.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,
igraph/include/gengraph_graph_molloy_hash.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -209,7 +209,7 @@       // same, but when multiple shortest path are possible, average the weights.       double *vertex_betweenness_asp(bool trivial_path);     //___________________________________________________________________________________-    //*/+    */  }; 
igraph/include/gengraph_graph_molloy_optimized.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -265,7 +265,7 @@       bool try_shuffle(int T, int K);      //___________________________________________________________________________________-    //*/+    */      /*___________________________________________________________________________________       Not to use anymore : replaced by vertex_betweenness()     22/04/2005@@ -277,7 +277,7 @@       // same, but when multiple shortest path are possible, average the weights.       double *vertex_betweenness_asp(bool trivial_path);     //___________________________________________________________________________________-    //*/+    */  }; 
igraph/include/gengraph_hash.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,
igraph/include/gengraph_header.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -41,17 +41,6 @@ }  }--#ifdef _WIN32-#include <process.h>-#include <windows.h>-void set_priority_low() {-    HANDLE hProcess = OpenProcess(PROCESS_ALL_ACCESS, TRUE, _getpid());-    SetPriorityClass(hProcess, IDLE_PRIORITY_CLASS);-}-#else-#include <unistd.h>-#endif  namespace gengraph { 
igraph/include/gengraph_powerlaw.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,
igraph/include/gengraph_qsort.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -24,10 +24,6 @@ #include <assert.h> #include <stdio.h> -#ifndef register-    #define register-#endif- namespace gengraph {  //___________________________________________________________________________@@ -63,7 +59,7 @@         return;     }     for (int i = 1; i < t; i++) {-        register int *w = v + i;+        int *w = v + i;         int tmp = *w;         while (w != v && *(w - 1) > tmp) {             *w = *(w - 1);@@ -147,7 +143,7 @@         return;     }     for (int i = 1; i < t; i++) {-        register double *w = v + i;+        double *w = v + i;         double tmp = *w;         while (w != v && *(w - 1) > tmp) {             *w = *(w - 1);@@ -260,7 +256,7 @@     int mx = mem[0];     int mn = mem[0];     for (yo = mem + n - 1; yo != mem; yo--) {-        register int x = *yo;+        int x = *yo;         if (x > mx) {             mx = x;         }@@ -399,7 +395,7 @@         return;     }     for (int i = 1; i < t; i++) {-        register int *w = v + i;+        int *w = v + i;         int tmp = *w;         while (w != v && lex_comp(l[tmp], l[*(w - 1)], s) < 0) {             *w = *(w - 1);@@ -521,7 +517,7 @@         return;     }     for (int i = 1; i < t; i++) {-        register int *w = v + i;+        int *w = v + i;         int tmp = *w;         while (w != v && mix_comp_indirect(key, tmp, *(w - 1), neigh, degs) < 0) {             *w = *(w - 1);
igraph/include/gengraph_random.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -22,8 +22,6 @@ #define RNG_H  #include "igraph_random.h"-#include <iostream>-using namespace std;  namespace KW_RNG { 
igraph/include/gengraph_vertex_cover.h view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -28,10 +28,7 @@ // Moreover, vertex_cover() keeps links[] intact, permuting only the adjacency lists  #include "gengraph_box_list.h"--#ifndef register-    #define register-#endif+#include <cstddef>  namespace gengraph { @@ -57,9 +54,9 @@         if (!bl.is_empty()) {             v = bl.get_max();             int *w = neigh[v];-            register int v2 = *(w++);-            register int dm = deg[v2];-            register int k = deg[v] - 1;+            int v2 = *(w++);+            int dm = deg[v2];+            int k = deg[v] - 1;             while (k--) if (deg[*(w++)] > dm) {                     v2 = *(w - 1);                     dm = deg[v2];
igraph/include/heap.pmt view
@@ -33,6 +33,12 @@ #define LEFTCHILD(x)  (((x)+1)*2-1) #define RIGHTCHILD(x) (((x)+1)*2) +/* Define internal functions */+void FUNCTION(igraph_heap, i_build)(BASE* arr, long int size, long int head);+void FUNCTION(igraph_heap, i_shift_up)(BASE* arr, long int size, long int elem);+void FUNCTION(igraph_heap, i_sink)(BASE* arr, long int size, long int head);+void FUNCTION(igraph_heap, i_switch)(BASE* arr, long int e1, long int e2);+ /**  * \ingroup heap  * \function igraph_heap_init
igraph/include/hrg_dendro.h view
@@ -65,18 +65,15 @@ #ifndef IGRAPH_HRG_DENDRO #define IGRAPH_HRG_DENDRO -#include <iostream>-#include <fstream>-#include <cstdio>-#include <cmath>- #include "hrg_graph.h" #include "hrg_rbtree.h" #include "hrg_splittree_eq.h"  #include "igraph_hrg.h" -using namespace std;+#include <string>+#include <cmath>+ using namespace fitHRG;  namespace fitHRG {@@ -105,7 +102,7 @@     int    x;     int y;     short int t;-    string sp;+    std::string sp; }; struct child {     int index;@@ -147,7 +144,7 @@  class split { public:-    string s;           // partition assignment of leaf vertices+    std::string s;           // partition assignment of leaf vertices     split(): s("") { }     ~split() { }     void initializeSplit(const int n) {@@ -157,7 +154,7 @@         }     }     bool checkSplit() {-        if (s.empty() || s.find("-", 0) != string::npos) {+        if (s.empty() || s.find("-", 0) != std::string::npos) {             return false;         } else {             return true;@@ -181,7 +178,7 @@ class interns { private:     ipair* edgelist;   // list of internal edges represented-    string* splitlist; // split representation of the internal edges+    std::string* splitlist; // split representation of the internal edges     int** indexLUT;    // table of indices of internal edges in edgelist     int q;         // number of internal edges     int count;         // (for adding edges) edgelist index of new edge to add@@ -196,9 +193,9 @@     // returns a uniformly random internal edge, O(1)     ipair* getRandomEdge();     // returns the ith split of the splitlist, O(1)-    string getSplit(const int);+    std::string getSplit(const int);     // replace an existing split, O(1)-    bool replaceSplit(const int, const string);+    bool replaceSplit(const int, const std::string);     // swaps two edges, O(1)     bool swapEdges(const int, const int, const short int, const int,                    const int, const short int);@@ -250,12 +247,12 @@     // return path to root from leaf     list* binarySearchFind(const double);     // build split for this internal edge-    string buildSplit(elementd*);+    std::string buildSplit(elementd*);     // compute number of edges between two internal subtrees     int computeEdgeCount(const int, const short int, const int,                          const short int);     // (consensus tree) counts children-    int countChildren(const string);+    int countChildren(const std::string);     // find internal node of D that is common ancestor of i,j     elementd* findCommonAncestor(list**, const int, const int);     // return reverse of path to leaf from root
igraph/include/hrg_graph.h view
@@ -61,13 +61,11 @@ #ifndef IGRAPH_HRG_GRAPH #define IGRAPH_HRG_GRAPH -#include <cstdio>-#include <cstring>-#include <cstdlib>- #include "hrg_rbtree.h" -using namespace std;+#include <string>+#include <cstring>+#include <cstdlib>  namespace fitHRG { @@ -96,7 +94,7 @@ #define IGRAPH_HRG_VERT class vert { public:-    string name;           // (external) name of vertex+    std::string name;           // (external) name of vertex     int degree;            // degree of this vertex      vert(): name(""), degree(0) { }@@ -122,7 +120,7 @@     // returns degree of vertex i     int getDegree(const int);     // returns name of vertex i-    string getName(const int);+    std::string getName(const int);     // returns edge list of vertex i     edge* getNeighborList(const int);     // return ptr to histogram of edge (i,j)@@ -148,7 +146,7 @@     // allocate edge histograms     void setAdjacencyHistograms(const int);     // set name of vertex i-    bool setName(const int, const string);+    bool setName(const int, const std::string);  private:     bool predict;      // do we need prediction?
igraph/include/hrg_graph_simp.h view
@@ -60,14 +60,11 @@ #ifndef IGRAPH_HRG_SIMPLEGRAPH #define IGRAPH_HRG_SIMPLEGRAPH -#include <cstdio>-#include <cstring>-#include <cstdlib>- #include "hrg_rbtree.h" #include "hrg_dendro.h" -using namespace std;+#include <cstring>+#include <cstdlib>  namespace fitHRG { @@ -89,7 +86,7 @@ #define IGRAPH_HRG_SIMPLEVERT class simpleVert { public:-    string name;          // (external) name of vertex+    std::string name;          // (external) name of vertex     int degree;           // degree of this vertex     int group_true;       // index of vertex's true group @@ -129,7 +126,7 @@     // returns group label of vertex i     int getGroupLabel(const int);     // returns name of vertex i-    string getName(const int);+    std::string getName(const int);     // returns edge list of vertex i     simpleEdge* getNeighborList(const int);     // return pointer to a node@@ -141,7 +138,7 @@     // returns n     int getNumNodes();     // set name of vertex i-    bool setName(const int, const string);+    bool setName(const int, const std::string);  private:     simpleVert* nodes;        // list of nodes
igraph/include/hrg_rbtree.h view
@@ -55,10 +55,6 @@ #ifndef IGRAPH_HRG_RBTREE #define IGRAPH_HRG_RBTREE -#include <iostream>--using namespace std;- namespace fitHRG {  // ******** Basic Structures *********************************************
igraph/include/hrg_splittree_eq.h view
@@ -62,9 +62,7 @@ #ifndef IGRAPH_HRG_SPLITTREE #define IGRAPH_HRG_SPLITTREE -#include <iostream>--using namespace std;+#include <string>  namespace fitHRG { @@ -74,7 +72,7 @@ #define IGRAPH_HRG_SLIST class slist { public:-    string x;         // stored elementd in linked-list+    std::string x;         // stored elementd in linked-list     slist* next;          // pointer to next elementd     slist(): x(""), next(0) { }     ~slist() { }@@ -83,7 +81,7 @@  class keyValuePairSplit { public:-    string x;         // elementsp split (string)+    std::string x;         // elementsp split (string)     double y;         // stored weight   (double)     int c;            // stored count    (int)     keyValuePairSplit* next;  // linked-list pointer@@ -95,7 +93,7 @@  class elementsp { public:-    string split;             // split represented as a string+    std::string split;             // split represented as a string     double weight;            // total weight of this split     int count;                // number of observations of this split @@ -149,21 +147,21 @@     // default constructor/destructor     splittree(); ~splittree();     // returns value associated with searchKey-    double returnValue(const string);+    double returnValue(const std::string);     // returns T if searchKey found, and points foundNode at the     // corresponding node-    elementsp* findItem(const string);+    elementsp* findItem(const std::string);     // update total_count and total_weight     void finishedThisRound();     // insert a new key with stored value-    bool insertItem(string, double);+    bool insertItem(std::string, double);     void clearTree();     // delete a node with given key-    void deleteItem(string);+    void deleteItem(std::string);     // delete the entire tree     void deleteTree();     // return array of keys in tree-    string* returnArrayOfKeys();+    std::string* returnArrayOfKeys();     // return list of keys in tree     slist* returnListOfKeys();     // return the tree as a list of keyValuePairSplits
igraph/include/igraph_adjlist.h view
@@ -59,13 +59,12 @@ /*                 igraph_integer_t no); */ /**  * \define igraph_adjlist_get- * Query a vector in an adjlist+ * \brief Query a vector in an adjacency list.  *  * Returns a pointer to an <type>igraph_vector_int_t</type> object from an  * adjacency list. The vector can be modified as desired.  * \param al The adjacency list object.- * \param no The vertex of which the vertex of adjacent vertices are- *   returned.+ * \param no The vertex whose adjacent vertices will be returned.  * \return Pointer to the <type>igraph_vector_int_t</type> object.  *  * Time complexity: O(1).@@ -93,7 +92,7 @@  /**  * \define igraph_inclist_get- * Query a vector in an incidence list+ * \brief Query a vector in an incidence list.  *  * Returns a pointer to an <type>igraph_vector_int_t</type> object from an  * incidence list containing edge ids. The vector can be modified,@@ -124,14 +123,14 @@ /*                     igraph_integer_t no); */ /**  * \define igraph_lazy_adjlist_get- * Query neighbor vertices+ * \brief Query neighbor vertices.  *  * If the function is called for the first time for a vertex then the  * result is stored in the adjacency list and no further query  * operations are needed when the neighbors of the same vertex are  * queried again.  * \param al The lazy adjacency list.- * \param no The vertex id to query.+ * \param no The vertex ID to query.  * \return Pointer to a vector. It is allowed to modify it and  *   modification does not affect the original graph.  *@@ -159,7 +158,7 @@  /**  * \define igraph_lazy_inclist_get- * Query incident edges+ * \brief Query incident edges.  *  * If the function is called for the first time for a vertex, then the  * result is stored in the incidence list and no further query@@ -195,7 +194,7 @@  /**  * \define igraph_adjedgelist_get- * Query a vector in an incidence list+ * \brief Query a vector in an incidence list.  *  * This macro was superseded by \ref igraph_inclist_get() in igraph 0.6.  * Please use \ref igraph_inclist_get() instead of this macro.@@ -214,7 +213,7 @@  /**  * \define igraph_lazy_adjedgelist_get- * Query a vector in a lazy incidence list+ * \brief Query a vector in a lazy incidence list.  *  * This macro was superseded by \ref igraph_lazy_inclist_get() in igraph 0.6.  * Please use \ref igraph_lazy_inclist_get() instead of this macro.
igraph/include/igraph_arpack.h view
@@ -25,8 +25,8 @@ #include "igraph_vector.h" #include "igraph_matrix.h" -#ifndef ARPACK_H-#define ARPACK_H+#ifndef IGRAPH_ARPACK_H+#define IGRAPH_ARPACK_H  #include "igraph_decls.h" @@ -222,34 +222,34 @@  typedef struct igraph_arpack_options_t {     /* INPUT */-    char bmat[1];         /* I-standard problem, G-generalized */-    int n;            /* Dimension of the eigenproblem */-    char which[2];        /* LA, SA, LM, SM, BE */-    int nev;                 /* Number of eigenvalues to be computed */-    igraph_real_t tol;        /* Stopping criterion */-    int ncv;          /* Number of columns in V */-    int ldv;          /* Leading dimension of V */-    int ishift;       /* 0-reverse comm., 1-exact with tridiagonal */-    int mxiter;              /* Maximum number of update iterations to take */-    int nb;           /* Block size on the recurrence, only 1 works */-    int mode;     /* The kind of problem to be solved (1-5)-                   1: A*x=l*x, A symmetric-                   2: A*x=l*M*x, A symm. M pos. def.-                   3: K*x = l*M*x, K symm., M pos. semidef.-                   4: K*x = l*KG*x, K s. pos. semidef. KG s. indef.-                   5: A*x = l*M*x, A symm., M symm. pos. semidef. */-    int start;        /* 0: random, 1: use the supplied vector */-    int lworkl;       /* Size of temporary storage, default is fine */-    igraph_real_t sigma;          /* The shift for modes 3,4,5 */-    igraph_real_t sigmai;     /* The imaginary part of shift for rnsolve */+    char bmat[1];          /* I-standard problem, G-generalized */+    int n;                 /* Dimension of the eigenproblem */+    char which[2];         /* LA, SA, LM, SM, BE */+    int nev;               /* Number of eigenvalues to be computed */+    igraph_real_t tol;     /* Stopping criterion */+    int ncv;               /* Number of columns in V */+    int ldv;               /* Leading dimension of V */+    int ishift;            /* 0-reverse comm., 1-exact with tridiagonal */+    int mxiter;            /* Maximum number of update iterations to take */+    int nb;                /* Block size on the recurrence, only 1 works */+    int mode;              /* The kind of problem to be solved (1-5)+                               1: A*x=l*x, A symmetric+                               2: A*x=l*M*x, A symm. M pos. def.+                               3: K*x = l*M*x, K symm., M pos. semidef.+                               4: K*x = l*KG*x, K s. pos. semidef. KG s. indef.+                               5: A*x = l*M*x, A symm., M symm. pos. semidef. */+    int start;             /* 0: random, 1: use the supplied vector */+    int lworkl;            /* Size of temporary storage, default is fine */+    igraph_real_t sigma;   /* The shift for modes 3,4,5 */+    igraph_real_t sigmai;  /* The imaginary part of shift for rnsolve */     /* OUTPUT */-    int info;     /* What happened, see docs */-    int ierr;     /* What happened  in the dseupd call */-    int noiter;       /* The number of iterations taken */+    int info;              /* What happened, see docs */+    int ierr;              /* What happened  in the dseupd call */+    int noiter;            /* The number of iterations taken */     int nconv;-    int numop;        /* Number of OP*x operations */-    int numopb;       /* Number of B*x operations if BMAT='G' */-    int numreo;       /* Number of steps of re-orthogonalizations */+    int numop;             /* Number of OP*x operations */+    int numopb;            /* Number of B*x operations if BMAT='G' */+    int numreo;            /* Number of steps of re-orthogonalizations */     /* INTERNAL */     int iparam[11];     int ipntr[14];
igraph/include/igraph_array_pmt.h view
@@ -36,16 +36,16 @@     #define ARRAY3(m,i,j,k) ((m).data.stor_begin[(m).n1n2*(k)+(m).n1*(j)+(i)]) #endif -int FUNCTION(igraph_array3, init)(TYPE(igraph_array3) *a, long int n1, long int n2,+DECLDIR int FUNCTION(igraph_array3, init)(TYPE(igraph_array3) *a, long int n1, long int n2,                                   long int n3);-void FUNCTION(igraph_array3, destroy)(TYPE(igraph_array3) *a);-long int FUNCTION(igraph_array3, size)(const TYPE(igraph_array3) *a);-long int FUNCTION(igraph_array3, n)(const TYPE(igraph_array3) *a, long int idx);-int FUNCTION(igraph_array3, resize)(TYPE(igraph_array3) *a, long int n1, long int n2,+DECLDIR void FUNCTION(igraph_array3, destroy)(TYPE(igraph_array3) *a);+DECLDIR long int FUNCTION(igraph_array3, size)(const TYPE(igraph_array3) *a);+DECLDIR long int FUNCTION(igraph_array3, n)(const TYPE(igraph_array3) *a, long int idx);+DECLDIR int FUNCTION(igraph_array3, resize)(TYPE(igraph_array3) *a, long int n1, long int n2,                                     long int n3);-void FUNCTION(igraph_array3, null)(TYPE(igraph_array3) *a);-BASE FUNCTION(igraph_array3, sum)(const TYPE(igraph_array3) *a);-void FUNCTION(igraph_array3, scale)(TYPE(igraph_array3) *a, BASE by);-void FUNCTION(igraph_array3, fill)(TYPE(igraph_array3) *a, BASE e);-int FUNCTION(igraph_array3, update)(TYPE(igraph_array3) *to,+DECLDIR void FUNCTION(igraph_array3, null)(TYPE(igraph_array3) *a);+DECLDIR BASE FUNCTION(igraph_array3, sum)(const TYPE(igraph_array3) *a);+DECLDIR void FUNCTION(igraph_array3, scale)(TYPE(igraph_array3) *a, BASE by);+DECLDIR void FUNCTION(igraph_array3, fill)(TYPE(igraph_array3) *a, BASE e);+DECLDIR int FUNCTION(igraph_array3, update)(TYPE(igraph_array3) *to,                                     const TYPE(igraph_array3) *from);
igraph/include/igraph_attributes.h view
@@ -21,8 +21,8 @@  */ -#ifndef REST_ATTRIBUTES_H-#define REST_ATTRIBUTES_H+#ifndef IGRAPH_ATTRIBUTES_H+#define IGRAPH_ATTRIBUTES_H  #include "igraph_decls.h" #include "igraph_datatype.h"@@ -385,7 +385,7 @@  /* Experimental attribute handler in C */ -extern const igraph_attribute_table_t igraph_cattribute_table;+DECLDIR extern const igraph_attribute_table_t igraph_cattribute_table;  DECLDIR igraph_real_t igraph_cattribute_GAN(const igraph_t *graph, const char *name); DECLDIR igraph_bool_t igraph_cattribute_GAB(const igraph_t *graph, const char *name);@@ -778,7 +778,7 @@ #define SETVASV(graph,n,v) (igraph_cattribute_VAS_setv((graph),(n),(v))) /**  * \define SETEANV- *  Set a numeric edge attribute for all vertices+ *  Set a numeric edge attribute for all edges  *  * This is a shorthand for \ref igraph_cattribute_EAN_setv().  * \param graph The graph.@@ -788,7 +788,7 @@ #define SETEANV(graph,n,v) (igraph_cattribute_EAN_setv((graph),(n),(v))) /**  * \define SETEABV- *  Set a boolean edge attribute for all vertices+ *  Set a boolean edge attribute for all edges  *  * This is a shorthand for \ref igraph_cattribute_EAB_setv().  * \param graph The graph.@@ -798,7 +798,7 @@ #define SETEABV(graph,n,v) (igraph_cattribute_EAB_setv((graph),(n),(v))) /**  * \define SETEASV- *  Set a string edge attribute for all vertices+ *  Set a string edge attribute for all edges  *  * This is a shorthand for \ref igraph_cattribute_EAS_setv().  * \param graph The graph.
igraph/include/igraph_blas.h view
@@ -21,8 +21,8 @@  */ -#ifndef BLAS_H-#define BLAS_H+#ifndef IGRAPH_BLAS_H+#define IGRAPH_BLAS_H  #include "igraph_types.h" #include "igraph_vector.h"@@ -59,6 +59,9 @@                                      igraph_real_t beta, igraph_real_t* y);  DECLDIR igraph_real_t igraph_blas_dnrm2(const igraph_vector_t *v);++DECLDIR int igraph_blas_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2,+                               igraph_real_t *res);  __END_DECLS 
igraph/include/igraph_blas_internal.h view
@@ -34,13 +34,13 @@  #ifndef INTERNAL_BLAS     #define igraphdaxpy_    daxpy_-    #define igraphdger_ dger_+    #define igraphdger_     dger_     #define igraphdcopy_    dcopy_     #define igraphdscal_    dscal_     #define igraphdswap_    dswap_     #define igraphdgemm_    dgemm_     #define igraphdgemv_    dgemv_-    #define igraphddot_ ddot_+    #define igraphddot_     ddot_     #define igraphdnrm2_    dnrm2_     #define igraphlsame_    lsame_     #define igraphdrot_     drot_@@ -50,6 +50,11 @@     #define igraphdtrsm_    dtrsm_     #define igraphdtrsv_    dtrsv_     #define igraphdnrm2_    dnrm2_+    #define igraphdsymv_    dsymv_+    #define igraphdsyr2_    dsyr2_+    #define igraphdsyr2k_   dsyr2k_+    #define igraphdtrmv_    dtrmv_+    #define igraphdsyrk_    dsyrk_ #endif  int igraphdgemv_(char *trans, int *m, int *n, igraph_real_t *alpha,@@ -61,5 +66,7 @@                  double *beta, double *c__, int *ldc);  double igraphdnrm2_(int *n, double *x, int *incx);++double igraphddot_(int *n, double *dx, int *incx, double *dy, int *incy);  #endif
igraph/include/igraph_cliques.h view
@@ -83,7 +83,7 @@  /**  * \typedef igraph_clique_handler_t- * \brief Type of clique handler functions+ * \brief Type of clique handler functions.  *  * Callback type, called when a clique was found.  *
igraph/include/igraph_coloring.h view
@@ -1,3 +1,23 @@+/*+  Heuristic graph coloring algorithms.+  Copyright (C) 2017 Szabolcs Horvat <szhorvat@gmail.com>++  This program is free software; you can redistribute it and/or modify+  it under the terms of the GNU General Public License as published by+  the Free Software Foundation; either version 2 of the License, or+  (at your option) any later version.++  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License for more details.++  You should have received a copy of the GNU General Public License+  along with this program; if not, write to the Free Software+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA+  02110-1301 USA+*/+ #ifndef IGRAPH_COLORING_H #define IGRAPH_COLORING_H @@ -7,7 +27,9 @@  /**  * \typedef igraph_coloring_greedy_t- * Ordering heuristics for igraph_vertex_coloring_greedy+ * \brief Ordering heuristics for greedy graph coloring.+ *+ * Ordering heuristics for \ref igraph_vertex_coloring_greedy().  *  * \enumval IGRAPH_COLORING_GREEDY_COLORED_NEIGHBORS  Choose vertex with largest number of already colored neighbors.  *
igraph/include/igraph_datatype.h view
@@ -57,11 +57,14 @@  * - <b>is</b> This is basically the same as <b>os</b>, but this time  *   for the incoming edges.  *- * For undirected graph, the same edge list is stored, ie. an- * undirected edge is stored only once, and for checking whether there- * is an undirected edge from \c v1 to \c v2 one- * should search for both \c from=v1, \c to=v2 and- * \c from=v2, \c to=v1.+ * For undirected graphs, the same edge list is stored, i.e. an+ * undirected edge is stored only once. Currently, undirected edges+ * are canonicalized so that the index of the 'from' vertex is not greater+ * than the index of the 'to' vertex. Thus, if v1 <= v2, only the edge (v1, v2)+ * needs to be searched for, not (v2, v1), to determine if v1 and v2 are connected.+ * However, this fact is NOT guaranteed by the documented public API, + * and should not be relied upon by the implementation of any functions, + * except those belonging to the minimal API in type_indexededgelist.c.  *  * The storage requirements for a graph with \c |V| vertices  * and \c |E| edges is \c O(|E|+|V|).
igraph/include/igraph_decls.h view
@@ -8,18 +8,15 @@     #define __END_DECLS /* empty */ #endif +/* In igraph 0.8, we use DECLDIR only with MSVC, not other compilers on Windows. */ #undef DECLDIR-#if defined (_WIN32) || defined (WIN32) || defined (_WIN64) || defined (WIN64)-    #if defined (__MINGW32__) || defined (__CYGWIN32__)+#if defined (_MSC_VER)+    #ifdef IGRAPH_EXPORTS+        #define DECLDIR __declspec(dllexport)+    #elif defined(IGRAPH_STATIC)         #define DECLDIR /**/     #else-        #ifdef IGRAPH_EXPORTS-            #define DECLDIR __declspec(dllexport)-        #elif defined(IGRAPH_STATIC)-            #define DECLDIR /**/-        #else-            #define DECLDIR __declspec(dllimport)-        #endif+        #define DECLDIR __declspec(dllimport)     #endif #else     #define DECLDIR /**/
igraph/include/igraph_dqueue_pmt.h view
@@ -44,6 +44,6 @@ DECLDIR BASE FUNCTION(igraph_dqueue, head)    (const TYPE(igraph_dqueue)* q); DECLDIR BASE FUNCTION(igraph_dqueue, back)    (const TYPE(igraph_dqueue)* q); DECLDIR int FUNCTION(igraph_dqueue, push)    (TYPE(igraph_dqueue)* q, BASE elem);-int FUNCTION(igraph_dqueue, print)(const TYPE(igraph_dqueue)* q);-int FUNCTION(igraph_dqueue, fprint)(const TYPE(igraph_dqueue)* q, FILE *file);+DECLDIR int FUNCTION(igraph_dqueue, print)(const TYPE(igraph_dqueue)* q);+DECLDIR int FUNCTION(igraph_dqueue, fprint)(const TYPE(igraph_dqueue)* q, FILE *file); DECLDIR BASE FUNCTION(igraph_dqueue, e)(const TYPE(igraph_dqueue) *q, long int idx);
igraph/include/igraph_error.h view
@@ -112,7 +112,7 @@  * function of type \ref igraph_error_handler_t and calling  * \ref igraph_set_error_handler(). This feature is useful for interface  * writers, as \a igraph will have the chance to- * signal errors the appropriate way, eg. the R interface defines an+ * signal errors the appropriate way, e.g. the R interface defines an  * error handler which calls the <function>error()</function>  * function, as required by R, while the Python interface has an error  * handler which raises an exception according to the Python way.@@ -217,7 +217,7 @@  * program.  */ -extern igraph_error_handler_t igraph_error_handler_abort;+DECLDIR igraph_error_handler_t igraph_error_handler_abort;  /**  * \var igraph_error_handler_ignore@@ -227,7 +227,7 @@  * with the error code.  */ -extern igraph_error_handler_t igraph_error_handler_ignore;+DECLDIR igraph_error_handler_t igraph_error_handler_ignore;  /**  * \var igraph_error_handler_printignore@@ -237,7 +237,7 @@  * standard error and returns with the error code.  */ -extern igraph_error_handler_t igraph_error_handler_printignore;+DECLDIR igraph_error_handler_t igraph_error_handler_printignore;  /**  * \function igraph_set_error_handler@@ -268,7 +268,7 @@  * \enumval IGRAPH_ENOMEM There wasn't enough memory to allocate  *    on the heap.  * \enumval IGRAPH_PARSEERROR A parse error was found in a file.- * \enumval IGRAPH_EINVAL A parameter's value is invalid. Eg. negative+ * \enumval IGRAPH_EINVAL A parameter's value is invalid. E.g. negative  *    number was specified as the number of vertices.  * \enumval IGRAPH_EXISTS A graph/vertex/edge attribute is already  *    installed with the given name.@@ -278,7 +278,7 @@  * \enumval IGRAPH_NONSQUARE A non-square matrix was received while a  *    square matrix was expected.  * \enumval IGRAPH_EINVMODE Invalid mode parameter.- * \enumval IGRAPH_EFILE A file operation failed. Eg. a file doesn't exist,+ * \enumval IGRAPH_EFILE A file operation failed. E.g. a file doesn't exist,  *   or the user has no rights to open it.  * \enumval IGRAPH_UNIMPLEMENTED Attempted to call an unimplemented or  *   disabled (at compile-time) function.@@ -330,8 +330,6 @@  * \enumval IGRAPH_ERWSTUCK Random walk got stuck.  */ -/* Each enum value below must have a corresponding error string in- * igraph_i_error_strings[] in igraph_error.c */ typedef enum {     IGRAPH_SUCCESS           = 0,     IGRAPH_FAILURE           = 1,@@ -394,6 +392,8 @@     IGRAPH_ERWSTUCK          = 59,     IGRAPH_STOP              = 60, /* undocumented, used internally; signals a request to stop in functions like igraph_i_maximal_cliques_bk */ } igraph_error_type_t;+/* Each enum value above must have a corresponding error string in+ * igraph_i_error_strings[] in igraph_error.c */  /**  * \define IGRAPH_ERROR@@ -408,7 +408,7 @@  * \ref igraph_error() directly.  * \param reason Textual description of the error. This should be  *   something more descriptive than the text associated with the error- *   code. Eg. if the error code is \c IGRAPH_EINVAL,+ *   code. E.g. if the error code is \c IGRAPH_EINVAL,  *   its associated text (see  \ref igraph_strerror()) is "Invalid  *   value" and this string should explain which parameter was invalid  *   and maybe why.@@ -448,7 +448,7 @@  * \brief Trigger an error, printf-like version.  *  * \param reason Textual description of the error, interpreted as- *               a printf format string.+ *               a \c printf format string.  * \param file The source file in which the error was noticed.  * \param line The line in the source file which triggered the error.  * \param igraph_errno The \a igraph error code.@@ -564,7 +564,13 @@  */  #define IGRAPH_FINALLY(func,ptr) \-    IGRAPH_FINALLY_REAL((igraph_finally_func_t*)(func), (ptr))+    { \+        /* the following branch makes the compiler check the compatibility of \+         * func and ptr to detect cases when we are accidentally invoking an \+         * incorrect destructor function with the pointer */ \+        if (0) { func(ptr); } \+        IGRAPH_FINALLY_REAL((igraph_finally_func_t*)(func), (ptr)); \+    }  #if !defined(GCC_VERSION_MAJOR) && defined(__GNUC__)     #define GCC_VERSION_MAJOR  __GNUC__@@ -578,6 +584,19 @@     #define IGRAPH_LIKELY(a)   a #endif +#if IGRAPH_VERIFY_FINALLY_STACK == 1+#define IGRAPH_CHECK(a) \+        do { \+            int enter_stack_size = IGRAPH_FINALLY_STACK_SIZE(); \+            int igraph_i_ret=(a); \+            if (IGRAPH_UNLIKELY(igraph_i_ret != 0)) {\+                IGRAPH_ERROR("", igraph_i_ret); \+            } \+            if (IGRAPH_UNLIKELY(enter_stack_size != IGRAPH_FINALLY_STACK_SIZE())) { \+                IGRAPH_ERROR("Non-matching number of IGRAPH_FINALLY and IGRAPH_FINALLY_CLEAN", IGRAPH_FAILURE); \+            } \+        } while (0)+#else /**  * \define IGRAPH_CHECK  * \brief Check the return value of a function call.@@ -596,18 +615,19 @@  * igraph_error_handler_printignore), and the \a igraph function  * signalling the error is called from another \a igraph function  * then we need to make sure that the error is propagated back to- * the auxiliary (ie. non-igraph) calling function. This is achieved+ * the auxiliary (i.e. non-igraph) calling function. This is achieved  * by using <function>IGRAPH_CHECK</function> on every \a igraph  * call which can return an error code.  */- #define IGRAPH_CHECK(a) do { \         int igraph_i_ret=(a); \         if (IGRAPH_UNLIKELY(igraph_i_ret != 0)) {\             IGRAPH_ERROR("", igraph_i_ret); \         } } while (0)+#endif  + /**  * \section about_igraph_warnings Warning messages  *@@ -658,8 +678,8 @@  DECLDIR igraph_warning_handler_t* igraph_set_warning_handler(igraph_warning_handler_t* new_handler); -extern igraph_warning_handler_t igraph_warning_handler_ignore;-extern igraph_warning_handler_t igraph_warning_handler_print;+DECLDIR igraph_warning_handler_t igraph_warning_handler_ignore;+DECLDIR igraph_warning_handler_t igraph_warning_handler_print;  /**  * \function igraph_warning
igraph/include/igraph_flow.h view
@@ -33,7 +33,7 @@ __BEGIN_DECLS  /* -------------------------------------------------- */-/* MAximum flows, minimum cuts & such                 */+/* Maximum flows, minimum cuts & such                 */ /* -------------------------------------------------- */  /**
+ igraph/include/igraph_handle_exceptions.h view
@@ -0,0 +1,14 @@+#ifndef IGRAPH_HANDLE_EXCEPTIONS_H+#define IGRAPH_HANDLE_EXCEPTIONS_H++#include <exception>+#include <new>++#define IGRAPH_HANDLE_EXCEPTIONS(code) \+    try { code; } \+    catch (const std::bad_alloc &e) { IGRAPH_ERROR(e.what(), IGRAPH_ENOMEM); } \+    catch (const std::exception &e) { IGRAPH_ERROR(e.what(), IGRAPH_FAILURE); } \+    catch (...) { IGRAPH_ERROR("Unknown exception caught", IGRAPH_FAILURE); }+++#endif // IGRAPH_HANDLE_EXCEPTIONS_H
igraph/include/igraph_heap_pmt.h view
@@ -37,9 +37,3 @@ DECLDIR BASE FUNCTION(igraph_heap, delete_top)(TYPE(igraph_heap)* h); DECLDIR long int FUNCTION(igraph_heap, size)(TYPE(igraph_heap)* h); DECLDIR int FUNCTION(igraph_heap, reserve)(TYPE(igraph_heap)* h, long int size);--void FUNCTION(igraph_heap, i_build)(BASE* arr, long int size, long int head);-void FUNCTION(igraph_heap, i_shift_up)(BASE* arr, long int size, long int elem);-void FUNCTION(igraph_heap, i_sink)(BASE* arr, long int size, long int head);-void FUNCTION(igraph_heap, i_switch)(BASE* arr, long int e1, long int e2);-
igraph/include/igraph_hrg.h view
@@ -81,6 +81,7 @@ DECLDIR int igraph_hrg_sample(const igraph_t *graph,                               igraph_t *sample,                               igraph_vector_ptr_t *samples,+                              igraph_integer_t no_samples,                               igraph_hrg_t *hrg,                               igraph_bool_t start); 
igraph/include/igraph_interface.h view
@@ -76,10 +76,49 @@ DECLDIR int igraph_incident(const igraph_t *graph, igraph_vector_t *eids, igraph_integer_t vid,                             igraph_neimode_t mode); -#define IGRAPH_FROM(g,e) ((igraph_integer_t)(VECTOR((g)->from)[(long int)(e)]))-#define IGRAPH_TO(g,e)   ((igraph_integer_t)(VECTOR((g)->to)  [(long int)(e)]))-#define IGRAPH_OTHER(g,e,v) \-    ((igraph_integer_t)(IGRAPH_TO(g,(e))==(v) ? IGRAPH_FROM((g),(e)) : IGRAPH_TO((g),(e))))+/**+ * \define IGRAPH_FROM+ * \brief The source vertex of an edge.+ *+ * Faster than \ref igraph_edge(), but no error checking is done: \p eid is assumed to be valid.+ *+ * \param graph The graph.+ * \param eid   The edge ID.+ * \return The source vertex of the edge.+ * \sa \ref igraph_edge() if error checking is desired.+ */+#define IGRAPH_FROM(graph,eid) ((igraph_integer_t)(VECTOR((graph)->from)[(long int)(eid)]))++/**+ * \define IGRAPH_TO+ * \brief The target vertex of an edge.+ *+ * Faster than \ref igraph_edge(), but no error checking is done: \p eid is assumed to be valid.+ *+ * \param graph The graph object.+ * \param eid   The edge ID.+ * \return The target vertex of the edge.+ * \sa \ref igraph_edge() if error checking is desired.+ */+#define IGRAPH_TO(graph,eid)   ((igraph_integer_t)(VECTOR((graph)->to)  [(long int)(eid)]))++/**+ * \define IGRAPH_OTHER+ * \brief The other endpoint of an edge.+ *+ * Typically used with undirected edges when one endpoint of the edge is known,+ * and the other endpoint is needed. No error checking is done:+ * \p eid and \p vid are assumed to be valid.+ *+ * \param graph The graph object.+ * \param eid   The edge ID.+ * \param vid   The vertex ID of one endpoint of an edge.+ * \return The other endpoint of the edge.+ * \sa \ref IGRAPH_TO() and \ref IGRAPH_FROM() to get the source and target+ *     of directed edges.+ */+#define IGRAPH_OTHER(graph,eid,vid) \+    ((igraph_integer_t)(IGRAPH_TO(graph,(eid))==(vid) ? IGRAPH_FROM((graph),(eid)) : IGRAPH_TO((graph),(eid))))  __END_DECLS 
+ igraph/include/igraph_isoclasses.h view
@@ -0,0 +1,54 @@+/* -*- mode: C -*-  */+/*+   IGraph library.+   Copyright (C) 2008-2020  The igraph development team+   334 Harvard street, Cambridge, MA 02139 USA++   This program is free software; you can redistribute it and/or modify+   it under the terms of the GNU General Public License as published by+   the Free Software Foundation; either version 2 of the License, or+   (at your option) any later version.++   This program is distributed in the hope that it will be useful,+   but WITHOUT ANY WARRANTY; without even the implied warranty of+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+   GNU General Public License for more details.++   You should have received a copy of the GNU General Public License+   along with this program; if not, write to the Free Software+   Foundation, Inc.,  51 Franklin Street, Fifth Floor, Boston, MA+   02110-1301 USA++*/++#ifndef IGRAPH_ISOCLASSES_H+#define IGRAPH_ISOCLASSES_H++#undef __BEGIN_DECLS+#undef __END_DECLS+#ifdef __cplusplus+    #define __BEGIN_DECLS extern "C" {+    #define __END_DECLS }+#else+    #define __BEGIN_DECLS /* empty */+    #define __END_DECLS /* empty */+#endif++__BEGIN_DECLS++extern const unsigned int igraph_i_isoclass_3[];+extern const unsigned int igraph_i_isoclass_4[];+extern const unsigned int igraph_i_isoclass_3u[];+extern const unsigned int igraph_i_isoclass_4u[];+extern const unsigned int igraph_i_isoclass2_3[];+extern const unsigned int igraph_i_isoclass2_4[];+extern const unsigned int igraph_i_isoclass2_3u[];+extern const unsigned int igraph_i_isoclass2_4u[];+extern const unsigned int igraph_i_isoclass_3_idx[];+extern const unsigned int igraph_i_isoclass_4_idx[];+extern const unsigned int igraph_i_isoclass_3u_idx[];+extern const unsigned int igraph_i_isoclass_4u_idx[];++__END_DECLS++#endif
igraph/include/igraph_lsap.h view
@@ -1,6 +1,6 @@ -#ifndef IGRAPH_LSAP-#define IGRAPH_LSAP+#ifndef IGRAPH_LSAP_H+#define IGRAPH_LSAP_H  #include "igraph_types.h" #include "igraph_vector.h"
igraph/include/igraph_matrix.h view
@@ -89,11 +89,11 @@  */ #define MATRIX(m,i,j) ((m).data.stor_begin[(m).nrow*(j)+(i)]) -igraph_bool_t igraph_matrix_all_e_tol(const igraph_matrix_t *lhs,+DECLDIR igraph_bool_t igraph_matrix_all_e_tol(const igraph_matrix_t *lhs,                                       const igraph_matrix_t *rhs,                                       igraph_real_t tol); -int igraph_matrix_zapsmall(igraph_matrix_t *m, igraph_real_t tol);+DECLDIR int igraph_matrix_zapsmall(igraph_matrix_t *m, igraph_real_t tol);  __END_DECLS 
igraph/include/igraph_matrix_pmt.h view
@@ -44,7 +44,7 @@ /* MATRIX */ DECLDIR BASE FUNCTION(igraph_matrix, e)(const TYPE(igraph_matrix) *m,                                         long int row, long int col);-BASE* FUNCTION(igraph_matrix, e_ptr)(const TYPE(igraph_matrix) *m,+DECLDIR BASE* FUNCTION(igraph_matrix, e_ptr)(const TYPE(igraph_matrix) *m,                                      long int row, long int col); DECLDIR void FUNCTION(igraph_matrix, set)(TYPE(igraph_matrix)* m, long int row, long int col,         BASE value);@@ -60,7 +60,7 @@ /* Matrix views          */ /*-----------------------*/ -const TYPE(igraph_matrix) *FUNCTION(igraph_matrix, view)(const TYPE(igraph_matrix) *m,+DECLDIR const TYPE(igraph_matrix) *FUNCTION(igraph_matrix, view)(const TYPE(igraph_matrix) *m,         const BASE *data,         long int nrow,         long int ncol);@@ -207,37 +207,33 @@ /* Print as text          */ /*------------------------*/ -int FUNCTION(igraph_matrix, print)(const TYPE(igraph_matrix) *m);-int FUNCTION(igraph_matrix, printf)(const TYPE(igraph_matrix) *m,+DECLDIR int FUNCTION(igraph_matrix, print)(const TYPE(igraph_matrix) *m);+DECLDIR int FUNCTION(igraph_matrix, printf)(const TYPE(igraph_matrix) *m,                                     const char *format);-int FUNCTION(igraph_matrix, fprint)(const TYPE(igraph_matrix) *m,+DECLDIR int FUNCTION(igraph_matrix, fprint)(const TYPE(igraph_matrix) *m,                                     FILE *file);  #ifdef BASE_COMPLEX -int igraph_matrix_complex_real(const igraph_matrix_complex_t *v,+DECLDIR int igraph_matrix_complex_real(const igraph_matrix_complex_t *v,                                igraph_matrix_t *real);-int igraph_matrix_complex_imag(const igraph_matrix_complex_t *v,+DECLDIR int igraph_matrix_complex_imag(const igraph_matrix_complex_t *v,                                igraph_matrix_t *imag);-int igraph_matrix_complex_realimag(const igraph_matrix_complex_t *v,+DECLDIR int igraph_matrix_complex_realimag(const igraph_matrix_complex_t *v,                                    igraph_matrix_t *real,                                    igraph_matrix_t *imag);-int igraph_matrix_complex_create(igraph_matrix_complex_t *v,+DECLDIR int igraph_matrix_complex_create(igraph_matrix_complex_t *v,                                  const igraph_matrix_t *real,                                  const igraph_matrix_t *imag);-int igraph_matrix_complex_create_polar(igraph_matrix_complex_t *v,+DECLDIR int igraph_matrix_complex_create_polar(igraph_matrix_complex_t *v,                                        const igraph_matrix_t *r,                                        const igraph_matrix_t *theta);  #endif -/* ----------------------------------------------------------------------------*/-/* For internal use only, may be removed, rewritten ... */-/* ----------------------------------------------------------------------------*/--int FUNCTION(igraph_matrix, permdelete_rows)(TYPE(igraph_matrix) *m,+DECLDIR int FUNCTION(igraph_matrix, permdelete_rows)(TYPE(igraph_matrix) *m,         long int *index, long int nremove);-int FUNCTION(igraph_matrix, delete_rows_neg)(TYPE(igraph_matrix) *m,+DECLDIR int FUNCTION(igraph_matrix, delete_rows_neg)(TYPE(igraph_matrix) *m,         const igraph_vector_t *neg,         long int nremove); 
igraph/include/igraph_memory.h view
@@ -21,8 +21,8 @@  */ -#ifndef REST_MEMORY_H-#define REST_MEMORY_H+#ifndef IGRAPH_MEMORY_H+#define IGRAPH_MEMORY_H  #include <stdlib.h> #include "igraph_decls.h"
igraph/include/igraph_nongraph.h view
@@ -72,7 +72,6 @@  DECLDIR int igraph_running_mean(const igraph_vector_t *data, igraph_vector_t *res,                                 igraph_integer_t binwidth);-DECLDIR int igraph_fisher_yates_shuffle(igraph_vector_t *seq); DECLDIR int igraph_random_sample(igraph_vector_t *res, igraph_real_t l, igraph_real_t h,                                  igraph_integer_t length); DECLDIR int igraph_convex_hull(const igraph_matrix_t *data, igraph_vector_t *resverts,
igraph/include/igraph_scg.h view
@@ -48,94 +48,94 @@                IGRAPH_SCG_DIRECTION_RIGHT = 3              } igraph_scg_direction_t; -int igraph_scg_grouping(const igraph_matrix_t *V,-                        igraph_vector_t *groups,-                        igraph_integer_t nt,-                        const igraph_vector_t *nt_vec,-                        igraph_scg_matrix_t mtype,-                        igraph_scg_algorithm_t algo,-                        const igraph_vector_t *p,-                        igraph_integer_t maxiter);+DECLDIR int igraph_scg_grouping(const igraph_matrix_t *V,+                                igraph_vector_t *groups,+                                igraph_integer_t nt,+                                const igraph_vector_t *nt_vec,+                                igraph_scg_matrix_t mtype,+                                igraph_scg_algorithm_t algo,+                                const igraph_vector_t *p,+                                igraph_integer_t maxiter); -int igraph_scg_semiprojectors(const igraph_vector_t *groups,-                              igraph_scg_matrix_t mtype,-                              igraph_matrix_t *L,-                              igraph_matrix_t *R,-                              igraph_sparsemat_t *Lsparse,-                              igraph_sparsemat_t *Rsparse,-                              const igraph_vector_t *p,-                              igraph_scg_norm_t norm);+DECLDIR int igraph_scg_semiprojectors(const igraph_vector_t *groups,+                                      igraph_scg_matrix_t mtype,+                                      igraph_matrix_t *L,+                                      igraph_matrix_t *R,+                                      igraph_sparsemat_t *Lsparse,+                                      igraph_sparsemat_t *Rsparse,+                                      const igraph_vector_t *p,+                                      igraph_scg_norm_t norm); -int igraph_scg_norm_eps(const igraph_matrix_t *V,-                        const igraph_vector_t *groups,-                        igraph_vector_t *eps,-                        igraph_scg_matrix_t mtype,-                        const igraph_vector_t *p,-                        igraph_scg_norm_t norm);+DECLDIR int igraph_scg_norm_eps(const igraph_matrix_t *V,+                                const igraph_vector_t *groups,+                                igraph_vector_t *eps,+                                igraph_scg_matrix_t mtype,+                                const igraph_vector_t *p,+                                igraph_scg_norm_t norm); -int igraph_scg_adjacency(const igraph_t *graph,-                         const igraph_matrix_t *matrix,-                         const igraph_sparsemat_t *sparsemat,-                         const igraph_vector_t *ev,-                         igraph_integer_t nt,-                         const igraph_vector_t *nt_vec,-                         igraph_scg_algorithm_t algo,-                         igraph_vector_t *values,-                         igraph_matrix_t *vectors,-                         igraph_vector_t *groups,-                         igraph_bool_t use_arpack,-                         igraph_integer_t maxiter,-                         igraph_t *scg_graph,-                         igraph_matrix_t *scg_matrix,-                         igraph_sparsemat_t *scg_sparsemat,-                         igraph_matrix_t *L,-                         igraph_matrix_t *R,-                         igraph_sparsemat_t *Lsparse,-                         igraph_sparsemat_t *Rsparse);+DECLDIR int igraph_scg_adjacency(const igraph_t *graph,+                                 const igraph_matrix_t *matrix,+                                 const igraph_sparsemat_t *sparsemat,+                                 const igraph_vector_t *ev,+                                 igraph_integer_t nt,+                                 const igraph_vector_t *nt_vec,+                                 igraph_scg_algorithm_t algo,+                                 igraph_vector_t *values,+                                 igraph_matrix_t *vectors,+                                 igraph_vector_t *groups,+                                 igraph_bool_t use_arpack,+                                 igraph_integer_t maxiter,+                                 igraph_t *scg_graph,+                                 igraph_matrix_t *scg_matrix,+                                 igraph_sparsemat_t *scg_sparsemat,+                                 igraph_matrix_t *L,+                                 igraph_matrix_t *R,+                                 igraph_sparsemat_t *Lsparse,+                                 igraph_sparsemat_t *Rsparse); -int igraph_scg_stochastic(const igraph_t *graph,-                          const igraph_matrix_t *matrix,-                          const igraph_sparsemat_t *sparsemat,-                          const igraph_vector_t *ev,-                          igraph_integer_t nt,-                          const igraph_vector_t *nt_vec,-                          igraph_scg_algorithm_t algo,-                          igraph_scg_norm_t norm,-                          igraph_vector_complex_t *values,-                          igraph_matrix_complex_t *vectors,-                          igraph_vector_t *groups,-                          igraph_vector_t *p,-                          igraph_bool_t use_arpack,-                          igraph_integer_t maxiter,-                          igraph_t *scg_graph,-                          igraph_matrix_t *scg_matrix,-                          igraph_sparsemat_t *scg_sparsemat,-                          igraph_matrix_t *L,-                          igraph_matrix_t *R,-                          igraph_sparsemat_t *Lsparse,-                          igraph_sparsemat_t *Rsparse);+DECLDIR int igraph_scg_stochastic(const igraph_t *graph,+                                  const igraph_matrix_t *matrix,+                                  const igraph_sparsemat_t *sparsemat,+                                  const igraph_vector_t *ev,+                                  igraph_integer_t nt,+                                  const igraph_vector_t *nt_vec,+                                  igraph_scg_algorithm_t algo,+                                  igraph_scg_norm_t norm,+                                  igraph_vector_complex_t *values,+                                  igraph_matrix_complex_t *vectors,+                                  igraph_vector_t *groups,+                                  igraph_vector_t *p,+                                  igraph_bool_t use_arpack,+                                  igraph_integer_t maxiter,+                                  igraph_t *scg_graph,+                                  igraph_matrix_t *scg_matrix,+                                  igraph_sparsemat_t *scg_sparsemat,+                                  igraph_matrix_t *L,+                                  igraph_matrix_t *R,+                                  igraph_sparsemat_t *Lsparse,+                                  igraph_sparsemat_t *Rsparse); -int igraph_scg_laplacian(const igraph_t *graph,-                         const igraph_matrix_t *matrix,-                         const igraph_sparsemat_t *sparsemat,-                         const igraph_vector_t *ev,-                         igraph_integer_t nt,-                         const igraph_vector_t *nt_vec,-                         igraph_scg_algorithm_t algo,-                         igraph_scg_norm_t norm,-                         igraph_scg_direction_t direction,-                         igraph_vector_complex_t *values,-                         igraph_matrix_complex_t *vectors,-                         igraph_vector_t *groups,-                         igraph_bool_t use_arpack,-                         igraph_integer_t maxiter,-                         igraph_t *scg_graph,-                         igraph_matrix_t *scg_matrix,-                         igraph_sparsemat_t *scg_sparsemat,-                         igraph_matrix_t *L,-                         igraph_matrix_t *R,-                         igraph_sparsemat_t *Lsparse,-                         igraph_sparsemat_t *Rsparse);+DECLDIR int igraph_scg_laplacian(const igraph_t *graph,+                                 const igraph_matrix_t *matrix,+                                 const igraph_sparsemat_t *sparsemat,+                                 const igraph_vector_t *ev,+                                 igraph_integer_t nt,+                                 const igraph_vector_t *nt_vec,+                                 igraph_scg_algorithm_t algo,+                                 igraph_scg_norm_t norm,+                                 igraph_scg_direction_t direction,+                                 igraph_vector_complex_t *values,+                                 igraph_matrix_complex_t *vectors,+                                 igraph_vector_t *groups,+                                 igraph_bool_t use_arpack,+                                 igraph_integer_t maxiter,+                                 igraph_t *scg_graph,+                                 igraph_matrix_t *scg_matrix,+                                 igraph_sparsemat_t *scg_sparsemat,+                                 igraph_matrix_t *L,+                                 igraph_matrix_t *R,+                                 igraph_sparsemat_t *Lsparse,+                                 igraph_sparsemat_t *Rsparse);  __END_DECLS 
igraph/include/igraph_sparsemat.h view
@@ -59,228 +59,226 @@     int col; } igraph_sparsemat_iterator_t; -int igraph_sparsemat_init(igraph_sparsemat_t *A, int rows, int cols, int nzmax);-int igraph_sparsemat_copy(igraph_sparsemat_t *to,+DECLDIR int igraph_sparsemat_init(igraph_sparsemat_t *A, int rows, int cols, int nzmax);+DECLDIR int igraph_sparsemat_copy(igraph_sparsemat_t *to,                           const igraph_sparsemat_t *from);-void igraph_sparsemat_destroy(igraph_sparsemat_t *A);-int igraph_sparsemat_realloc(igraph_sparsemat_t *A, int nzmax);+DECLDIR void igraph_sparsemat_destroy(igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_realloc(igraph_sparsemat_t *A, int nzmax); -long int igraph_sparsemat_nrow(const igraph_sparsemat_t *A);-long int igraph_sparsemat_ncol(const igraph_sparsemat_t *B);-igraph_sparsemat_type_t igraph_sparsemat_type(const igraph_sparsemat_t *A);-igraph_bool_t igraph_sparsemat_is_triplet(const igraph_sparsemat_t *A);-igraph_bool_t igraph_sparsemat_is_cc(const igraph_sparsemat_t *A);+DECLDIR long int igraph_sparsemat_nrow(const igraph_sparsemat_t *A);+DECLDIR long int igraph_sparsemat_ncol(const igraph_sparsemat_t *B);+DECLDIR igraph_sparsemat_type_t igraph_sparsemat_type(const igraph_sparsemat_t *A);+DECLDIR igraph_bool_t igraph_sparsemat_is_triplet(const igraph_sparsemat_t *A);+DECLDIR igraph_bool_t igraph_sparsemat_is_cc(const igraph_sparsemat_t *A); -int igraph_sparsemat_permute(const igraph_sparsemat_t *A,-                             const igraph_vector_int_t *p,-                             const igraph_vector_int_t *q,-                             igraph_sparsemat_t *res);+DECLDIR int igraph_sparsemat_permute(const igraph_sparsemat_t *A,+                                     const igraph_vector_int_t *p,+                                     const igraph_vector_int_t *q,+                                     igraph_sparsemat_t *res); -int igraph_sparsemat_index(const igraph_sparsemat_t *A,-                           const igraph_vector_int_t *p,-                           const igraph_vector_int_t *q,-                           igraph_sparsemat_t *res,-                           igraph_real_t *constres);+DECLDIR int igraph_sparsemat_index(const igraph_sparsemat_t *A,+                                   const igraph_vector_int_t *p,+                                   const igraph_vector_int_t *q,+                                   igraph_sparsemat_t *res,+                                   igraph_real_t *constres); -int igraph_sparsemat_entry(igraph_sparsemat_t *A, int row, int col,-                           igraph_real_t elem);-int igraph_sparsemat_compress(const igraph_sparsemat_t *A,-                              igraph_sparsemat_t *res);-int igraph_sparsemat_transpose(const igraph_sparsemat_t *A,-                               igraph_sparsemat_t *res, int values);-igraph_bool_t igraph_sparsemat_is_symmetric(const igraph_sparsemat_t *A);-int igraph_sparsemat_dupl(igraph_sparsemat_t *A);-int igraph_sparsemat_fkeep(igraph_sparsemat_t *A,-                           int (*fkeep)(int, int, igraph_real_t, void*),-                           void *other);-int igraph_sparsemat_dropzeros(igraph_sparsemat_t *A);-int igraph_sparsemat_droptol(igraph_sparsemat_t *A, igraph_real_t tol);-int igraph_sparsemat_multiply(const igraph_sparsemat_t *A,-                              const igraph_sparsemat_t *B,-                              igraph_sparsemat_t *res);-int igraph_sparsemat_add(const igraph_sparsemat_t *A,-                         const igraph_sparsemat_t *B,-                         igraph_real_t alpha,-                         igraph_real_t beta,-                         igraph_sparsemat_t *res);-int igraph_sparsemat_gaxpy(const igraph_sparsemat_t *A,-                           const igraph_vector_t *x,-                           igraph_vector_t *res);+DECLDIR int igraph_sparsemat_entry(igraph_sparsemat_t *A, int row, int col,+                                   igraph_real_t elem);+DECLDIR int igraph_sparsemat_compress(const igraph_sparsemat_t *A,+                                      igraph_sparsemat_t *res);+DECLDIR int igraph_sparsemat_transpose(const igraph_sparsemat_t *A,+                                       igraph_sparsemat_t *res, int values);+DECLDIR igraph_bool_t igraph_sparsemat_is_symmetric(const igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_dupl(igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_fkeep(igraph_sparsemat_t *A,+                                   int (*fkeep)(int, int, igraph_real_t, void*),+                                   void *other);+DECLDIR int igraph_sparsemat_dropzeros(igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_droptol(igraph_sparsemat_t *A, igraph_real_t tol);+DECLDIR int igraph_sparsemat_multiply(const igraph_sparsemat_t *A,+                                      const igraph_sparsemat_t *B,+                                      igraph_sparsemat_t *res);+DECLDIR int igraph_sparsemat_add(const igraph_sparsemat_t *A,+                                 const igraph_sparsemat_t *B,+                                 igraph_real_t alpha,+                                 igraph_real_t beta,+                                 igraph_sparsemat_t *res);+DECLDIR int igraph_sparsemat_gaxpy(const igraph_sparsemat_t *A,+                                   const igraph_vector_t *x,+                                   igraph_vector_t *res); -int igraph_sparsemat_lsolve(const igraph_sparsemat_t *A,-                            const igraph_vector_t *b,-                            igraph_vector_t *res);-int igraph_sparsemat_ltsolve(const igraph_sparsemat_t *A,-                             const igraph_vector_t *b,-                             igraph_vector_t *res);-int igraph_sparsemat_usolve(const igraph_sparsemat_t *A,-                            const igraph_vector_t *b,-                            igraph_vector_t *res);-int igraph_sparsemat_utsolve(const igraph_sparsemat_t *A,-                             const igraph_vector_t *b,-                             igraph_vector_t *res);+DECLDIR int igraph_sparsemat_lsolve(const igraph_sparsemat_t *A,+                                    const igraph_vector_t *b,+                                    igraph_vector_t *res);+DECLDIR int igraph_sparsemat_ltsolve(const igraph_sparsemat_t *A,+                                     const igraph_vector_t *b,+                                     igraph_vector_t *res);+DECLDIR int igraph_sparsemat_usolve(const igraph_sparsemat_t *A,+                                    const igraph_vector_t *b,+                                    igraph_vector_t *res);+DECLDIR int igraph_sparsemat_utsolve(const igraph_sparsemat_t *A,+                                     const igraph_vector_t *b,+                                     igraph_vector_t *res); -int igraph_sparsemat_cholsol(const igraph_sparsemat_t *A,-                             const igraph_vector_t *b,-                             igraph_vector_t *res,-                             int order);+DECLDIR int igraph_sparsemat_cholsol(const igraph_sparsemat_t *A,+                                     const igraph_vector_t *b,+                                     igraph_vector_t *res,+                                     int order); -int igraph_sparsemat_lusol(const igraph_sparsemat_t *A,-                           const igraph_vector_t *b,-                           igraph_vector_t *res,-                           int order,-                           igraph_real_t tol);+DECLDIR int igraph_sparsemat_lusol(const igraph_sparsemat_t *A,+                                   const igraph_vector_t *b,+                                   igraph_vector_t *res,+                                   int order,+                                   igraph_real_t tol); -int igraph_sparsemat_print(const igraph_sparsemat_t *A,-                           FILE *outstream);+DECLDIR int igraph_sparsemat_print(const igraph_sparsemat_t *A,+                                   FILE *outstream); -int igraph_sparsemat_eye(igraph_sparsemat_t *A, int n, int nzmax,-                         igraph_real_t value,-                         igraph_bool_t compress);+DECLDIR int igraph_sparsemat_eye(igraph_sparsemat_t *A, int n, int nzmax,+                                 igraph_real_t value,+                                 igraph_bool_t compress); -int igraph_sparsemat_diag(igraph_sparsemat_t *A, int nzmax,-                          const igraph_vector_t *values,-                          igraph_bool_t compress);+DECLDIR int igraph_sparsemat_diag(igraph_sparsemat_t *A, int nzmax,+                                  const igraph_vector_t *values,+                                  igraph_bool_t compress); -int igraph_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A,-                     igraph_bool_t directed);+DECLDIR int igraph_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A,+                             igraph_bool_t directed); -int igraph_weighted_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A,-                              igraph_bool_t directed, const char *attr,-                              igraph_bool_t loops);+DECLDIR int igraph_weighted_sparsemat(igraph_t *graph, const igraph_sparsemat_t *A,+                                      igraph_bool_t directed, const char *attr,+                                      igraph_bool_t loops); -int igraph_get_sparsemat(const igraph_t *graph, igraph_sparsemat_t *res);+DECLDIR int igraph_get_sparsemat(const igraph_t *graph, igraph_sparsemat_t *res); -int igraph_matrix_as_sparsemat(igraph_sparsemat_t *res,-                               const igraph_matrix_t *mat,-                               igraph_real_t tol);+DECLDIR int igraph_matrix_as_sparsemat(igraph_sparsemat_t *res,+                                       const igraph_matrix_t *mat,+                                       igraph_real_t tol); -int igraph_sparsemat_as_matrix(igraph_matrix_t *res,-                               const igraph_sparsemat_t *spmat);+DECLDIR int igraph_sparsemat_as_matrix(igraph_matrix_t *res,+                                       const igraph_sparsemat_t *spmat);  typedef enum { IGRAPH_SPARSEMAT_SOLVE_LU,                IGRAPH_SPARSEMAT_SOLVE_QR              } igraph_sparsemat_solve_t; -int igraph_sparsemat_arpack_rssolve(const igraph_sparsemat_t *A,-                                    igraph_arpack_options_t *options,-                                    igraph_arpack_storage_t *storage,-                                    igraph_vector_t *values,-                                    igraph_matrix_t *vectors,-                                    igraph_sparsemat_solve_t solvemethod);+DECLDIR int igraph_sparsemat_arpack_rssolve(const igraph_sparsemat_t *A,+                                            igraph_arpack_options_t *options,+                                            igraph_arpack_storage_t *storage,+                                            igraph_vector_t *values,+                                            igraph_matrix_t *vectors,+                                            igraph_sparsemat_solve_t solvemethod); -int igraph_sparsemat_arpack_rnsolve(const igraph_sparsemat_t *A,-                                    igraph_arpack_options_t *options,-                                    igraph_arpack_storage_t *storage,-                                    igraph_matrix_t *values,-                                    igraph_matrix_t *vectors);+DECLDIR int igraph_sparsemat_arpack_rnsolve(const igraph_sparsemat_t *A,+                                            igraph_arpack_options_t *options,+                                            igraph_arpack_storage_t *storage,+                                            igraph_matrix_t *values,+                                            igraph_matrix_t *vectors); -int igraph_sparsemat_lu(const igraph_sparsemat_t *A,-                        const igraph_sparsemat_symbolic_t *dis,-                        igraph_sparsemat_numeric_t *din, double tol);+DECLDIR int igraph_sparsemat_lu(const igraph_sparsemat_t *A,+                                const igraph_sparsemat_symbolic_t *dis,+                                igraph_sparsemat_numeric_t *din, double tol); -int igraph_sparsemat_qr(const igraph_sparsemat_t *A,-                        const igraph_sparsemat_symbolic_t *dis,-                        igraph_sparsemat_numeric_t *din);+DECLDIR int igraph_sparsemat_qr(const igraph_sparsemat_t *A,+                                const igraph_sparsemat_symbolic_t *dis,+                                igraph_sparsemat_numeric_t *din); -int igraph_sparsemat_luresol(const igraph_sparsemat_symbolic_t *dis,-                             const igraph_sparsemat_numeric_t *din,-                             const igraph_vector_t *b,-                             igraph_vector_t *res);+DECLDIR int igraph_sparsemat_luresol(const igraph_sparsemat_symbolic_t *dis,+                                     const igraph_sparsemat_numeric_t *din,+                                     const igraph_vector_t *b,+                                     igraph_vector_t *res); -int igraph_sparsemat_qrresol(const igraph_sparsemat_symbolic_t *dis,-                             const igraph_sparsemat_numeric_t *din,-                             const igraph_vector_t *b,-                             igraph_vector_t *res);+DECLDIR int igraph_sparsemat_qrresol(const igraph_sparsemat_symbolic_t *dis,+                                     const igraph_sparsemat_numeric_t *din,+                                     const igraph_vector_t *b,+                                     igraph_vector_t *res); -int igraph_sparsemat_symbqr(long int order, const igraph_sparsemat_t *A,-                            igraph_sparsemat_symbolic_t *dis);+DECLDIR int igraph_sparsemat_symbqr(long int order, const igraph_sparsemat_t *A,+                                    igraph_sparsemat_symbolic_t *dis); -int igraph_sparsemat_symblu(long int order, const igraph_sparsemat_t *A,-                            igraph_sparsemat_symbolic_t *dis);+DECLDIR int igraph_sparsemat_symblu(long int order, const igraph_sparsemat_t *A,+                                    igraph_sparsemat_symbolic_t *dis);  -void igraph_sparsemat_symbolic_destroy(igraph_sparsemat_symbolic_t *dis);-void igraph_sparsemat_numeric_destroy(igraph_sparsemat_numeric_t *din);+DECLDIR void igraph_sparsemat_symbolic_destroy(igraph_sparsemat_symbolic_t *dis);+DECLDIR void igraph_sparsemat_numeric_destroy(igraph_sparsemat_numeric_t *din); -igraph_real_t igraph_sparsemat_max(igraph_sparsemat_t *A);-igraph_real_t igraph_sparsemat_min(igraph_sparsemat_t *A);-int igraph_sparsemat_minmax(igraph_sparsemat_t *A,-                            igraph_real_t *min, igraph_real_t *max);+DECLDIR igraph_real_t igraph_sparsemat_max(igraph_sparsemat_t *A);+DECLDIR igraph_real_t igraph_sparsemat_min(igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_minmax(igraph_sparsemat_t *A,+                                    igraph_real_t *min, igraph_real_t *max); -long int igraph_sparsemat_count_nonzero(igraph_sparsemat_t *A);-long int igraph_sparsemat_count_nonzerotol(igraph_sparsemat_t *A,-        igraph_real_t tol);-int igraph_sparsemat_rowsums(const igraph_sparsemat_t *A,-                             igraph_vector_t *res);-int igraph_sparsemat_colsums(const igraph_sparsemat_t *A,-                             igraph_vector_t *res);+DECLDIR long int igraph_sparsemat_count_nonzero(igraph_sparsemat_t *A);+DECLDIR long int igraph_sparsemat_count_nonzerotol(igraph_sparsemat_t *A,+                                                   igraph_real_t tol);+DECLDIR int igraph_sparsemat_rowsums(const igraph_sparsemat_t *A,+                                     igraph_vector_t *res);+DECLDIR int igraph_sparsemat_colsums(const igraph_sparsemat_t *A,+                                     igraph_vector_t *res); -int igraph_sparsemat_rowmins(igraph_sparsemat_t *A,-                             igraph_vector_t *res);-int igraph_sparsemat_colmins(igraph_sparsemat_t *A,-                             igraph_vector_t *res);+DECLDIR int igraph_sparsemat_rowmins(igraph_sparsemat_t *A,+                                     igraph_vector_t *res);+DECLDIR int igraph_sparsemat_colmins(igraph_sparsemat_t *A,+                                     igraph_vector_t *res); -int igraph_sparsemat_rowmaxs(igraph_sparsemat_t *A,-                             igraph_vector_t *res);-int igraph_sparsemat_colmaxs(igraph_sparsemat_t *A,-                             igraph_vector_t *res);+DECLDIR int igraph_sparsemat_rowmaxs(igraph_sparsemat_t *A,+                                     igraph_vector_t *res);+DECLDIR int igraph_sparsemat_colmaxs(igraph_sparsemat_t *A,+                                     igraph_vector_t *res); -int igraph_sparsemat_which_min_rows(igraph_sparsemat_t *A,-                                    igraph_vector_t *res,-                                    igraph_vector_int_t *pos);-int igraph_sparsemat_which_min_cols(igraph_sparsemat_t *A,-                                    igraph_vector_t *res,-                                    igraph_vector_int_t *pos);+DECLDIR int igraph_sparsemat_which_min_rows(igraph_sparsemat_t *A,+                                            igraph_vector_t *res,+                                            igraph_vector_int_t *pos);+DECLDIR int igraph_sparsemat_which_min_cols(igraph_sparsemat_t *A,+                                            igraph_vector_t *res,+                                            igraph_vector_int_t *pos); -int igraph_sparsemat_scale(igraph_sparsemat_t *A, igraph_real_t by);+DECLDIR int igraph_sparsemat_scale(igraph_sparsemat_t *A, igraph_real_t by);  -int igraph_sparsemat_add_rows(igraph_sparsemat_t *A, long int n);-int igraph_sparsemat_add_cols(igraph_sparsemat_t *A, long int n);-int igraph_sparsemat_resize(igraph_sparsemat_t *A, long int nrow,-                            long int ncol, int nzmax);-int igraph_sparsemat_nonzero_storage(const igraph_sparsemat_t *A);-int igraph_sparsemat_getelements(const igraph_sparsemat_t *A,-                                 igraph_vector_int_t *i,-                                 igraph_vector_int_t *j,-                                 igraph_vector_t *x);-int igraph_sparsemat_getelements_sorted(const igraph_sparsemat_t *A,-                                        igraph_vector_int_t *i,-                                        igraph_vector_int_t *j,-                                        igraph_vector_t *x);-int igraph_sparsemat_scale_rows(igraph_sparsemat_t *A,-                                const igraph_vector_t *fact);-int igraph_sparsemat_scale_cols(igraph_sparsemat_t *A,-                                const igraph_vector_t *fact);-int igraph_sparsemat_multiply_by_dense(const igraph_sparsemat_t *A,-                                       const igraph_matrix_t *B,-                                       igraph_matrix_t *res);-int igraph_sparsemat_dense_multiply(const igraph_matrix_t *A,-                                    const igraph_sparsemat_t *B,-                                    igraph_matrix_t *res);+DECLDIR int igraph_sparsemat_add_rows(igraph_sparsemat_t *A, long int n);+DECLDIR int igraph_sparsemat_add_cols(igraph_sparsemat_t *A, long int n);+DECLDIR int igraph_sparsemat_resize(igraph_sparsemat_t *A, long int nrow,+                                    long int ncol, int nzmax);+DECLDIR int igraph_sparsemat_nonzero_storage(const igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_getelements(const igraph_sparsemat_t *A,+                                         igraph_vector_int_t *i,+                                         igraph_vector_int_t *j,+                                         igraph_vector_t *x);+DECLDIR int igraph_sparsemat_getelements_sorted(const igraph_sparsemat_t *A,+                                                igraph_vector_int_t *i,+                                                igraph_vector_int_t *j,+                                                igraph_vector_t *x);+DECLDIR int igraph_sparsemat_scale_rows(igraph_sparsemat_t *A,+                                        const igraph_vector_t *fact);+DECLDIR int igraph_sparsemat_scale_cols(igraph_sparsemat_t *A,+                                        const igraph_vector_t *fact);+DECLDIR int igraph_sparsemat_multiply_by_dense(const igraph_sparsemat_t *A,+                                               const igraph_matrix_t *B,+                                               igraph_matrix_t *res);+DECLDIR int igraph_sparsemat_dense_multiply(const igraph_matrix_t *A,+                                            const igraph_sparsemat_t *B,+                                            igraph_matrix_t *res); -int igraph_i_sparsemat_view(igraph_sparsemat_t *A, int nzmax, int m, int n,-                            int *p, int *i, double *x, int nz);+DECLDIR int igraph_i_sparsemat_view(igraph_sparsemat_t *A, int nzmax, int m, int n,+                                    int *p, int *i, double *x, int nz); -int igraph_sparsemat_sort(const igraph_sparsemat_t *A,-                          igraph_sparsemat_t *sorted);+DECLDIR int igraph_sparsemat_sort(const igraph_sparsemat_t *A,+                                  igraph_sparsemat_t *sorted); -int igraph_sparsemat_nzmax(const igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_nzmax(const igraph_sparsemat_t *A); -int igraph_sparsemat_neg(igraph_sparsemat_t *A);+DECLDIR int igraph_sparsemat_neg(igraph_sparsemat_t *A); -int igraph_sparsemat_iterator_init(igraph_sparsemat_iterator_t *it,-                                   igraph_sparsemat_t *sparsemat);-int igraph_sparsemat_iterator_reset(igraph_sparsemat_iterator_t *it);-igraph_bool_t-igraph_sparsemat_iterator_end(const igraph_sparsemat_iterator_t *it);-int igraph_sparsemat_iterator_row(const igraph_sparsemat_iterator_t *it);-int igraph_sparsemat_iterator_col(const igraph_sparsemat_iterator_t *it);-int igraph_sparsemat_iterator_idx(const igraph_sparsemat_iterator_t *it);-igraph_real_t-igraph_sparsemat_iterator_get(const igraph_sparsemat_iterator_t *it);-int igraph_sparsemat_iterator_next(igraph_sparsemat_iterator_t *it);+DECLDIR int igraph_sparsemat_iterator_init(igraph_sparsemat_iterator_t *it,+                                           igraph_sparsemat_t *sparsemat);+DECLDIR int igraph_sparsemat_iterator_reset(igraph_sparsemat_iterator_t *it);+DECLDIR igraph_bool_t igraph_sparsemat_iterator_end(const igraph_sparsemat_iterator_t *it);+DECLDIR int igraph_sparsemat_iterator_row(const igraph_sparsemat_iterator_t *it);+DECLDIR int igraph_sparsemat_iterator_col(const igraph_sparsemat_iterator_t *it);+DECLDIR int igraph_sparsemat_iterator_idx(const igraph_sparsemat_iterator_t *it);+DECLDIR igraph_real_t igraph_sparsemat_iterator_get(const igraph_sparsemat_iterator_t *it);+DECLDIR int igraph_sparsemat_iterator_next(igraph_sparsemat_iterator_t *it);  __END_DECLS 
igraph/include/igraph_statusbar.h view
@@ -21,8 +21,8 @@  */ -#ifndef IGRAPH_STATUSBAR-#define IGRAPH_STATUSBAR+#ifndef IGRAPH_STATUSBAR_H+#define IGRAPH_STATUSBAR_H  #include "igraph_decls.h" 
igraph/include/igraph_strvector.h view
@@ -57,7 +57,7 @@ #define IGRAPH_STRVECTOR_NULL { 0,0 } #define IGRAPH_STRVECTOR_INIT_FINALLY(v, size) \     do { IGRAPH_CHECK(igraph_strvector_init(v, size)); \-        IGRAPH_FINALLY( (igraph_finally_func_t*) igraph_strvector_destroy, v); } while (0)+        IGRAPH_FINALLY( igraph_strvector_destroy, v); } while (0)  DECLDIR int igraph_strvector_init(igraph_strvector_t *sv, long int len); DECLDIR void igraph_strvector_destroy(igraph_strvector_t *sv);
igraph/include/igraph_types.h view
@@ -21,8 +21,8 @@  */ -#ifndef REST_TYPES_H-#define REST_TYPES_H+#ifndef IGRAPH_TYPES_H+#define IGRAPH_TYPES_H  #include "igraph_decls.h" 
igraph/include/igraph_vector.h view
@@ -28,14 +28,6 @@ #include "igraph_types.h" #include "igraph_complex.h" -#ifdef HAVE_STDINT_H-    #include <stdint.h>-#else-    #if defined(HAVE_SYS_INT_TYPES_H) && HAVE_SYS_INT_TYPES_H-        #include <sys/int_types.h>    /* for Solaris */-    #endif-#endif- __BEGIN_DECLS  /* -------------------------------------------------- */@@ -144,6 +136,11 @@     do { IGRAPH_CHECK(igraph_vector_bool_init(v, size)); \         IGRAPH_FINALLY(igraph_vector_bool_destroy, v); } while (0) #endif+#ifndef IGRAPH_VECTOR_CHAR_INIT_FINALLY+#define IGRAPH_VECTOR_CHAR_INIT_FINALLY(v, size) \+  do { IGRAPH_CHECK(igraph_vector_char_init(v, size)); \+  IGRAPH_FINALLY(igraph_vector_char_destroy, v); } while (0)+#endif #ifndef IGRAPH_VECTOR_INT_INIT_FINALLY #define IGRAPH_VECTOR_INT_INIT_FINALLY(v, size) \     do { IGRAPH_CHECK(igraph_vector_int_init(v, size)); \@@ -168,15 +165,14 @@  DECLDIR int igraph_vector_zapsmall(igraph_vector_t *v, igraph_real_t tol); -/* These are for internal use only */-int igraph_vector_order(const igraph_vector_t* v, const igraph_vector_t *v2,+DECLDIR int igraph_vector_order(const igraph_vector_t* v, const igraph_vector_t *v2,                         igraph_vector_t* res, igraph_real_t maxval);-int igraph_vector_order1(const igraph_vector_t* v,+DECLDIR int igraph_vector_order1(const igraph_vector_t* v,                          igraph_vector_t* res, igraph_real_t maxval);-int igraph_vector_order1_int(const igraph_vector_t* v,+DECLDIR int igraph_vector_order1_int(const igraph_vector_t* v,                              igraph_vector_int_t* res, igraph_real_t maxval);-int igraph_vector_order2(igraph_vector_t *v);-int igraph_vector_rank(const igraph_vector_t *v, igraph_vector_t *res,+DECLDIR int igraph_vector_order2(igraph_vector_t *v);+DECLDIR int igraph_vector_rank(const igraph_vector_t *v, igraph_vector_t *res,                        long int nodes);  __END_DECLS
igraph/include/igraph_vector_pmt.h view
@@ -40,29 +40,29 @@ /*--------------------*/  #ifndef VECTOR-    /**-    * \ingroup vector-    * \define VECTOR-    * \brief Accessing an element of a vector.-    *-    * Usage:-    * \verbatim VECTOR(v)[0] \endverbatim-    * to access the first element of the vector, you can also use this in-    * assignments, like:-    * \verbatim VECTOR(v)[10]=5; \endverbatim-    *-    * Note that there are no range checks right now.-    * This functionality might be redefined later as a real function-    * instead of a <code>#define</code>.-    * \param v The vector object.-    *-    * Time complexity: O(1).-    */-    #define VECTOR(v) ((v).stor_begin)+/**+ * \ingroup vector+ * \define VECTOR+ * \brief Accessing an element of a vector.+ *+ * Usage:+ * \verbatim VECTOR(v)[0] \endverbatim+ * to access the first element of the vector, you can also use this in+ * assignments, like:+ * \verbatim VECTOR(v)[10]=5; \endverbatim+ *+ * Note that there are no range checks right now.+ * This functionality might be redefined later as a real function+ * instead of a <code>#define</code>.+ * \param v The vector object.+ *+ * Time complexity: O(1).+ */+#define VECTOR(v) ((v).stor_begin) #endif  DECLDIR BASE FUNCTION(igraph_vector, e)(const TYPE(igraph_vector)* v, long int pos);-BASE* FUNCTION(igraph_vector, e_ptr)(const TYPE(igraph_vector)* v, long int pos);+DECLDIR BASE* FUNCTION(igraph_vector, e_ptr)(const TYPE(igraph_vector)* v, long int pos); DECLDIR void FUNCTION(igraph_vector, set)(TYPE(igraph_vector)* v, long int pos, BASE value); DECLDIR BASE FUNCTION(igraph_vector, tail)(const TYPE(igraph_vector) *v); @@ -177,6 +177,9 @@ DECLDIR igraph_bool_t FUNCTION(igraph_vector, search)(const TYPE(igraph_vector) *v,         long int from, BASE what,         long int *pos);+DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch_slice)(const TYPE(igraph_vector) *v,+        BASE what, long int *pos,+        long int start, long int end); DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch)(const TYPE(igraph_vector) *v,         BASE what, long int *pos); DECLDIR igraph_bool_t FUNCTION(igraph_vector, binsearch2)(const TYPE(igraph_vector) *v,@@ -202,6 +205,7 @@ /*-----------*/  DECLDIR void FUNCTION(igraph_vector, sort)(TYPE(igraph_vector) *v);+DECLDIR void FUNCTION(igraph_vector, reverse_sort)(TYPE(igraph_vector) *v); DECLDIR long int FUNCTION(igraph_vector, qsort_ind)(TYPE(igraph_vector) *v,         igraph_vector_t *inds, igraph_bool_t descending); @@ -209,10 +213,10 @@ /* Printing  */ /*-----------*/ -int FUNCTION(igraph_vector, print)(const TYPE(igraph_vector) *v);-int FUNCTION(igraph_vector, printf)(const TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, print)(const TYPE(igraph_vector) *v);+DECLDIR int FUNCTION(igraph_vector, printf)(const TYPE(igraph_vector) *v,                                     const char *format);-int FUNCTION(igraph_vector, fprint)(const TYPE(igraph_vector) *v, FILE *file);+DECLDIR int FUNCTION(igraph_vector, fprint)(const TYPE(igraph_vector) *v, FILE *file);  #ifdef BASE_COMPLEX @@ -232,34 +236,30 @@  #endif -/* ----------------------------------------------------------------------------*/-/* For internal use only, may be removed, rewritten ... */-/* ----------------------------------------------------------------------------*/--int FUNCTION(igraph_vector, init_real)(TYPE(igraph_vector)*v, int no, ...);-int FUNCTION(igraph_vector, init_int)(TYPE(igraph_vector)*v, int no, ...);-int FUNCTION(igraph_vector, init_real_end)(TYPE(igraph_vector)*v, BASE endmark, ...);-int FUNCTION(igraph_vector, init_int_end)(TYPE(igraph_vector)*v, int endmark, ...);+DECLDIR int FUNCTION(igraph_vector, init_real)(TYPE(igraph_vector)*v, int no, ...);+DECLDIR int FUNCTION(igraph_vector, init_int)(TYPE(igraph_vector)*v, int no, ...);+DECLDIR int FUNCTION(igraph_vector, init_real_end)(TYPE(igraph_vector)*v, BASE endmark, ...);+DECLDIR int FUNCTION(igraph_vector, init_int_end)(TYPE(igraph_vector)*v, int endmark, ...); -int FUNCTION(igraph_vector, move_interval)(TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, move_interval)(TYPE(igraph_vector) *v,         long int begin, long int end, long int to);-int FUNCTION(igraph_vector, move_interval2)(TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, move_interval2)(TYPE(igraph_vector) *v,         long int begin, long int end, long int to);-void FUNCTION(igraph_vector, permdelete)(TYPE(igraph_vector) *v,+DECLDIR void FUNCTION(igraph_vector, permdelete)(TYPE(igraph_vector) *v,         const igraph_vector_t *index,         long int nremove);-int FUNCTION(igraph_vector, filter_smaller)(TYPE(igraph_vector) *v, BASE elem);-int FUNCTION(igraph_vector, get_interval)(const TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, filter_smaller)(TYPE(igraph_vector) *v, BASE elem);+DECLDIR int FUNCTION(igraph_vector, get_interval)(const TYPE(igraph_vector) *v,         TYPE(igraph_vector) *res,         long int from, long int to);-int FUNCTION(igraph_vector, difference_sorted)(const TYPE(igraph_vector) *v1,+DECLDIR int FUNCTION(igraph_vector, difference_sorted)(const TYPE(igraph_vector) *v1,         const TYPE(igraph_vector) *v2, TYPE(igraph_vector) *result);-int FUNCTION(igraph_vector, intersect_sorted)(const TYPE(igraph_vector) *v1,+DECLDIR int FUNCTION(igraph_vector, intersect_sorted)(const TYPE(igraph_vector) *v1,         const TYPE(igraph_vector) *v2, TYPE(igraph_vector) *result); -int FUNCTION(igraph_vector, index)(const TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, index)(const TYPE(igraph_vector) *v,                                    TYPE(igraph_vector) *newv,                                    const igraph_vector_t *idx); -int FUNCTION(igraph_vector, index_int)(TYPE(igraph_vector) *v,+DECLDIR int FUNCTION(igraph_vector, index_int)(TYPE(igraph_vector) *v,                                        const igraph_vector_int_t *idx);
igraph/include/igraph_version.h view
@@ -28,13 +28,13 @@  __BEGIN_DECLS -#define IGRAPH_VERSION "0.8.0"+#define IGRAPH_VERSION "0.8.5" #define IGRAPH_VERSION_MAJOR 0 #define IGRAPH_VERSION_MINOR 8-#define IGRAPH_VERSION_PATCH 0+#define IGRAPH_VERSION_PATCH 5 #define IGRAPH_VERSION_PRERELEASE "" -int igraph_version(const char **version_string,+DECLDIR int igraph_version(const char **version_string,                    int *major,                    int *minor,                    int *subminor);
igraph/include/igraph_visitor.h view
@@ -62,7 +62,7 @@  *    as a request to stop the BFS and return to the caller. If a BFS  *    is terminated like this, then all elements of the result vectors  *    that were not yet calculated at the point of the termination- *    contain \c IGRAPH_NAN.+ *    contain NaN.  *  * \sa \ref igraph_bfs()  */@@ -109,7 +109,7 @@  *    as a request to stop the DFS and return to the caller. If a DFS  *    is terminated like this, then all elements of the result vectors  *    that were not yet calculated at the point of the termination- *    contain \c IGRAPH_NAN.+ *    contain NaN.  *  * \sa \ref igraph_dfs()  */
igraph/include/infomap_FlowGraph.h view
@@ -62,7 +62,7 @@     double alpha, beta;      int Ndanglings;-    vector<int> danglings; // id of dangling nodes+    std::vector<int> danglings; // id of dangling nodes      double exit;                  //     double exitFlow;              //
igraph/include/infomap_Greedy.h view
@@ -69,16 +69,16 @@     double alpha, beta;     // local copy of fgraph alpha, beta (=alpha -  Nnode = graph->Nnode;1) -    vector<int> node_index;  // module number of each node+    std::vector<int> node_index;  // module number of each node      int Nempty;-    vector<int> mod_empty;+    std::vector<int> mod_empty; -    vector<double> mod_exit;  // version tmp de node-    vector<double> mod_size;-    vector<double> mod_danglingSize;-    vector<double> mod_teleportWeight;-    vector<int> mod_members;+    std::vector<double> mod_exit;  // version tmp de node+    std::vector<double> mod_size;+    std::vector<double> mod_danglingSize;+    std::vector<double> mod_teleportWeight;+    std::vector<int> mod_members; };  void delete_Greedy(Greedy *greedy);
igraph/include/infomap_Node.h view
@@ -30,18 +30,15 @@  #include "igraph_interface.h" -class Node;-using namespace std;- class Node { public:      Node();     Node(int modulenr, double tpweight); -    vector<int> members;-    vector< pair<int, double> > inLinks;-    vector< pair<int, double> > outLinks;+    std::vector<int> members;+    std::vector< std::pair<int, double> > inLinks;+    std::vector< std::pair<int, double> > outLinks;     double selfLink;      double teleportWeight;
igraph/include/plfit/error.h view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
igraph/include/plfit/gss.h view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -55,7 +55,7 @@  * The gss() function calls this function to obtain the values of the objective  * function when needed. A client program must implement this function to evaluate  * the value of the objective function, given the location.- *  + *  * @param  instance    The user data sent for the gss() function by the client.  * @param  x           The current value of the variable.  * @retval double      The value of the objective function for the current
+ igraph/include/plfit/hzeta.h view
@@ -0,0 +1,96 @@+/* This file was imported from a private scientific library+ * based on GSL coined Home Scientific Libray (HSL) by its author+ * Jerome Benoit; this very material is itself inspired from the+ * material written by G. Jungan and distributed by GSL.+ * Ultimately, some modifications were done in order to render the+ * imported material independent from the rest of GSL.+ */++/* `hsl/hsl_sf_zeta.h' C header file+// HSL - Home Scientific Library+// Copyright (C) 2005-2018  Jerome Benoit+//+// HSL is free software; you can redistribute it and/or+// modify it under the terms of the GNU General Public License+// as published by the Free Software Foundation; either version 2+// of the License, or (at your option) any later version.+//+// This program is distributed in the hope that it will be useful,+// but WITHOUT ANY WARRANTY; without even the implied warranty of+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+// GNU General Public License for more details.+//+// You should have received a copy of the GNU General Public License+// along with this program; if not, write to the Free Software+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.+*/++/* For futher details, see its source conterpart src/hzeta.c */++/* Author:  Jerome G. Benoit < jgmbenoit _at_ rezozer _dot_ net > */++#ifndef __HZETA_H__+#define __HZETA_H__++#undef __BEGIN_DECLS+#undef __END_DECLS+#ifdef __cplusplus+# define __BEGIN_DECLS extern "C" {+# define __END_DECLS }+#else+# define __BEGIN_DECLS /* empty */+# define __END_DECLS /* empty */+#endif++__BEGIN_DECLS+++/* Hurwitz Zeta Function+ * zeta(s,q) = Sum[ (k+q)^(-s), {k,0,Infinity} ]+ *+ * s > 1.0, q > 0.0+ */+double hsl_sf_hzeta(const double s, const double q);++/* First Derivative of Hurwitz Zeta Function+ * zeta'(s,q) = - Sum[ Ln(k+q)/(k+q)^(s), {k,0,Infinity} ]+ *+ * s > 1.0, q > 0.0+ */+double hsl_sf_hzeta_deriv(const double s, const double q);++/* Second Derivative of Hurwitz Zeta Function+ * zeta''(s,q) = + Sum[ Ln(k+q)^2/(k+q)^(s), {k,0,Infinity} ]+ *+ * s > 1.0, q > 0.0+ */+double hsl_sf_hzeta_deriv2(const double s, const double q);++/* Logarithm of Hurwitz Zeta Function+ * lnzeta(s,q) = ln(zeta(s,q))+ *+ * s > 1.0, q > 0.0 (and q >> 1)+ */+double hsl_sf_lnhzeta(const double s, const double q);++/* Logarithmic Derivative of Hurwitz Zeta Function+ * lnzeta'(s,q) = zeta'(s,q)/zeta(s,q)+ *+ * s > 1.0, q > 0.0 (and q >> 1)+ */+double hsl_sf_lnhzeta_deriv(const double s, const double q);++/* Logarithm and Logarithmic Derivative of Hurwitz Zeta Function:+ * nonredundant computation version:+ * - lnzeta(s,q) and lnzeta'(s,q) are stored in *deriv0 and *deriv1, respectively;+ * - the return value and the value stored in *deriv0 are the same;+ * - deriv0 and deriv1 must be effective pointers, that is, not the NULL pointer.+ *+ * s > 1.0, q > 0.0 (and q >> 1)+ */+double hsl_sf_lnhzeta_deriv_tuple(const double s, const double q, double * deriv0, double * deriv1);+++__END_DECLS++#endif // __HZETA_H__
igraph/include/plfit/kolmogorov.h view
@@ -1,17 +1,17 @@ /* kolmogorov.h- * + *  * Copyright (C) 2010-2011 Tamas Nepusz- * + *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ igraph/include/plfit/mt.h view
@@ -0,0 +1,103 @@+/* mt.h+ *+ * Mersenne Twister random number generator, based on the implementation of+ * Michael Brundage (which has been placed in the public domain).+ *+ * Author: Tamas Nepusz (original by Michael Brundage)+ *+ * See the following URL for the original implementation:+ * http://www.qbrundage.com/michaelb/pubs/essays/random_number_generation.html+ *+ * This file has been placed in the public domain.+ */++#ifndef __MT_H__+#define __MT_H__++/* VS 2010, i.e. _MSC_VER == 1600, already has stdint.h */+#if defined(_MSC_VER) && _MSC_VER < 1600+#  define uint32_t __int32+#else+#  include <stdint.h>+#endif++#undef __BEGIN_DECLS+#undef __END_DECLS+#ifdef __cplusplus+# define __BEGIN_DECLS extern "C" {+# define __END_DECLS }+#else+# define __BEGIN_DECLS /* empty */+# define __END_DECLS /* empty */+#endif++__BEGIN_DECLS++#define MT_LEN       624++/**+ * \def MT_RAND_MAX+ *+ * The maximum random number that \c mt_random() can generate.+ */+#define MT_RAND_MAX 0xFFFFFFFF++/**+ * Struct that stores the internal state of a Mersenne Twister random number+ * generator.+ */+typedef struct {+    int mt_index;+    uint32_t mt_buffer[MT_LEN];+} mt_rng_t;++/**+ * \brief Initializes a Mersenne Twister random number generator.+ *+ * The random number generator is seeded with random 32-bit numbers obtained+ * from the \em built-in random number generator using consecutive calls to+ * \c rand().+ *+ * \param  rng  the random number generator to initialize+ */+void mt_init(mt_rng_t* rng);++/**+ * \brief Initializes a Mersenne Twister random number generator, seeding it+ *        from another one.+ *+ * The random number generator is seeded with random 32-bit numbers obtained+ * from another, initialized Mersenne Twister random number generator.+ *+ * \param  rng     the random number generator to initialize+ * \param  seeder  the random number generator that will seed the one being+ *                 initialized. When null, the random number generator will+ *                 be initialized from the built-in RNG as if \ref mt_init()+ *                 was called.+ */+void mt_init_from_rng(mt_rng_t* rng, mt_rng_t* seeder);++/**+ * \brief Returns the next 32-bit random number from the given Mersenne Twister+ * random number generator.+ *+ * \param  rng  the random number generator to use+ * \return the next 32-bit random number from the generator+ */+uint32_t mt_random(mt_rng_t* rng);++/**+ * \brief Returns a uniformly distributed double from the interval [0;1)+ * based on the next value of the given Mersenne Twister random number+ * generator.+ *+ * \param  rng  the random number generator to use+ * \return a uniformly distributed random number from the interval [0;1)+ */+double mt_uniform_01(mt_rng_t* rng);++__END_DECLS++#endif++
igraph/include/plfit/platform.h view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -34,11 +34,22 @@  __BEGIN_DECLS +#if defined(_MSC_VER) && _MSC_VER < 1900+#include <math.h>++#define snprintf igraph_i_snprintf+#define isnan(x) ((x) != (x))+#define isfinite(x) _finite(x)++extern double _plfit_fmin(double a, double b);+extern double _plfit_round(double x);++#define fmin _plfit_fmin+#define round _plfit_round+#endif+ #ifdef _MSC_VER-#define snprintf sprintf_s #define inline  __inline-#define isnan(x) _isnan(x)-#define isfinite(x) _finite(x) #endif  #ifndef INFINITY@@ -46,7 +57,7 @@ #endif  #ifndef NAN-#  define NAN (INFINITY-INFINITY)+#  define NAN ((double)0.0 / (double)DBL_MIN) #endif  __END_DECLS
igraph/include/plfit/plfit.h view
@@ -1,17 +1,18 @@+/* vim:set ts=4 sw=4 sts=4 et: */ /* plfit.h- * + *  * Copyright (C) 2010-2011 Tamas Nepusz- * + *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -21,6 +22,7 @@ #define __PLFIT_H__  #include <stdlib.h>+#include "mt.h"  #undef __BEGIN_DECLS #undef __END_DECLS@@ -35,47 +37,61 @@ __BEGIN_DECLS  #define PLFIT_VERSION_MAJOR 0-#define PLFIT_VERSION_MINOR 6-#define PLFIT_VERSION_STRING "0.6"+#define PLFIT_VERSION_MINOR 8+#define PLFIT_VERSION_STRING "0.8"  typedef unsigned short int plfit_bool_t;  typedef enum {-	PLFIT_GSS_OR_LINEAR,-	PLFIT_LINEAR_ONLY,-	PLFIT_DEFAULT_CONTINUOUS_METHOD = PLFIT_GSS_OR_LINEAR+    PLFIT_LINEAR_ONLY,+    PLFIT_STRATIFIED_SAMPLING,+    PLFIT_GSS_OR_LINEAR,+    PLFIT_DEFAULT_CONTINUOUS_METHOD = PLFIT_STRATIFIED_SAMPLING } plfit_continuous_method_t;  typedef enum {-	PLFIT_LBFGS,-	PLFIT_LINEAR_SCAN,-	PLFIT_PRETEND_CONTINUOUS,-	PLFIT_DEFAULT_DISCRETE_METHOD = PLFIT_LBFGS+    PLFIT_LBFGS,+    PLFIT_LINEAR_SCAN,+    PLFIT_PRETEND_CONTINUOUS,+    PLFIT_DEFAULT_DISCRETE_METHOD = PLFIT_LBFGS } plfit_discrete_method_t; +typedef enum {+    PLFIT_P_VALUE_SKIP,+    PLFIT_P_VALUE_APPROXIMATE,+    PLFIT_P_VALUE_EXACT,+    PLFIT_DEFAULT_P_VALUE_METHOD = PLFIT_P_VALUE_EXACT+} plfit_p_value_method_t;+ typedef struct _plfit_result_t {-	double alpha;     /* fitted power-law exponent */-	double xmin;      /* cutoff where the power-law behaviour kicks in */-	double L;         /* log-likelihood of the sample */-	double D;         /* test statistic for the KS test */-	double p;         /* p-value of the KS test */+    double alpha;     /* fitted power-law exponent */+    double xmin;      /* cutoff where the power-law behaviour kicks in */+    double L;         /* log-likelihood of the sample */+    double D;         /* test statistic for the KS test */+    double p;         /* p-value of the KS test */ } plfit_result_t;  /********** structure that holds the options of plfit **********/  typedef struct _plfit_continuous_options_t {-	plfit_bool_t finite_size_correction;-	plfit_continuous_method_t xmin_method;+    plfit_bool_t finite_size_correction;+    plfit_continuous_method_t xmin_method;+    plfit_p_value_method_t p_value_method;+    double p_value_precision;+    mt_rng_t* rng; } plfit_continuous_options_t;  typedef struct _plfit_discrete_options_t {-	plfit_bool_t finite_size_correction;-	plfit_discrete_method_t alpha_method;-	struct {-		double min;-		double max;-		double step;-	} alpha;+    plfit_bool_t finite_size_correction;+    plfit_discrete_method_t alpha_method;+    struct {+        double min;+        double max;+        double step;+    } alpha;+    plfit_p_value_method_t p_value_method;+    double p_value_precision;+    mt_rng_t* rng; } plfit_discrete_options_t;  int plfit_continuous_options_init(plfit_continuous_options_t* options);@@ -87,23 +103,41 @@ /********** continuous power law distribution fitting **********/  int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha,-		double xmin, double* l);+        double xmin, double* l); int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin,         const plfit_continuous_options_t* options, plfit_result_t* result);-int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin,-        const plfit_continuous_options_t* options, plfit_result_t* result); int plfit_continuous(double* xs, size_t n,-		const plfit_continuous_options_t* options, plfit_result_t* result);+        const plfit_continuous_options_t* options, plfit_result_t* result); -/********** discrete power law distribution fitting **********/+/*********** discrete power law distribution fitting ***********/  int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin,         const plfit_discrete_options_t* options, plfit_result_t *result); int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* l); int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options,-		plfit_result_t* result);+        plfit_result_t* result); +/***** resampling routines to generate synthetic replicates ****/++int plfit_resample_continuous(double* xs, size_t n, double alpha, double xmin,+        size_t num_samples, mt_rng_t* rng, double* result);+int plfit_resample_discrete(double* xs, size_t n, double alpha, double xmin,+        size_t num_samples, mt_rng_t* rng, double* result);++/******** calculating the p-value of a fitted model only *******/++int plfit_calculate_p_value_continuous(double* xs, size_t n,+        const plfit_continuous_options_t* options, plfit_bool_t xmin_fixed,+        plfit_result_t *result);+int plfit_calculate_p_value_discrete(double* xs, size_t n,+        const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed,+        plfit_result_t *result);++/************* calculating descriptive statistics **************/++int plfit_moments(double* data, size_t n, double* mean, double* variance,+        double* skewness, double* kurtosis);+ __END_DECLS  #endif /* __PLFIT_H__ */-
+ igraph/include/plfit/sampling.h view
@@ -0,0 +1,177 @@+/* sampling.h+ *+ * Copyright (C) 2012 Tamas Nepusz+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or (at+ * your option) any later version.+ *+ * This program is distributed in the hope that it will be useful, but+ * WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU+ * General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License+ * along with this program; if not, write to the Free Software+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.+ */++#ifndef __SAMPLING_H__+#define __SAMPLING_H__++#include <stdlib.h>+#include "mt.h"++#undef __BEGIN_DECLS+#undef __END_DECLS+#ifdef __cplusplus+# define __BEGIN_DECLS extern "C" {+# define __END_DECLS }+#else+# define __BEGIN_DECLS /* empty */+# define __END_DECLS /* empty */+#endif++__BEGIN_DECLS++/**+ * Draws a sample from a binomial distribution with the given count and+ * probability values.+ *+ * This function is borrowed from R; see the corresponding license in+ * \c rbinom.c. The return value is always an integer.+ *+ * The function is \em not thread-safe.+ *+ * \param  n    the number of trials+ * \param  p    the success probability of each trial+ * \param  rng  the Mersenne Twister random number generator to use+ * \return the value drawn from the given binomial distribution.+ */+double plfit_rbinom(double n, double p, mt_rng_t* rng);++/**+ * Draws a sample from a Pareto distribution with the given minimum value and+ * power-law exponent.+ *+ * \param  xmin    the minimum value of the distribution. Must be positive.+ * \param  alpha   the exponent. Must be positive+ * \param  rng     the Mersenne Twister random number generator to use+ *+ * \return the sample or NaN if one of the parameters is invalid+ */+extern double plfit_rpareto(double xmin, double alpha, mt_rng_t* rng);++/**+ * Draws a given number of samples from a Pareto distribution with the given+ * minimum value and power-law exponent.+ *+ * \param  xmin    the minimum value of the distribution. Must be positive.+ * \param  alpha   the exponent. Must be positive+ * \param  n       the number of samples to draw+ * \param  rng     the Mersenne Twister random number generator to use+ * \param  result  the array where the result should be written. It must+ *                 have enough space to store n items+ *+ * \return \c PLFIT_EINVAL if one of the parameters is invalid, zero otherwise+ */+int plfit_rpareto_array(double xmin, double alpha, size_t n, mt_rng_t* rng,+        double* result);++/**+ * Draws a sample from a zeta distribution with the given minimum value and+ * power-law exponent.+ *+ * \param  xmin    the minimum value of the distribution. Must be positive.+ * \param  alpha   the exponent. Must be positive+ * \param  rng     the Mersenne Twister random number generator to use+ *+ * \return the sample or NaN if one of the parameters is invalid+ */+extern double plfit_rzeta(long int xmin, double alpha, mt_rng_t* rng);++/**+ * Draws a given number of samples from a zeta distribution with the given+ * minimum value and power-law exponent.+ *+ * \param  xmin    the minimum value of the distribution. Must be positive.+ * \param  alpha   the exponent. Must be positive+ * \param  n       the number of samples to draw+ * \param  rng     the Mersenne Twister random number generator to use+ * \param  result  the array where the result should be written. It must+ *                 have enough space to store n items+ *+ * \return \c PLFIT_EINVAL if one of the parameters is invalid, zero otherwise+ */+int plfit_rzeta_array(long int xmin, double alpha, size_t n, mt_rng_t* rng,+        double* result);++/**+ * Draws a sample from a uniform distribution with the given lower and+ * upper bounds.+ *+ * The lower bound is inclusive, the uppoer bound is not.+ *+ * \param  lo   the lower bound+ * \param  hi   the upper bound+ * \param  rng  the Mersenne Twister random number generator to use+ * \return the value drawn from the given uniform distribution.+ */+extern double plfit_runif(double lo, double hi, mt_rng_t* rng);++/**+ * Draws a sample from a uniform distribution over the [0; 1) interval.+ *+ * The interval is closed from the left and open from the right.+ *+ * \param  rng  the Mersenne Twister random number generator to use+ * \return the value drawn from the given uniform distribution.+ */+extern double plfit_runif_01(mt_rng_t* rng);++/**+ * Random sampler using Walker's alias method.+ */+typedef struct {+    long int num_bins;            /**< Number of bins */+    long int* indexes;            /**< Index of the "other" element in each bin */+    double* probs;                /**< Probability of drawing the "own" element from a bin */+} plfit_walker_alias_sampler_t;++/**+ * \brief Initializes the sampler with item probabilities.+ *+ * \param  sampler  the sampler to initialize+ * \param  ps   pointer to an array containing a value proportional to the+ *              sampling probability of each item in the set being sampled.+ * \param  n    the number of items in the array+ * \return error code+ */+int plfit_walker_alias_sampler_init(plfit_walker_alias_sampler_t* sampler,+        double* ps, size_t n);++/**+ * \brief Destroys an initialized sampler and frees the allocated memory.+ *+ * \param  sampler  the sampler to destroy+ */+void plfit_walker_alias_sampler_destroy(plfit_walker_alias_sampler_t* sampler);++/**+ * \brief Draws a given number of samples from the sampler and writes them+ *        to a given array.+ *+ * \param  sampler  the sampler to use+ * \param  xs       pointer to an array where the sampled items should be+ *                  written+ * \param  n        the number of samples to draw+ * \param  rng      the Mersenne Twister random number generator to use+ * \return error code+ */+int plfit_walker_alias_sampler_sample(const plfit_walker_alias_sampler_t* sampler,+        long int* xs, size_t n, mt_rng_t* rng);++__END_DECLS++#endif
− igraph/include/plfit/zeta.h 
@@ -1,53 +0,0 @@-/* specfunc/gsl_sf_zeta.h- * - * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2004 Gerard Jungman- * - * This program is free software; you can redistribute it and/or modify- * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at- * your option) any later version.- * - * This program is distributed in the hope that it will be useful, but- * WITHOUT ANY WARRANTY; without even the implied warranty of- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU- * General Public License for more details.- * - * You should have received a copy of the GNU General Public License- * along with this program; if not, write to the Free Software- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.- */--/* Author:  G. Jungman */--/* This file was taken from the GNU Scientific Library. Some modifications- * were done in order to make it independent from the rest of GSL- */--#ifndef __ZETA_H__-#define __ZETA_H__--#undef __BEGIN_DECLS-#undef __END_DECLS-#ifdef __cplusplus-# define __BEGIN_DECLS extern "C" {-# define __END_DECLS }-#else-# define __BEGIN_DECLS /* empty */-# define __END_DECLS /* empty */-#endif--__BEGIN_DECLS---/* Hurwitz Zeta Function- * zeta(s,q) = Sum[ (k+q)^(-s), {k,0,Infinity} ]- *- * s > 1.0, q > 0.0- */-double gsl_sf_hzeta(const double s, const double q);---__END_DECLS--#endif /* __ZETA_H__ */-
igraph/include/pottsmodel_2.h view
igraph/include/prpack/prpack_base_graph.h view
@@ -37,6 +37,6 @@             void normalize_weights();     }; -};+}  #endif
igraph/include/prpack/prpack_csc.h view
@@ -25,6 +25,6 @@             int64_t* heads;             int64_t* tails;     };-};+}  #endif
igraph/include/prpack/prpack_csr.h view
@@ -11,6 +11,6 @@             int* tails;     }; -};+}  #endif
igraph/include/prpack/prpack_edge_list.h view
@@ -11,6 +11,6 @@             int* tails;     }; -};+}  #endif
igraph/include/prpack/prpack_igraph_graph.h view
@@ -17,7 +17,7 @@ 					igraph_bool_t directed = true);     }; -};+}  // PRPACK_IGRAPH_SUPPORT  #endif 
igraph/include/prpack/prpack_preprocessed_ge_graph.h view
@@ -21,6 +21,6 @@             ~prpack_preprocessed_ge_graph();     }; -};+}  #endif
igraph/include/prpack/prpack_preprocessed_graph.h view
@@ -12,6 +12,6 @@             double* d;     }; -};+}  #endif
igraph/include/prpack/prpack_preprocessed_gs_graph.h view
@@ -25,6 +25,6 @@             ~prpack_preprocessed_gs_graph();     }; -};+}  #endif
igraph/include/prpack/prpack_preprocessed_scc_graph.h view
@@ -34,6 +34,6 @@             ~prpack_preprocessed_scc_graph();     }; -};+}  #endif
igraph/include/prpack/prpack_preprocessed_schur_graph.h view
@@ -28,6 +28,6 @@             ~prpack_preprocessed_schur_graph();     }; -};+}  #endif
igraph/include/prpack/prpack_result.h view
@@ -1,6 +1,8 @@ #ifndef PRPACK_RESULT #define PRPACK_RESULT +#include <string>+ namespace prpack {      // Result class.@@ -14,7 +16,7 @@             double preprocess_time;             double compute_time;             long num_es_touched;-            const char* method;+            std::string method;             int converged;             // constructor             prpack_result();@@ -22,6 +24,6 @@             ~prpack_result();     }; -};+}  #endif
igraph/include/prpack/prpack_solver.h view
@@ -173,6 +173,6 @@                     const char* method);     }; -};+}  #endif
igraph/include/prpack/prpack_utils.h view
@@ -28,7 +28,7 @@             static double* permute(const int length, const double* a, const int* coding);     }; -};+}  #endif 
igraph/include/scg_headers.h view
@@ -55,11 +55,11 @@ #ifndef SCG_HEADERS_H #define SCG_HEADERS_H -#include <stdio.h>-#include <stdlib.h>- #include "igraph_types.h" #include "igraph_vector.h"++#include <stdio.h>+#include <stdlib.h>  typedef struct ind_val {     int ind;
igraph/include/vector.pmt view
@@ -754,17 +754,27 @@  /**  * \ingroup vector+ * \function igraph_vector_reverse_sort_cmp+ * \brief Internal comparison function of vector elements, used by+ * \ref igraph_vector_reverse_sort().+ */++int FUNCTION(igraph_vector, reverse_sort_cmp)(const void *a, const void *b) {+    const BASE *da = (const BASE *) a;+    const BASE *db = (const BASE *) b;++    return (*da < *db) - (*da > *db);+}++/**+ * \ingroup vector  * \function igraph_vector_sort  * \brief Sorts the elements of the vector into ascending order.  *- * </para><para>- * This function uses the built-in sort function of the C library.  * \param v Pointer to an initialized vector object.  *- * Time complexity: should be- * O(nlogn) for- * n- * elements.+ * Time complexity:+ * O(n log n) for n elements.  */  void FUNCTION(igraph_vector, sort)(TYPE(igraph_vector) *v) {@@ -775,6 +785,24 @@ }  /**+ * \ingroup vector+ * \function igraph_vector_reverse_sort+ * \brief Sorts the elements of the vector into descending order.+ *+ * \param v Pointer to an initialized vector object.+ *+ * Time complexity:+ * O(n log n) for n elements.+ */++void FUNCTION(igraph_vector, reverse_sort)(TYPE(igraph_vector) *v) {+    assert(v != NULL);+    assert(v->stor_begin != NULL);+    igraph_qsort(v->stor_begin, (size_t) FUNCTION(igraph_vector, size)(v),+                 sizeof(BASE), FUNCTION(igraph_vector, reverse_sort_cmp));+}++/**  * Ascending comparison function passed to qsort from  igraph_vector_qsort_ind  */ int FUNCTION(igraph_vector, i_qsort_ind_cmp_asc)(const void *p1, const void *p2) {@@ -1710,6 +1738,51 @@             0, FUNCTION(igraph_vector, size)(v)); } +/**+ * \ingroup vector+ * \function igraph_vector_binsearch_slice+ * \brief Finds an element by binary searching a sorted slice of a vector.+ *+ * </para><para>++ * It is assumed that the indicated slice of the vector, from \p start to \p end,+ * is sorted. If the specified element (\p what) is not in the slice of the+ * vector, then the position of where it should be inserted (to keep the vector+ * sorted) is returned.+ * \param v The \type igraph_vector_t object.+ * \param what The element to search for.+ * \param pos Pointer to a \type long int. This is set to the position of an+ *        instance of \p what in the slice of the vector if it is present. If \p+ *        v does not contain \p what then \p pos is set to the position to which+ *        it should be inserted (to keep the the vector sorted).+ * \param start The start position of the slice to search (inclusive).+ * \param end The end position of the slice to search (exclusive).+ * \return Positive integer (true) if \p what is found in the vector,+ *         zero (false) otherwise.+ *+ * Time complexity: O(log(n)),+ * n is the number of elements in the slice of \p v, i.e. \p end - \p start.+ */++igraph_bool_t FUNCTION(igraph_vector, binsearch_slice)(const TYPE(igraph_vector) *v,+        BASE what, long int *pos,+        long int start, long int end) {+    long int left  = start;+    long int right = end - 1;++    if (left < 0)+        IGRAPH_ERROR("Invalid start position.", IGRAPH_EINVAL);++    if (right >= FUNCTION(igraph_vector, size)(v))+        IGRAPH_ERROR("Invalid end position.", IGRAPH_EINVAL);++    if (left > right)+        IGRAPH_ERROR("Invalid slice, start position must be smaller than end position.",+                     IGRAPH_EINVAL);++    return FUNCTION(igraph_i_vector, binsearch_slice)(v, what, pos, start, end);+}+ igraph_bool_t FUNCTION(igraph_i_vector, binsearch_slice)(const TYPE(igraph_vector) *v,         BASE what, long int *pos,         long int start, long int end) {@@ -1930,7 +2003,7 @@  * \function igraph_vector_append  * \brief Append a vector to another one.  *- * The target vector will be resized (except \p from is empty).+ * The target vector will be resized (except when \p from is empty).  * \param to The vector to append to.  * \param from The vector to append, it is kept unchanged.  * \return Error code.@@ -2008,8 +2081,8 @@  * \brief Update a vector from another one.  *  * After this operation the contents of \p to will be exactly the same- * \p from. \p to will be resized if it was originally shorter or- * longer than \p from.+ * as that of \p from. The vector \p to will be resized if it was originally+ * shorter or longer than \p from.  * \param to The vector to update.  * \param from The vector to update from.  * \return Error code.@@ -2063,8 +2136,8 @@  * Note that currently no range checking is performed.  * \param v The input vector.  * \param i Index of the first element.- * \param j index of the second element. (Might be the same as the- * first.)+ * \param j Index of the second element (may be the same as the+ * first one).  * \return Error code, currently always \c IGRAPH_SUCCESS.  *  * Time complexity: O(1).@@ -2110,7 +2183,7 @@  * \brief Shuffles a vector in-place using the Fisher-Yates method  *  * </para><para>- * The Fisher-Yates shuffle ensures that every implementation is+ * The Fisher-Yates shuffle ensures that every permutation is  * equally probable when using a proper randomness source. Of course  * this does not apply to pseudo-random generators as the cycle of  * these generators is less than the number of possible permutations
igraph/include/walktrap_communities.h view
@@ -54,12 +54,11 @@ // see readme.txt for more details  -#ifndef COMMUNITIES_H-#define COMMUNITIES_H+#ifndef WALKTRAP_COMMUNITIES_H+#define WALKTRAP_COMMUNITIES_H  #include "walktrap_graph.h" #include "walktrap_heap.h"- #include "igraph_community.h" #include "config.h" @@ -173,4 +172,4 @@ } }       /* end of namespaces */ -#endif+#endif // WALKTRAP_COMMUNITIES_H
igraph/include/walktrap_graph.h view
@@ -55,9 +55,8 @@ /* FSF address above was fixed by Tamas Nepusz */  -#ifndef GRAPH_H-#define GRAPH_H-#include <iostream>+#ifndef WALKTRAP_GRAPH_H+#define WALKTRAP_GRAPH_H  #include "igraph_community.h" @@ -65,8 +64,6 @@  namespace walktrap { -using namespace std;- class Edge {            // code an edge of a given vertex public:     int neighbor;         // the number of the neighbor vertex@@ -104,5 +101,5 @@ } }        /* end of namespaces */ -#endif+#endif // WALKTRAP_GRAPH_H 
igraph/include/walktrap_heap.h view
@@ -53,8 +53,8 @@ //----------------------------------------------------------------------------- // see readme.txt for more details -#ifndef HEAP_H-#define HEAP_H+#ifndef WALKTRAP_HEAP_H+#define WALKTRAP_HEAP_H  namespace igraph { @@ -130,5 +130,5 @@ } }        /* end of namespaces */ -#endif+#endif // WALKTRAP_HEAP_H 
igraph/src/DensityGrid.cpp view
@@ -33,17 +33,14 @@ // This file contains the member definitions of the DensityGrid.h class // This code is modified from the original code by B.N. Wylie -#include <string>+#include "drl_Node.h"+#include "DensityGrid.h"+#include "igraph_error.h"+ #include <deque>-#include <iostream> #include <cmath>-#include <cstdlib>  using namespace std;--#include "drl_Node.h"-#include "DensityGrid.h"-#include "igraph_error.h"  #define GET_BIN(y, x) (Bins[y*GRID_SIZE+x]) 
igraph/src/DensityGrid_3d.cpp view
@@ -33,17 +33,14 @@ // This file contains the member definitions of the DensityGrid.h class // This code is modified from the original code by B.N. Wylie -#include <string>+#include "drl_Node_3d.h"+#include "DensityGrid_3d.h"+#include "igraph_error.h"+ #include <deque>-#include <iostream> #include <cmath>-#include <cstdlib>  using namespace std;--#include "drl_Node_3d.h"-#include "DensityGrid_3d.h"-#include "igraph_error.h"  #define GET_BIN(z, y, x) (Bins[(z*GRID_SIZE+y)*GRID_SIZE+x]) 
igraph/src/NetDataTypes.cpp view
@@ -43,10 +43,9 @@ #ifdef HAVE_CONFIG_H     #include <config.h> #endif-#include <cstdlib>-#include <cstdio>-#include <cstring>+ #include "NetDataTypes.h"+#include <cstring>  //################################################################################# //###############################################################################
igraph/src/NetRoutines.cpp view
@@ -40,15 +40,15 @@  *   (at your option) any later version.                                   *  *                                                                         *  ***************************************************************************/-#include <cstdlib>-#include <cstdio>-#include <cstring>+ #include "NetRoutines.h" #include "NetDataTypes.h"  #include "igraph_types.h" #include "igraph_interface.h" #include "igraph_conversion.h"++#include <cstring>  int igraph_i_read_network(const igraph_t *graph,                           const igraph_vector_t *weights,
igraph/src/adjlist.c view
@@ -37,7 +37,7 @@  * neighbor vertices or incident edges of a given vertex. Typically,  * this representation is good if we need to iterate over the neighbors  * of all vertices many times. E.g. when finding the shortest paths- * between every pairs of vertices or calculating closeness centrality+ * between all pairs of vertices or calculating closeness centrality  * for all the vertices.</para>  *  * <para>The <type>igraph_adjlist_t</type> stores the adjacency lists@@ -61,7 +61,7 @@  * the neighbors of v are queried and stored in a vector of the  * adjacency list, so they don't need to be queried again. Lazy  * adjacency lists are handy if you have an at least linear operation- * (because initialization is generally linear in terms of number of+ * (because initialization is generally linear in terms of the number of  * vertices), but you don't know how many vertices you will visit  * during the computation.  * </para>@@ -73,9 +73,9 @@  /**  * \function igraph_adjlist_init- * Initialize an adjacency list of vertices from a given graph+ * \brief Constructs an adjacency list of vertices from a given graph.  *- * Create a list of vectors containing the neighbors of all vertices+ * Creates a list of vectors containing the neighbors of all vertices  * in a graph. The adjacency list is independent of the graph after  * creation, e.g. the graph can be destroyed and modified, the  * adjacency list contains the state of the graph at the time of its@@ -133,7 +133,7 @@  /**  * \function igraph_adjlist_init_empty- * Initialize an empty adjacency list+ * \brief Initializes an empty adjacency list.  *  * Creates a list of vectors, one for each vertex. This is useful when you  * are \em constructing a graph using an adjacency list representation as@@ -165,7 +165,7 @@  /**  * \function igraph_adjlist_init_complementer- * Adjacency lists for the complementer graph+ * \brief Adjacency lists for the complementer graph.  *  * This function creates adjacency lists for the complementer  * of the input graph. In the complementer graph all edges are present@@ -248,7 +248,7 @@  /**  * \function igraph_adjlist_destroy- * Deallocate memory+ * \brief Deallocates an adjacency list.  *  * Free all memory allocated for an adjacency list.  * \param al The adjacency list to destroy.@@ -283,7 +283,7 @@  /**  * \function igraph_adjlist_size- * Number of vertices in an adjacency list.+ * \brief Number of vertices in an adjacency list.  *  * \param al The adjacency list.  * \return The number of elements.@@ -301,7 +301,7 @@  /**  * \function igraph_adjlist_sort- * Sort each vector in an adjacency list.+ * \brief Sorts each vector in an adjacency list.  *  * Sorts every vector of the adjacency list.  * \param al The adjacency list.@@ -319,9 +319,10 @@  /**  * \function igraph_adjlist_simplify- * Simplify+ * \brief Simplifies an adjacency list.  *- * Simplify an adjacency list, ie. remove loop and multiple edges.+ * Simplifies an adjacency list, i.e. removes loop and multiple edges.+ *  * \param al The adjacency list.  * \return Error code.  *@@ -359,21 +360,27 @@  int igraph_adjlist_remove_duplicate(const igraph_t *graph,                                     igraph_adjlist_t *al) {-    long int i;-    long int n = al->length;+    long int i, j, l, n, p;+    igraph_vector_int_t *v;+     IGRAPH_UNUSED(graph);++    n = al->length;     for (i = 0; i < n; i++) {-        igraph_vector_int_t *v = &al->adjs[i];-        long int j, p = 1, l = igraph_vector_int_size(v);-        for (j = 1; j < l; j++) {-            long int e = (long int) VECTOR(*v)[j];-            /* Non-loop edges, and one end of loop edges are fine. */-            /* We use here, that the vector is sorted and we also keep it sorted */-            if (e != i || VECTOR(*v)[j - 1] != e) {-                VECTOR(*v)[p++] = e;+        v = &al->adjs[i];+        l = igraph_vector_int_size(v);+        if (l > 0) {+            p = 1;+            for (j = 1; j < l; j++) {+                long int e = (long int) VECTOR(*v)[j];+                /* Non-loop edges, and one end of loop edges are fine. */+                /* We assume that the vector is sorted and we also keep it sorted */+                if (e != i || VECTOR(*v)[j - 1] != e) {+                    VECTOR(*v)[p++] = e;+                }             }+            igraph_vector_int_resize(v, p);         }-        igraph_vector_int_resize(v, p);     }      return 0;@@ -466,7 +473,7 @@  /**  * \function igraph_adjedgelist_init- * Initialize an incidence list of edges+ * \brief Initializes an incidence list of edges.  *  * This function was superseded by \ref igraph_inclist_init() in igraph 0.6.  * Please use \ref igraph_inclist_init() instead of this function.@@ -484,7 +491,7 @@  /**  * \function igraph_adjedgelist_destroy- * Frees all memory allocated for an incidence list.+ * \brief Frees all memory allocated for an incidence list.  *  * This function was superseded by \ref igraph_inclist_destroy() in igraph 0.6.  * Please use \ref igraph_inclist_destroy() instead of this function.@@ -500,21 +507,25 @@  int igraph_inclist_remove_duplicate(const igraph_t *graph,                                     igraph_inclist_t *al) {-    long int i;-    long int n = al->length;+    long int i, j, l, n, p;+    igraph_vector_int_t* v;++    n = al->length;     for (i = 0; i < n; i++) {-        igraph_vector_int_t *v = &al->incs[i];-        long int j, p = 1, l = igraph_vector_int_size(v);-        for (j = 1; j < l; j++) {-            long int e = (long int) VECTOR(*v)[j];-            /* Non-loop edges and one end of loop edges are fine. */-            /* We use here, that the vector is sorted and we also keep it sorted */-            if (IGRAPH_FROM(graph, e) != IGRAPH_TO(graph, e) ||-                VECTOR(*v)[j - 1] != e) {-                VECTOR(*v)[p++] = e;+        v = &al->incs[i];+        l = igraph_vector_int_size(v);+        if (l > 0) {+            p = 1;+            for (j = 1; j < l; j++) {+                long int e = (long int) VECTOR(*v)[j];+                /* Non-loop edges and one end of loop edges are fine. */+                /* We assume that the vector is sorted and we also keep it sorted */+                if (VECTOR(*v)[j - 1] != e) {+                    VECTOR(*v)[p++] = e;+                }             }+            igraph_vector_int_resize(v, p);         }-        igraph_vector_int_resize(v, p);     }      return 0;@@ -544,13 +555,21 @@  /**  * \function igraph_inclist_init- * Initialize an incidence list of edges+ * \brief Initializes an incidence list.  *- * Create a list of vectors containing the incident edges for all+ * Creates a list of vectors containing the incident edges for all  * vertices. The incidence list is independent of the graph after  * creation, subsequent changes of the graph object do not update the  * incidence list, and changes to the incidence list do not update the  * graph.+ *+ * </para><para>+ * When \p mode is \c IGRAPH_IN or \c IGRAPH_OUT, each edge ID will appear+ * in the incidence list \em once. When \p mode is \c IGRAPH_ALL, each edge ID+ * will appear in the incidence list \em twice, once for the source vertex+ * and once for the target edge. It also means that the edge IDs of loop edges+ * will appear \em twice for the \em same vertex.+ *  * \param graph The input graph.  * \param il Pointer to an uninitialized incidence list.  * \param mode Constant specifying whether incoming edges@@ -605,7 +624,7 @@  /**  * \function igraph_inclist_init_empty- * \brief Initialize an incidence list corresponding to an empty graph.+ * \brief Initializes an incidence list corresponding to an empty graph.  *  * This function essentially creates a list of empty vectors that may  * be treated as an incidence list for a graph with a given number of@@ -638,7 +657,7 @@  /**  * \function igraph_inclist_destroy- * Frees all memory allocated for an incidence list.+ * \brief Frees all memory allocated for an incidence list.  *  * \param eal The incidence list to destroy.  *@@ -657,7 +676,7 @@  /**  * \function igraph_inclist_clear- * Removes all edges from an incidence list.+ * \brief Removes all edges from an incidence list.  *  * \param il The incidence list.  * Time complexity: depends on memory management, typically O(n), where n is@@ -672,7 +691,7 @@  /**  * \function igraph_lazy_adjlist_init- * Constructor+ * \brief Initialized a lazy adjacency list.  *  * Create a lazy adjacency list for vertices. This function only  * allocates some memory for storing the vectors of an adjacency list,@@ -720,7 +739,7 @@  /**  * \function igraph_lazy_adjlist_destroy- * Deallocate memory+ * \brief Deallocate a lazt adjacency list.  *  * Free all allocated memory for a lazy adjacency list.  * \param al The adjacency list to deallocate.@@ -735,7 +754,7 @@  /**  * \function igraph_lazy_adjlist_clear- * Removes all edges from a lazy adjacency list.+ * \brief Removes all edges from a lazy adjacency list.  *  * \param al The lazy adjacency list.  * Time complexity: depends on memory management, typically O(n), where n is@@ -789,7 +808,7 @@  /**  * \function igraph_lazy_adjedgelist_init- * Initializes a lazy incidence list of edges+ * \brief Initializes a lazy incidence list of edges.  *  * This function was superseded by \ref igraph_lazy_inclist_init() in igraph 0.6.  * Please use \ref igraph_lazy_inclist_init() instead of this function.@@ -807,7 +826,7 @@  /**  * \function igraph_lazy_adjedgelist_destroy- * Frees all memory allocated for an incidence list.+ * \brief Frees all memory allocated for an incidence list.  *  * This function was superseded by \ref igraph_lazy_inclist_destroy() in igraph 0.6.  * Please use \ref igraph_lazy_inclist_destroy() instead of this function.@@ -830,17 +849,25 @@  /**  * \function igraph_lazy_inclist_init- * Initializes a lazy incidence list of edges+ * \brief Initializes a lazy incidence list of edges.  *  * Create a lazy incidence list for edges. This function only  * allocates some memory for storing the vectors of an incidence list,  * but the incident edges are not queried, only when \ref  * igraph_lazy_inclist_get() is called.+ *+ * </para><para>+ * When \p mode is \c IGRAPH_IN or \c IGRAPH_OUT, each edge ID will appear+ * in the incidence list \em once. When \p mode is \c IGRAPH_ALL, each edge ID+ * will appear in the incidence list \em twice, once for the source vertex+ * and once for the target edge. It also means that the edge IDs of loop edges+ * will appear \em twice for the \em same vertex.+ *  * \param graph The input graph.  * \param al Pointer to an uninitialized incidence list.  * \param mode Constant, it gives whether incoming edges  *   (<code>IGRAPH_IN</code>), outgoing edges- *   (<code>IGRPAH_OUT</code>) or both types of edges+ *   (<code>IGRAPH_OUT</code>) or both types of edges  *   (<code>IGRAPH_ALL</code>) are considered. It is ignored for  *   undirected graphs.  * \return Error code.@@ -876,7 +903,7 @@  /**  * \function igraph_lazy_inclist_destroy- * Deallocates memory+ * \brief Deallocates a lazy incidence list.  *  * Frees all allocated memory for a lazy incidence list.  * \param al The incidence list to deallocate.@@ -891,9 +918,10 @@  /**  * \function igraph_lazy_inclist_clear- * Removes all edges from a lazy incidence list.+ * \brief Removes all edges from a lazy incidence list.  *  * \param il The lazy incidence list.+ *  * Time complexity: depends on memory management, typically O(n), where n is  * the total number of elements in the incidence list.  */
igraph/src/arpack.c view
@@ -32,7 +32,7 @@  /* The ARPACK example file dssimp.f is used as a template */ -int igraph_i_arpack_err_dsaupd(int error) {+static int igraph_i_arpack_err_dsaupd(int error) {     switch (error) {     case  1:      return IGRAPH_ARPACK_MAXIT;     case  3:      return IGRAPH_ARPACK_NOSHIFT;@@ -54,7 +54,7 @@     } } -int igraph_i_arpack_err_dseupd(int error) {+static int igraph_i_arpack_err_dseupd(int error) {     switch (error) {     case -1:      return IGRAPH_ARPACK_NPOS;     case -2:      return IGRAPH_ARPACK_NEVNPOS;@@ -76,7 +76,7 @@  } -int igraph_i_arpack_err_dnaupd(int error) {+static int igraph_i_arpack_err_dnaupd(int error) {     switch (error) {     case  1:      return IGRAPH_ARPACK_MAXIT;     case  3:      return IGRAPH_ARPACK_NOSHIFT;@@ -97,7 +97,7 @@     } } -int igraph_i_arpack_err_dneupd(int error) {+static int igraph_i_arpack_err_dneupd(int error) {     switch (error) {     case  1:      return IGRAPH_ARPACK_REORDER;     case -1:      return IGRAPH_ARPACK_NPOS;@@ -258,9 +258,9 @@  * "Solver" for 1x1 eigenvalue problems since ARPACK sometimes blows up with  * these.  */-int igraph_i_arpack_rssolve_1x1(igraph_arpack_function_t *fun, void *extra,-                                igraph_arpack_options_t* options,-                                igraph_vector_t* values, igraph_matrix_t* vectors) {+static int igraph_i_arpack_rssolve_1x1(igraph_arpack_function_t *fun, void *extra,+                                       igraph_arpack_options_t* options,+                                       igraph_vector_t* values, igraph_matrix_t* vectors) {     igraph_real_t a, b;     int nev = options->nev; @@ -294,9 +294,9 @@  * "Solver" for 1x1 eigenvalue problems since ARPACK sometimes blows up with  * these.  */-int igraph_i_arpack_rnsolve_1x1(igraph_arpack_function_t *fun, void *extra,-                                igraph_arpack_options_t* options,-                                igraph_matrix_t* values, igraph_matrix_t* vectors) {+static int igraph_i_arpack_rnsolve_1x1(igraph_arpack_function_t *fun, void *extra,+                                       igraph_arpack_options_t* options,+                                       igraph_matrix_t* values, igraph_matrix_t* vectors) {     igraph_real_t a, b;     int nev = options->nev; @@ -330,9 +330,9 @@  * "Solver" for 2x2 nonsymmetric eigenvalue problems since ARPACK sometimes  * blows up with these.  */-int igraph_i_arpack_rnsolve_2x2(igraph_arpack_function_t *fun, void *extra,-                                igraph_arpack_options_t* options, igraph_matrix_t* values,-                                igraph_matrix_t* vectors) {+static int igraph_i_arpack_rnsolve_2x2(igraph_arpack_function_t *fun, void *extra,+                                       igraph_arpack_options_t* options, igraph_matrix_t* values,+                                       igraph_matrix_t* vectors) {     igraph_real_t vec[2], mat[4];     igraph_real_t a, b, c, d;     igraph_real_t trace, det, tsq4_minus_d;@@ -484,9 +484,9 @@  * "Solver" for symmetric 2x2 eigenvalue problems since ARPACK sometimes blows  * up with these.  */-int igraph_i_arpack_rssolve_2x2(igraph_arpack_function_t *fun, void *extra,-                                igraph_arpack_options_t* options, igraph_vector_t* values,-                                igraph_matrix_t* vectors) {+static int igraph_i_arpack_rssolve_2x2(igraph_arpack_function_t *fun, void *extra,+                                       igraph_arpack_options_t* options, igraph_vector_t* values,+                                       igraph_matrix_t* vectors) {     igraph_real_t vec[2], mat[4];     igraph_real_t a, b, c, d;     igraph_real_t trace, det, tsq4_minus_d;@@ -778,7 +778,7 @@  * \brief Tries to set up the value of \c ncv in an \c igraph_arpack_options_t  *        automagically.  */-void igraph_i_arpack_auto_ncv(igraph_arpack_options_t* options) {+static void igraph_i_arpack_auto_ncv(igraph_arpack_options_t* options) {     /* This is similar to how Octave determines the value of ncv, with some      * modifications. */     int min_ncv = options->nev * 2 + 1;@@ -811,7 +811,7 @@  * \brief Prints a warning that informs the user that the ARPACK solver  *        did not converge.  */-void igraph_i_arpack_report_no_convergence(const igraph_arpack_options_t* options) {+static void igraph_i_arpack_report_no_convergence(const igraph_arpack_options_t* options) {     char buf[1024];     snprintf(buf, sizeof(buf), "ARPACK solver failed to converge (%d iterations, "              "%d/%d eigenvectors converged)", options->iparam[2],
igraph/src/attributes.c view
@@ -422,11 +422,7 @@          type = (igraph_attribute_combination_type_t)va_arg(ap, int);         if (type == IGRAPH_ATTRIBUTE_COMBINE_FUNCTION) {-#if defined(__GNUC__)-            func = va_arg(ap, void (*)(void));-#else-            func = va_arg(ap, void*);-#endif+            func = va_arg(ap, igraph_function_pointer_t);         }          if (strlen(name) == 0) {
igraph/src/bfgs.c view
@@ -24,7 +24,6 @@ #include "igraph_nongraph.h" #include "igraph_interrupt_internal.h" #include "igraph_statusbar.h"-#include "memory.h" #include "config.h"  #include <math.h>
igraph/src/bignum.c view
@@ -19,11 +19,10 @@  *  *  $Id: bignum.c,v 1.17 2005/07/23 02:55:53 pullmoll Exp $  ******************************************************************************/-#include <math.h>+ #include "bignum.h"-#include "config.h"-#include "math.h" #include "igraph_error.h"+#include "config.h"  #ifndef ASM_X86     #ifdef  X86
igraph/src/bipartite.c view
@@ -150,11 +150,11 @@     return 0; } -int igraph_i_bipartite_projection(const igraph_t *graph,-                                  const igraph_vector_bool_t *types,-                                  igraph_t *proj,-                                  int which,-                                  igraph_vector_t *multiplicity) {+static int igraph_i_bipartite_projection(const igraph_t *graph,+                                         const igraph_vector_bool_t *types,+                                         igraph_t *proj,+                                         int which,+                                         igraph_vector_t *multiplicity) {      long int no_of_nodes = igraph_vcount(graph);     long int i, j, k;
igraph/src/blas.c view
@@ -108,3 +108,20 @@     int one = 1;     return igraphdnrm2_(&n, VECTOR(*v), &one); }++int igraph_blas_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2,+                       igraph_real_t *res) {++    int n = igraph_vector_size(v1);+    int one = 1;++    if (igraph_vector_size(v2) != n) {+        IGRAPH_ERROR("Dot product of vectors with different dimensions",+                     IGRAPH_EINVAL);+    }++    *res = igraphddot_(&n, VECTOR(*v1), &one, VECTOR(*v2), &one);++    return 0;+}+
igraph/src/bliss.cc view
@@ -25,6 +25,7 @@ #include "igraph_datatype.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h"  using namespace bliss; using namespace std;@@ -53,7 +54,7 @@ }  -void bliss_free_graph(AbstractGraph *g) {+static void bliss_free_graph(AbstractGraph *g) {     delete g; } @@ -118,7 +119,7 @@  // this is the callback function used with AbstractGraph::find_automorphisms() // it collects the group generators into a pointer vector-void collect_generators(void *generators, unsigned int n, const unsigned int *aut) {+static void collect_generators(void *generators, unsigned int n, const unsigned int *aut) {     igraph_vector_ptr_t *gen = static_cast<igraph_vector_ptr_t *>(generators);     igraph_vector_t *newvector = igraph_Calloc(1, igraph_vector_t);     igraph_vector_init(newvector, n);@@ -153,24 +154,27 @@  */ int igraph_canonical_permutation(const igraph_t *graph, const igraph_vector_int_t *colors,                                  igraph_vector_t *labeling, igraph_bliss_sh_t sh, igraph_bliss_info_t *info) {-    AbstractGraph *g = bliss_from_igraph(graph);-    IGRAPH_FINALLY(bliss_free_graph, g);-    const unsigned int N = g->get_nof_vertices();+    IGRAPH_HANDLE_EXCEPTIONS(+        AbstractGraph *g = bliss_from_igraph(graph);+        IGRAPH_FINALLY(bliss_free_graph, g);+        const unsigned int N = g->get_nof_vertices(); -    IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));-    IGRAPH_CHECK(bliss_set_colors(g, colors));+        IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));+        IGRAPH_CHECK(bliss_set_colors(g, colors)); -    Stats stats;-    const unsigned int *cl = g->canonical_form(stats, NULL, NULL);-    IGRAPH_CHECK(igraph_vector_resize(labeling, N));-    for (unsigned int i = 0; i < N; i++) {-        VECTOR(*labeling)[i] = cl[i];-    }+        Stats stats;+        const unsigned int *cl = g->canonical_form(stats, NULL, NULL);+        IGRAPH_CHECK(igraph_vector_resize(labeling, N));+        for (unsigned int i = 0; i < N; i++) {+            VECTOR(*labeling)[i] = cl[i];+        } -    bliss_info_to_igraph(info, stats);+        bliss_info_to_igraph(info, stats); -    delete g;-    IGRAPH_FINALLY_CLEAN(1);+        delete g;+        IGRAPH_FINALLY_CLEAN(1);+    );+     return IGRAPH_SUCCESS; } @@ -199,19 +203,21 @@  */ int igraph_automorphisms(const igraph_t *graph, const igraph_vector_int_t *colors,                          igraph_bliss_sh_t sh, igraph_bliss_info_t *info) {-    AbstractGraph *g = bliss_from_igraph(graph);-    IGRAPH_FINALLY(bliss_free_graph, g);+    IGRAPH_HANDLE_EXCEPTIONS(+        AbstractGraph *g = bliss_from_igraph(graph);+        IGRAPH_FINALLY(bliss_free_graph, g); -    IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));-    IGRAPH_CHECK(bliss_set_colors(g, colors));+        IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));+        IGRAPH_CHECK(bliss_set_colors(g, colors)); -    Stats stats;-    g->find_automorphisms(stats, NULL, NULL);+        Stats stats;+        g->find_automorphisms(stats, NULL, NULL); -    bliss_info_to_igraph(info, stats);+        bliss_info_to_igraph(info, stats); -    delete g;-    IGRAPH_FINALLY_CLEAN(1);+        delete g;+        IGRAPH_FINALLY_CLEAN(1);+    );     return IGRAPH_SUCCESS; } @@ -241,20 +247,23 @@ int igraph_automorphism_group(     const igraph_t *graph, const igraph_vector_int_t *colors, igraph_vector_ptr_t *generators,     igraph_bliss_sh_t sh, igraph_bliss_info_t *info) {-    AbstractGraph *g = bliss_from_igraph(graph);-    IGRAPH_FINALLY(bliss_free_graph, g);+    IGRAPH_HANDLE_EXCEPTIONS(+        AbstractGraph *g = bliss_from_igraph(graph);+        IGRAPH_FINALLY(bliss_free_graph, g); -    IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));-    IGRAPH_CHECK(bliss_set_colors(g, colors));+        IGRAPH_CHECK(bliss_set_sh(g, sh, igraph_is_directed(graph)));+        IGRAPH_CHECK(bliss_set_colors(g, colors)); -    Stats stats;-    igraph_vector_ptr_resize(generators, 0);-    g->find_automorphisms(stats, collect_generators, generators);+        Stats stats;+        igraph_vector_ptr_resize(generators, 0);+        g->find_automorphisms(stats, collect_generators, generators); -    bliss_info_to_igraph(info, stats);+        bliss_info_to_igraph(info, stats); -    delete g;-    IGRAPH_FINALLY_CLEAN(1);+        delete g;+        IGRAPH_FINALLY_CLEAN(1);+    );+     return IGRAPH_SUCCESS; } 
igraph/src/bliss_heap.cc view
@@ -1,6 +1,6 @@-#include <stdlib.h>-#include <stdio.h>-#include <limits.h>+#include <cstdlib>+//#include <stdio.h>+#include <climits> #include "defs.hh" #include "heap.hh" 
igraph/src/cattributes.c view
@@ -23,10 +23,10 @@  #include "igraph_attributes.h" #include "igraph_memory.h"-#include "config.h" #include "igraph_math.h" #include "igraph_interface.h" #include "igraph_random.h"+#include "config.h"  #include <string.h> @@ -1577,7 +1577,8 @@      igraph_free(funcs);     igraph_free(TODO);-    IGRAPH_FINALLY_CLEAN(2);+    igraph_i_cattribute_permute_free(new_val);+    IGRAPH_FINALLY_CLEAN(3);      return 0; }@@ -2187,7 +2188,7 @@      igraph_free(funcs);     igraph_free(TODO);-    IGRAPH_FINALLY_CLEAN(2);+    IGRAPH_FINALLY_CLEAN(3);      return 0; }@@ -2638,7 +2639,7 @@  * is no attribute handler at all.</para>  *  * <para>The C attribute handler supports attaching real numbers and- * character strings as attributes. No vectors are allowed, ie. every+ * character strings as attributes. No vectors are allowed, i.e. every  * vertex might have an attribute called <code>name</code>, but it is  * not possible to have a <code>coords</code> graph (or other)  * attribute which is a vector of numbers.</para>@@ -3801,7 +3802,7 @@         IGRAPH_FINALLY(igraph_free, log);         rec->value = log;         IGRAPH_CHECK(igraph_vector_bool_copy(log, v));-        IGRAPH_FINALLY(igraph_vector_destroy, log);+        IGRAPH_FINALLY(igraph_vector_bool_destroy, log);         IGRAPH_CHECK(igraph_vector_ptr_push_back(val, rec));         IGRAPH_FINALLY_CLEAN(4);     }@@ -3878,7 +3879,7 @@  /**  * \function igraph_cattribute_EAN_setv- * Set a numeric edge attribute for all vertices.+ * Set a numeric edge attribute for all edges.  *  * The attribute will be added if not present yet.  * \param graph The graph.@@ -3944,7 +3945,7 @@  /**  * \function igraph_cattribute_EAB_setv- * Set a boolean edge attribute for all vertices.+ * Set a boolean edge attribute for all edges.  *  * The attribute will be added if not present yet.  * \param graph The graph.@@ -4010,7 +4011,7 @@  /**  * \function igraph_cattribute_EAS_setv- * Set a string edge attribute for all vertices.+ * Set a string edge attribute for all edges.  *  * The attribute will be added if not present yet.  * \param graph The graph.
igraph/src/centrality.c view
@@ -22,9 +22,6 @@  */ -#include <math.h>-#include <string.h>    /* memset */-#include <assert.h> #include "igraph_centrality.h" #include "igraph_math.h" #include "igraph_memory.h"@@ -42,6 +39,9 @@ #include "bigint.h" #include "prpack.h" +#include <math.h>+#include <string.h>    /* memset */+ int igraph_personalized_pagerank_arpack(const igraph_t *graph,                                         igraph_vector_t *vector,                                         igraph_real_t *value, const igraph_vs_t vids,@@ -50,7 +50,7 @@                                         const igraph_vector_t *weights,                                         igraph_arpack_options_t *options); -igraph_bool_t igraph_i_vector_mostly_negative(const igraph_vector_t *vector) {+static igraph_bool_t igraph_i_vector_mostly_negative(const igraph_vector_t *vector) {     /* Many of the centrality measures correspond to the eigenvector of some      * matrix. When v is an eigenvector, c*v is also an eigenvector, therefore      * it may happen that all the scores in the eigenvector are negative, in which@@ -89,8 +89,8 @@     return (mi < 1e-5) ? 1 : 0; } -int igraph_i_eigenvector_centrality(igraph_real_t *to, const igraph_real_t *from,-                                    int n, void *extra) {+static int igraph_i_eigenvector_centrality(igraph_real_t *to, const igraph_real_t *from,+                                           int n, void *extra) {     igraph_adjlist_t *adjlist = extra;     igraph_vector_int_t *neis;     long int i, j, nlen;@@ -115,8 +115,8 @@     const igraph_vector_t *weights; } igraph_i_eigenvector_centrality_t; -int igraph_i_eigenvector_centrality2(igraph_real_t *to, const igraph_real_t *from,-                                     int n, void *extra) {+static int igraph_i_eigenvector_centrality2(igraph_real_t *to, const igraph_real_t *from,+                                            int n, void *extra) {      igraph_i_eigenvector_centrality_t *data = extra;     const igraph_t *graph = data->graph;@@ -140,25 +140,6 @@     return 0; } -int igraph_i_eigenvector_centrality_loop(igraph_adjlist_t *adjlist) {--    long int i, j, k, nlen, n = igraph_adjlist_size(adjlist);-    igraph_vector_int_t *neis;--    for (i = 0; i < n; i++) {-        neis = igraph_adjlist_get(adjlist, i);-        nlen = igraph_vector_int_size(neis);-        for (j = 0; j < nlen && VECTOR(*neis)[j] < i; j++) ;-        for (k = j; k < nlen && VECTOR(*neis)[k] == i; k++) ;-        if (k != j) {-            /* First loop edge is 'j', first non-loop edge is 'k' */-            igraph_vector_int_remove_section(neis, j + (k - j) / 2, k);-        }-    }--    return 0;-}- int igraph_eigenvector_centrality_undirected(const igraph_t *graph, igraph_vector_t *vector,         igraph_real_t *value, igraph_bool_t scale,         const igraph_vector_t *weights,@@ -236,8 +217,6 @@         IGRAPH_CHECK(igraph_adjlist_init(graph, &adjlist, IGRAPH_ALL));         IGRAPH_FINALLY(igraph_adjlist_destroy, &adjlist); -        IGRAPH_CHECK(igraph_i_eigenvector_centrality_loop(&adjlist));-         IGRAPH_CHECK(igraph_arpack_rssolve(igraph_i_eigenvector_centrality,                                            &adjlist, options, 0, &values, &vectors)); @@ -252,8 +231,6 @@         IGRAPH_CHECK(igraph_inclist_init(graph, &inclist, IGRAPH_ALL));         IGRAPH_FINALLY(igraph_inclist_destroy, &inclist); -        IGRAPH_CHECK(igraph_inclist_remove_duplicate(graph, &inclist));-         IGRAPH_CHECK(igraph_arpack_rssolve(igraph_i_eigenvector_centrality2,                                            &data, options, 0, &values, &vectors)); @@ -504,21 +481,34 @@  *  * Eigenvector centrality is a measure of the importance of a node in a  * network. It assigns relative scores to all nodes in the network based- * on the principle that connections to high-scoring nodes contribute- * more to the score of the node in question than equal connections to- * low-scoring nodes. In practice, this is determined by calculating the+ * on the principle that connections from high-scoring nodes contribute+ * more to the score of the node in question than equal connections from+ * low-scoring nodes. Specifically, the eigenvector centrality of each+ * vertex is proportional to the sum of eigenvector centralities of its+ * neighbors. In practice, the centralities are determined by calculating the  * eigenvector corresponding to the largest positive eigenvalue of the- * adjacency matrix. The centrality scores returned by igraph are always- * normalized such that the largest eigenvector centrality score is one- * (with one exception, see below).+ * adjacency matrix. In the undirected case, this function considers+ * the diagonal entries of the adjacency matrix to be \em twice the number of+ * self-loops on the corresponding vertex.  *  * </para><para>- * Since the eigenvector centrality scores of nodes in different components- * do not affect each other, it may be beneficial for large graphs to- * decompose it first into weakly connected components and calculate the- * centrality scores individually for each component.+ * The centrality scores returned by igraph can be normalized+ * (using the \p scale parameter) such that the largest eigenvector centrality+ * score is 1 (with one exception, see below).  *  * </para><para>+ * In the directed case, the left eigenvector of the adjacency matrix is+ * calculated. In other words, the centrality of a vertex is proportional+ * to the sum of centralities of vertices pointing to it.+ *+ * </para><para>+ * Eigenvector centrality is meaningful only for connected graphs.+ * Graphs that are not connected should be decomposed into connected+ * components, and the eigenvector centrality calculated for each separately.+ * This function does not verify that the graph is connected. If it is not,+ * in the undirected case the scores of all but one component will be zeros.+ *+ * </para><para>  * Also note that the adjacency matrix of a directed acyclic graph or the  * adjacency matrix of an empty graph does not possess positive eigenvalues,  * therefore the eigenvector centrality is not defined for these graphs.@@ -529,7 +519,7 @@  * parameter, see below) and checking whether the eigenvalue is very close  * to zero.  *- * \param graph The input graph. It might be directed.+ * \param graph The input graph. It may be directed.  * \param vector Pointer to an initialized vector, it will be resized  *     as needed. The result of the computation is stored here. It can  *     be a null pointer, then it is ignored.@@ -591,9 +581,9 @@ } igraph_i_kleinberg_data2_t;  /* ARPACK auxiliary routine for the unweighted HITS algorithm */-int igraph_i_kleinberg_unweighted(igraph_real_t *to,-                                  const igraph_real_t *from,-                                  int n, void *extra) {+static int igraph_i_kleinberg_unweighted(igraph_real_t *to,+                                         const igraph_real_t *from,+                                         int n, void *extra) {     igraph_i_kleinberg_data_t *data = (igraph_i_kleinberg_data_t*)extra;     igraph_adjlist_t *in = data->in;     igraph_adjlist_t *out = data->out;@@ -625,9 +615,9 @@ }  /* ARPACK auxiliary routine for the weighted HITS algorithm */-int igraph_i_kleinberg_weighted(igraph_real_t *to,-                                const igraph_real_t *from,-                                int n, void *extra) {+static int igraph_i_kleinberg_weighted(igraph_real_t *to,+                                       const igraph_real_t *from,+                                       int n, void *extra) {      igraph_i_kleinberg_data2_t *data = (igraph_i_kleinberg_data2_t*)extra;     igraph_inclist_t *in = data->in;@@ -663,10 +653,10 @@     return 0; } -int igraph_i_kleinberg(const igraph_t *graph, igraph_vector_t *vector,-                       igraph_real_t *value, igraph_bool_t scale,-                       const igraph_vector_t *weights,-                       igraph_arpack_options_t *options, int inout) {+static int igraph_i_kleinberg(const igraph_t *graph, igraph_vector_t *vector,+                              igraph_real_t *value, igraph_bool_t scale,+                              const igraph_vector_t *weights,+                              igraph_arpack_options_t *options, int inout) {      igraph_adjlist_t myinadjlist, myoutadjlist;     igraph_inclist_t myininclist, myoutinclist;@@ -934,8 +924,8 @@     igraph_vector_t *reset; } igraph_i_pagerank_data2_t; -int igraph_i_pagerank(igraph_real_t *to, const igraph_real_t *from,-                      int n, void *extra) {+static int igraph_i_pagerank(igraph_real_t *to, const igraph_real_t *from,+                             int n, void *extra) {      igraph_i_pagerank_data_t *data = extra;     igraph_adjlist_t *adjlist = data->adjlist;@@ -996,8 +986,8 @@     return 0; } -int igraph_i_pagerank2(igraph_real_t *to, const igraph_real_t *from,-                       int n, void *extra) {+static int igraph_i_pagerank2(igraph_real_t *to, const igraph_real_t *from,+                              int n, void *extra) {      igraph_i_pagerank_data2_t *data = extra;     const igraph_t *graph = data->graph;@@ -1608,7 +1598,8 @@                                        nobigint); } -int igraph_i_betweenness_estimate_weighted(const igraph_t *graph,+static int igraph_i_betweenness_estimate_weighted(+        const igraph_t *graph,         igraph_vector_t *res,         const igraph_vs_t vids,         igraph_bool_t directed,@@ -1678,11 +1669,18 @@             igraph_vector_int_t *neis;             long int nlen; -            igraph_stack_push(&S, minnei);-            if (cutoff > 0 && VECTOR(dist)[minnei] >= cutoff + 1.0) {+            /* Ignore vertices that are more distant than the cutoff */+            if (cutoff >= 0 && mindist > cutoff + 1.0) {+                /* Reset variables if node is too distant */+                VECTOR(tmpscore)[minnei] = 0;+                VECTOR(dist)[minnei] = 0;+                VECTOR(nrgeo)[minnei] = 0;+                igraph_vector_int_clear(igraph_adjlist_get(&fathers, minnei));                 continue;             } +            igraph_stack_push(&S, minnei);+             /* Now check all neighbors of 'minnei' for a shorter path */             neis = igraph_inclist_get(&inclist, minnei);             nlen = igraph_vector_int_size(neis);@@ -1717,7 +1715,9 @@                      VECTOR(dist)[to] = altdist;                     IGRAPH_CHECK(igraph_2wheap_modify(&Q, to, -altdist));-                } else if (cmp_result == 0) {+                } else if (cmp_result == 0 &&+                    (altdist <= cutoff + 1.0 || cutoff < 0)) {+                    /* Only add if the node is not more distant than the cutoff */                     igraph_vector_int_t *v = igraph_adjlist_get(&fathers, to);                     igraph_vector_int_push_back(v, minnei);                     VECTOR(nrgeo)[to] += VECTOR(nrgeo)[minnei];@@ -1738,6 +1738,7 @@                 VECTOR(*tmpres)[w] += VECTOR(tmpscore)[w];             } +            /* Reset variables */             VECTOR(tmpscore)[w] = 0;             VECTOR(dist)[w] = 0;             VECTOR(nrgeo)[w] = 0;@@ -1784,7 +1785,7 @@     return 0; } -void igraph_i_destroy_biguints(igraph_biguint_t *p) {+static void igraph_i_destroy_biguints(igraph_biguint_t *p) {     igraph_biguint_t *p2 = p;     while ( *((long int*)(p)) ) {         igraph_biguint_destroy(p);@@ -1815,8 +1816,8 @@  * \param directed Logical, if true directed paths will be considered  *        for directed graphs. It is ignored for undirected graphs.  * \param cutoff The maximal length of paths that will be considered.- *        If zero or negative, the exact betweenness will be calculated- *        (no upper limit on path lengths).+ *        If negative or zero, the exact betweenness will be calculated, and+ *        there will be no upper limit on path lengths.  * \param weights An optional vector containing edge weights for  *        calculating weighted betweenness. Supply a null pointer here  *        for unweighted betweenness.@@ -1866,6 +1867,11 @@      igraph_biguint_t D, R, T; +    /* Ensure that 0 is interpreted as infinity in the igraph 0.8 series. TODO: remove for 0.9. */+    if (cutoff == 0) {+        cutoff = -1;+    }+     if (weights) {         return igraph_i_betweenness_estimate_weighted(graph, res, vids, directed,                 cutoff, weights, nobigint);@@ -1956,12 +1962,22 @@          while (!igraph_dqueue_empty(&q)) {             long int actnode = (long int) igraph_dqueue_pop(&q);-            IGRAPH_CHECK(igraph_stack_push(&stack, actnode)); -            if (cutoff > 0 && distance[actnode] >= cutoff + 1) {+            /* Ignore vertices that are more distant than the cutoff */+            if (cutoff >= 0 && distance[actnode] > cutoff + 1) {+                /* Reset variables if node is too distant */+                distance[actnode] = 0;+                if (nobigint) {+                    nrgeo[actnode] = 0;+                } else {+                    igraph_biguint_set_limb(&big_nrgeo[actnode], 0);+                }+                tmpscore[actnode] = 0;+                igraph_vector_int_clear(igraph_adjlist_get(adjlist_in_p, actnode));                 continue;             } +            IGRAPH_CHECK(igraph_stack_push(&stack, actnode));             neis = igraph_adjlist_get(adjlist_out_p, actnode);             nneis = igraph_vector_int_size(neis);             for (j = 0; j < nneis; j++) {@@ -1970,7 +1986,9 @@                     distance[neighbor] = distance[actnode] + 1;                     IGRAPH_CHECK(igraph_dqueue_push(&q, neighbor));                 }-                if (distance[neighbor] == distance[actnode] + 1) {+                if (distance[neighbor] == distance[actnode] + 1 &&+                    (distance[neighbor] <= cutoff + 1 || cutoff < 0)) {+                    /* Only add if the node is not more distant than the cutoff */                     igraph_vector_int_t *v = igraph_adjlist_get(adjlist_in_p,                                              neighbor);                     igraph_vector_int_push_back(v, actnode);@@ -2016,6 +2034,7 @@                 VECTOR(*tmpres)[actnode] += tmpscore[actnode];             } +            /* Reset variables */             distance[actnode] = 0;             if (nobigint) {                 nrgeo[actnode] = 0;@@ -2079,7 +2098,8 @@     return 0; } -int igraph_i_edge_betweenness_estimate_weighted(const igraph_t *graph,+static int igraph_i_edge_betweenness_estimate_weighted(+        const igraph_t *graph,         igraph_vector_t *result,         igraph_bool_t directed,         igraph_real_t cutoff,@@ -2518,8 +2538,7 @@  * \param graph The graph object.  * \param res The result of the computation, a vector containing the  *        closeness centrality scores for the given vertices.- * \param vids Vector giving the vertices for which the closeness- *        centrality scores will be computed.+ * \param vids The vertices for which the closeness centrality will be computed.  * \param mode The type of shortest paths to be used for the  *        calculation in directed graphs. Possible values:  *        \clist@@ -2563,13 +2582,13 @@                                      normalized); } -int igraph_i_closeness_estimate_weighted(const igraph_t *graph,-        igraph_vector_t *res,-        const igraph_vs_t vids,-        igraph_neimode_t mode,-        igraph_real_t cutoff,-        const igraph_vector_t *weights,-        igraph_bool_t normalized) {+static int igraph_i_closeness_estimate_weighted(const igraph_t *graph,+                                                igraph_vector_t *res,+                                                const igraph_vs_t vids,+                                                igraph_neimode_t mode,+                                                igraph_real_t cutoff,+                                                const igraph_vector_t *weights,+                                                igraph_bool_t normalized) {      /* See igraph_shortest_paths_dijkstra() for the implementation        details and the dirty tricks. */@@ -2727,8 +2746,7 @@  * \param graph The graph object.  * \param res The result of the computation, a vector containing the  *        closeness centrality scores for the given vertices.- * \param vids Vector giving the vertices for which the closeness- *        centrality scores will be computed.+ * \param vids The vertices for which the closeness centrality will be estimated.  * \param mode The type of shortest paths to be used for the  *        calculation in directed graphs. Possible values:  *        \clist
igraph/src/cliquer.c view
igraph/src/cliquer_graph.c view
igraph/src/cliques.c view
@@ -23,7 +23,6 @@  #include "igraph_cliques.h" #include "igraph_memory.h"-#include "igraph_random.h" #include "igraph_constants.h" #include "igraph_adjlist.h" #include "igraph_interrupt_internal.h"@@ -37,7 +36,7 @@ #include <assert.h> #include <string.h>    /* memset */ -void igraph_i_cliques_free_res(igraph_vector_ptr_t *res) {+static void igraph_i_cliques_free_res(igraph_vector_ptr_t *res) {     long i, n;      n = igraph_vector_ptr_size(res);@@ -50,14 +49,15 @@     igraph_vector_ptr_clear(res); } -int igraph_i_find_k_cliques(const igraph_t *graph,-                            long int size,-                            const igraph_real_t *member_storage,-                            igraph_real_t **new_member_storage,-                            long int old_clique_count,-                            long int *clique_count,-                            igraph_vector_t *neis,-                            igraph_bool_t independent_vertices) {+static int igraph_i_find_k_cliques(+        const igraph_t *graph,+        long int size,+        const igraph_real_t *member_storage,+        igraph_real_t **new_member_storage,+        long int old_clique_count,+        long int *clique_count,+        igraph_vector_t *neis,+        igraph_bool_t independent_vertices) {      long int j, k, l, m, n, new_member_storage_size;     const igraph_real_t *c1, *c2;@@ -188,9 +188,9 @@  * They are practically the same except that the complementer of the graph  * should be used in the latter case.  */-int igraph_i_cliques(const igraph_t *graph, igraph_vector_ptr_t *res,-                     igraph_integer_t min_size, igraph_integer_t max_size,-                     igraph_bool_t independent_vertices) {+static int igraph_i_cliques(const igraph_t *graph, igraph_vector_ptr_t *res,+                            igraph_integer_t min_size, igraph_integer_t max_size,+                            igraph_bool_t independent_vertices) {      igraph_integer_t no_of_nodes;     igraph_vector_t neis;@@ -303,7 +303,7 @@  /**  * \function igraph_cliques- * \brief Find all or some cliques in a graph+ * \brief Finds all or some cliques in a graph.  *  * </para><para>  * Cliques are fully connected subgraphs of a graph.@@ -312,17 +312,13 @@  * If you are only interested in the size of the largest clique in the graph,  * use \ref igraph_clique_number() instead.  *- * </para><para>The current implementation of this function searches- * for maximal independent vertex sets (see \ref- * igraph_maximal_independent_vertex_sets()) in the complementer graph- * using the algorithm published in:- * S. Tsukiyama, M. Ide, H. Ariyoshi and I. Shirawaka. A new algorithm- * for generating all the maximal independent sets. SIAM J Computing,- * 6:505--517, 1977.+ * </para><para>The current implementation of this function+ * uses version 1.21 of the Cliquer library by Sampo Niskanen and+ * Patric R. J. Östergård, http://users.aalto.fi/~pat/cliquer.html  *  * \param graph The input graph.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in a clique.  *   The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed.@@ -334,7 +330,7 @@  *  * \sa \ref igraph_largest_cliques() and \ref igraph_clique_number().  *- * Time complexity: TODO+ * Time complexity: Exponential  *  * \example examples/simple/igraph_cliques.c  */@@ -346,7 +342,7 @@  /**  * \function igraph_clique_size_hist- * \brief Count cliques of each size in the graph+ * \brief Counts cliques of each size in the graph.  *  * </para><para>  * Cliques are fully connected subgraphs of a graph.@@ -358,7 +354,7 @@  * \param graph The input graph.  * \param hist Pointer to an initialized vector. The result will be stored  * here. The first element will store the number of size-1 cliques, the second- * element the number of size-2 cliques, etc.  For cliques smaller than \c min_size,+ * element the number of size-2 cliques, etc.  For cliques smaller than \p min_size,  * zero counts will be returned.  * \param min_size Integer giving the minimum size of the cliques to be  *   returned. If negative or zero, no lower bound will be used.@@ -385,7 +381,7 @@  * Cliques are fully connected subgraphs of a graph. This function  * enumerates all cliques within the given size range and calls  * \p cliquehandler_fn for each of them. The cliques are passed to the- * callback function as an <type>igraph_vector_t *</type>.  Destroying and+ * callback function as a pointer to an \ref igraph_vector_t.  Destroying and  * freeing this vector is left up to the user.  Use \ref igraph_vector_destroy()  * to destroy it first, then free it using \ref igraph_free().  *@@ -399,7 +395,7 @@  * \param max_size Integer giving the maximum size of the cliques to be  *   returned. If negative or zero, no upper bound will be used.  * \param cliquehandler_fn Callback function to be called for each clique.- * See also igraph_clique_handler_t.+ * See also \ref igraph_clique_handler_t.  * \param arg Extra argument to supply to \p cliquehandler_fn.  * \return Error code.  *@@ -417,7 +413,7 @@  /**  * \function igraph_weighted_cliques- * \brief Find all cliques in a given weight range in a vertex weighted graph+ * \brief Finds all cliques in a given weight range in a vertex weighted graph.  *  * </para><para>  * Cliques are fully connected subgraphs of a graph.@@ -434,7 +430,7 @@  * \param vertex_weights A vector of vertex weights. The current implementation  *   will truncate all weights to their integer parts.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in a clique.  *   The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed.@@ -474,7 +470,7 @@  * \param vertex_weights A vector of vertex weights. The current implementation  *   will truncate all weights to their integer parts.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in a clique.  *   The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed.@@ -492,7 +488,7 @@  /**  * \function igraph_weighted_clique_number- * \brief Find the weight of the largest weight clique in the graph+ * \brief Finds the weight of the largest weight clique in the graph.  *  * </para><para>The current implementation of this function  * uses version 1.21 of the Cliquer library by Sampo Niskanen and@@ -524,9 +520,10 @@     igraph_integer_t max_size; } igraph_i_maximal_clique_data_t; -int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data);+static int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data); -int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph,+static int igraph_i_maximal_or_largest_cliques_or_indsets(+        const igraph_t *graph,         igraph_vector_ptr_t *res,         igraph_integer_t *clique_number,         igraph_bool_t keep_only_largest,@@ -534,7 +531,7 @@  /**  * \function igraph_independent_vertex_sets- * \brief Find all independent vertex sets in a graph+ * \brief Finds all independent vertex sets in a graph.  *  * </para><para>  * A vertex set is considered independent if there are no edges between@@ -553,7 +550,7 @@  *  * \param graph The input graph.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in an independent  *   vertex set. The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed.@@ -619,7 +616,8 @@     igraph_bool_t keep_only_largest;     /* True if we keep only the largest sets */ } igraph_i_max_ind_vsets_data_t; -int igraph_i_maximal_independent_vertex_sets_backtrack(const igraph_t *graph,+static int igraph_i_maximal_independent_vertex_sets_backtrack(+        const igraph_t *graph,         igraph_vector_ptr_t *res,         igraph_i_max_ind_vsets_data_t *clqdata,         igraph_integer_t level) {@@ -763,7 +761,7 @@     return 0; } -void igraph_i_free_set_array(igraph_set_t* array) {+static void igraph_i_free_set_array(igraph_set_t* array) {     long int i = 0;     while (igraph_set_inited(array + i)) {         igraph_set_destroy(array + i);@@ -774,7 +772,7 @@  /**  * \function igraph_maximal_independent_vertex_sets- * \brief Find all maximal independent vertex sets of a graph+ * \brief Finds all maximal independent vertex sets of a graph.  *  * </para><para>  * A maximal independent vertex set is an independent vertex set which@@ -797,7 +795,7 @@  *  * \param graph The input graph.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in an independent  *   vertex set. The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed.@@ -864,7 +862,7 @@  /**  * \function igraph_independence_number- * \brief Find the independence number of the graph+ * \brief Finds the independence number of the graph.  *  * </para><para>  * The independence number of a graph is the cardinality of the largest@@ -943,8 +941,8 @@ /* MAXIMAL CLIQUES, LARGEST CLIQUES                                      */ /*************************************************************************/ -int igraph_i_maximal_cliques_store_max_size(const igraph_vector_t* clique, void* data,-        igraph_bool_t* cont) {+static int igraph_i_maximal_cliques_store_max_size(const igraph_vector_t* clique, void* data,+                                                   igraph_bool_t* cont) {     igraph_integer_t* result = (igraph_integer_t*)data;     IGRAPH_UNUSED(cont);     if (*result < igraph_vector_size(clique)) {@@ -953,7 +951,7 @@     return IGRAPH_SUCCESS; } -int igraph_i_maximal_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) {+static int igraph_i_maximal_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) {     igraph_vector_ptr_t* result = (igraph_vector_ptr_t*)data;     igraph_vector_t* vec; @@ -969,7 +967,7 @@     return IGRAPH_SUCCESS; } -int igraph_i_maximal_cliques_store_size_check(const igraph_vector_t* clique, void* data_, igraph_bool_t* cont) {+static int igraph_i_maximal_cliques_store_size_check(const igraph_vector_t* clique, void* data_, igraph_bool_t* cont) {     igraph_i_maximal_clique_data_t* data = (igraph_i_maximal_clique_data_t*)data_;     igraph_vector_t* vec;     igraph_integer_t size = (igraph_integer_t) igraph_vector_size(clique);@@ -990,7 +988,7 @@     return IGRAPH_SUCCESS; } -int igraph_i_largest_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) {+static int igraph_i_largest_cliques_store(const igraph_vector_t* clique, void* data, igraph_bool_t* cont) {     igraph_vector_ptr_t* result = (igraph_vector_ptr_t*)data;     igraph_vector_t* vec;     long int i, n;@@ -1033,7 +1031,7 @@  *  * </para><para>  * Note that this is not necessarily the same as a maximal clique,- * ie. the largest cliques are always maximal but a maximal clique is+ * i.e. the largest cliques are always maximal but a maximal clique is  * not always largest.  *  * </para><para>The current implementation of this function searches@@ -1066,7 +1064,7 @@  /**  * \function igraph_clique_number- * \brief Find the clique number of the graph+ * \brief Finds the clique number of the graph.  *  * </para><para>  * The clique number of a graph is the size of the largest clique.@@ -1091,13 +1089,13 @@     igraph_vector_int_t cand_filtered; } igraph_i_maximal_cliques_stack_frame; -void igraph_i_maximal_cliques_stack_frame_destroy(igraph_i_maximal_cliques_stack_frame *frame) {+static void igraph_i_maximal_cliques_stack_frame_destroy(igraph_i_maximal_cliques_stack_frame *frame) {     igraph_vector_int_destroy(&frame->cand);     igraph_vector_int_destroy(&frame->fini);     igraph_vector_int_destroy(&frame->cand_filtered); } -void igraph_i_maximal_cliques_stack_destroy(igraph_stack_ptr_t *stack) {+static void igraph_i_maximal_cliques_stack_destroy(igraph_stack_ptr_t *stack) {     igraph_i_maximal_cliques_stack_frame *frame;      while (!igraph_stack_ptr_empty(stack)) {@@ -1109,7 +1107,7 @@     igraph_stack_ptr_destroy(stack); } -int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data) {+static int igraph_i_maximal_cliques(const igraph_t *graph, igraph_i_maximal_clique_func_t func, void* data) {     int directed = igraph_is_directed(graph);     long int i, j, k, l;     igraph_integer_t no_of_nodes, nodes_to_check, nodes_done;@@ -1331,7 +1329,7 @@     return IGRAPH_SUCCESS; } -int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph,+static int igraph_i_maximal_or_largest_cliques_or_indsets(const igraph_t *graph,         igraph_vector_ptr_t *res,         igraph_integer_t *clique_number,         igraph_bool_t keep_only_largest,
igraph/src/clustertool.cpp view
@@ -45,11 +45,6 @@     #include <config.h> #endif -#include <iostream>-#include <cstdlib>-#include <cstdio>-#include <ctime>- #include "NetDataTypes.h" #include "NetRoutines.h" #include "pottsmodel_2.h"@@ -61,22 +56,25 @@ #include "igraph_interface.h" #include "igraph_components.h" #include "igraph_interrupt_internal.h"+#include "igraph_handle_exceptions.h" -int igraph_i_community_spinglass_orig(const igraph_t *graph,-                                      const igraph_vector_t *weights,-                                      igraph_real_t *modularity,-                                      igraph_real_t *temperature,-                                      igraph_vector_t *membership,-                                      igraph_vector_t *csize,-                                      igraph_integer_t spins,-                                      igraph_bool_t parupdate,-                                      igraph_real_t starttemp,-                                      igraph_real_t stoptemp,-                                      igraph_real_t coolfact,-                                      igraph_spincomm_update_t update_rule,-                                      igraph_real_t gamma);+static int igraph_i_community_spinglass_orig(+        const igraph_t *graph,+        const igraph_vector_t *weights,+        igraph_real_t *modularity,+        igraph_real_t *temperature,+        igraph_vector_t *membership,+        igraph_vector_t *csize,+        igraph_integer_t spins,+        igraph_bool_t parupdate,+        igraph_real_t starttemp,+        igraph_real_t stoptemp,+        igraph_real_t coolfact,+        igraph_spincomm_update_t update_rule,+        igraph_real_t gamma); -int igraph_i_community_spinglass_negative(const igraph_t *graph,+static int igraph_i_community_spinglass_negative(+        const igraph_t *graph,         const igraph_vector_t *weights,         igraph_real_t *modularity,         igraph_real_t *temperature,@@ -89,9 +87,9 @@         igraph_real_t coolfact,         igraph_spincomm_update_t update_rule,         igraph_real_t gamma,-        /*                    igraph_matrix_t *adhesion, */-        /*                    igraph_matrix_t *normalised_adhesion, */-        /*                    igraph_real_t *polarization, */+        /* igraph_matrix_t *adhesion, */+        /* igraph_matrix_t *normalised_adhesion, */+        /* igraph_real_t *polarization, */         igraph_real_t gamma_minus);  /**@@ -205,45 +203,47 @@                                /*                 igraph_real_t *polarization, */                                igraph_real_t gamma_minus) { -    switch (implementation) {-    case IGRAPH_SPINCOMM_IMP_ORIG:-        return igraph_i_community_spinglass_orig(graph, weights, modularity,-                temperature, membership, csize,-                spins, parupdate, starttemp,-                stoptemp, coolfact, update_rule,-                gamma);-        break;-    case IGRAPH_SPINCOMM_IMP_NEG:-        return igraph_i_community_spinglass_negative(graph, weights, modularity,-                temperature, membership, csize,-                spins, parupdate, starttemp,-                stoptemp, coolfact,-                update_rule, gamma,-                /*                       adhesion, normalised_adhesion, */-                /*                       polarization, */-                gamma_minus);-        break;-    default:-        IGRAPH_ERROR("Unknown `implementation' in spinglass community finding",-                     IGRAPH_EINVAL);-    }-+    IGRAPH_HANDLE_EXCEPTIONS(+        switch (implementation) {+        case IGRAPH_SPINCOMM_IMP_ORIG:+            return igraph_i_community_spinglass_orig(graph, weights, modularity,+                    temperature, membership, csize,+                    spins, parupdate, starttemp,+                    stoptemp, coolfact, update_rule,+                    gamma);+            break;+        case IGRAPH_SPINCOMM_IMP_NEG:+            return igraph_i_community_spinglass_negative(graph, weights, modularity,+                    temperature, membership, csize,+                    spins, parupdate, starttemp,+                    stoptemp, coolfact,+                    update_rule, gamma,+                    /*                       adhesion, normalised_adhesion, */+                    /*                       polarization, */+                    gamma_minus);+            break;+        default:+            IGRAPH_ERROR("Unknown `implementation' in spinglass community finding",+                         IGRAPH_EINVAL);+        }+    );     return 0; } -int igraph_i_community_spinglass_orig(const igraph_t *graph,-                                      const igraph_vector_t *weights,-                                      igraph_real_t *modularity,-                                      igraph_real_t *temperature,-                                      igraph_vector_t *membership,-                                      igraph_vector_t *csize,-                                      igraph_integer_t spins,-                                      igraph_bool_t parupdate,-                                      igraph_real_t starttemp,-                                      igraph_real_t stoptemp,-                                      igraph_real_t coolfact,-                                      igraph_spincomm_update_t update_rule,-                                      igraph_real_t gamma) {+static int igraph_i_community_spinglass_orig(+        const igraph_t *graph,+        const igraph_vector_t *weights,+        igraph_real_t *modularity,+        igraph_real_t *temperature,+        igraph_vector_t *membership,+        igraph_vector_t *csize,+        igraph_integer_t spins,+        igraph_bool_t parupdate,+        igraph_real_t starttemp,+        igraph_real_t stoptemp,+        igraph_real_t coolfact,+        igraph_spincomm_update_t update_rule,+        igraph_real_t gamma) {      unsigned long changes, runs;     igraph_bool_t use_weights = 0;@@ -448,94 +448,96 @@                                       igraph_integer_t spins,                                       igraph_spincomm_update_t update_rule,                                       igraph_real_t gamma) {--    igraph_bool_t use_weights = 0;-    double prob;-    ClusterList<NNode*> *cl_cur;-    network *net;-    PottsModel *pm;-    char startnode[255];+    IGRAPH_HANDLE_EXCEPTIONS(+        igraph_bool_t use_weights = 0;+        double prob;+        ClusterList<NNode*> *cl_cur;+        network *net;+        PottsModel *pm;+        char startnode[255]; -    /* Check arguments */+        /* Check arguments */ -    if (spins < 2 || spins > 500) {-        IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL);-    }-    if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE &&-        update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) {-        IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL);-    }-    if (weights) {-        if (igraph_vector_size(weights) != igraph_ecount(graph)) {-            IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL);+        if (spins < 2 || spins > 500) {+            IGRAPH_ERROR("Invalid number of spins", IGRAPH_EINVAL);         }-        use_weights = 1;-    }-    if (gamma < 0.0) {-        IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL);-    }-    if (vertex < 0 || vertex > igraph_vcount(graph)) {-        IGRAPH_ERROR("Invalid vertex id", IGRAPH_EINVAL);-    }+        if (update_rule != IGRAPH_SPINCOMM_UPDATE_SIMPLE &&+            update_rule != IGRAPH_SPINCOMM_UPDATE_CONFIG) {+            IGRAPH_ERROR("Invalid update rule", IGRAPH_EINVAL);+        }+        if (weights) {+            if (igraph_vector_size(weights) != igraph_ecount(graph)) {+                IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL);+            }+            use_weights = 1;+        }+        if (gamma < 0.0) {+            IGRAPH_ERROR("Invalid gamme value", IGRAPH_EINVAL);+        }+        if (vertex < 0 || vertex > igraph_vcount(graph)) {+            IGRAPH_ERROR("Invalid vertex id", IGRAPH_EINVAL);+        } -    /* Check whether we have a single component */-    igraph_bool_t conn;-    IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK));-    if (!conn) {-        IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL);-    }+        /* Check whether we have a single component */+        igraph_bool_t conn;+        IGRAPH_CHECK(igraph_is_connected(graph, &conn, IGRAPH_WEAK));+        if (!conn) {+            IGRAPH_ERROR("Cannot work with unconnected graph", IGRAPH_EINVAL);+        } -    net = new network;-    net->node_list   = new DL_Indexed_List<NNode*>();-    net->link_list   = new DL_Indexed_List<NLink*>();-    net->cluster_list = new DL_Indexed_List<ClusterList<NNode*>*>();+        net = new network;+        net->node_list   = new DL_Indexed_List<NNode*>();+        net->link_list   = new DL_Indexed_List<NLink*>();+        net->cluster_list = new DL_Indexed_List<ClusterList<NNode*>*>(); -    /* Transform the igraph_t */-    IGRAPH_CHECK(igraph_i_read_network(graph, weights,-                                       net, use_weights, 0));+        /* Transform the igraph_t */+        IGRAPH_CHECK(igraph_i_read_network(graph, weights,+                                           net, use_weights, 0)); -    prob = 2.0 * net->sum_weights / double(net->node_list->Size())-           / double(net->node_list->Size() - 1);+        prob = 2.0 * net->sum_weights / double(net->node_list->Size())+               / double(net->node_list->Size() - 1); -    pm = new PottsModel(net, (unsigned int)spins, update_rule);+        pm = new PottsModel(net, (unsigned int)spins, update_rule); -    /* initialize the random number generator */-    RNG_BEGIN();+        /* initialize the random number generator */+        RNG_BEGIN(); -    /* to be exected, if we want to find the community around a particular node*/-    /* the initial conf is needed, because otherwise,-       the degree of the nodes is not in the weight property, stupid!!! */-    pm->assign_initial_conf(-1);-    snprintf(startnode, 255, "%li", (long int)vertex + 1);-    pm->FindCommunityFromStart(gamma, prob, startnode, community,-                               cohesion, adhesion, inner_links, outer_links);+        /* to be exected, if we want to find the community around a particular node*/+        /* the initial conf is needed, because otherwise,+           the degree of the nodes is not in the weight property, stupid!!! */+        pm->assign_initial_conf(-1);+        snprintf(startnode, 255, "%li", (long int)vertex + 1);+        pm->FindCommunityFromStart(gamma, prob, startnode, community,+                                   cohesion, adhesion, inner_links, outer_links); -    while (net->link_list->Size()) {-        delete net->link_list->Pop();-    }-    while (net->node_list->Size()) {-        delete net->node_list->Pop();-    }-    while (net->cluster_list->Size()) {-        cl_cur = net->cluster_list->Pop();-        while (cl_cur->Size()) {-            cl_cur->Pop();+        while (net->link_list->Size()) {+            delete net->link_list->Pop();         }-        delete cl_cur;-    }-    delete net->link_list;-    delete net->node_list;-    delete net->cluster_list;+        while (net->node_list->Size()) {+            delete net->node_list->Pop();+        }+        while (net->cluster_list->Size()) {+            cl_cur = net->cluster_list->Pop();+            while (cl_cur->Size()) {+                cl_cur->Pop();+            }+            delete cl_cur;+        }+        delete net->link_list;+        delete net->node_list;+        delete net->cluster_list; -    RNG_END();+        RNG_END(); -    delete net;-    delete pm;+        delete net;+        delete pm;+    );      return 0; } -int igraph_i_community_spinglass_negative(const igraph_t *graph,+static int igraph_i_community_spinglass_negative(+        const igraph_t *graph,         const igraph_vector_t *weights,         igraph_real_t *modularity,         igraph_real_t *temperature,@@ -548,9 +550,9 @@         igraph_real_t coolfact,         igraph_spincomm_update_t update_rule,         igraph_real_t gamma,-        /*                    igraph_matrix_t *adhesion, */-        /*                    igraph_matrix_t *normalised_adhesion, */-        /*                    igraph_real_t *polarization, */+        /* igraph_matrix_t *adhesion, */+        /* igraph_matrix_t *normalised_adhesion, */+        /* igraph_real_t *polarization, */         igraph_real_t gamma_minus) {      unsigned long changes, runs;
igraph/src/cocitation.c view
@@ -254,13 +254,10 @@     return 0; } -int igraph_i_neisets_intersect(const igraph_vector_t *v1,-                               const igraph_vector_t *v2, long int *len_union,-                               long int *len_intersection); -int igraph_i_neisets_intersect(const igraph_vector_t *v1,-                               const igraph_vector_t *v2, long int *len_union,-                               long int *len_intersection) {+static int igraph_i_neisets_intersect(const igraph_vector_t *v1,+                                      const igraph_vector_t *v2, long int *len_union,+                                      long int *len_intersection) {     /* ASSERT: v1 and v2 are sorted */     long int i, j, i0, jj0;     i0 = igraph_vector_size(v1); jj0 = igraph_vector_size(v2);@@ -460,7 +457,7 @@         if (seen == 0) {             IGRAPH_ERROR("cannot calculate Jaccard similarity", IGRAPH_ENOMEM);         }-        IGRAPH_FINALLY(free, seen);+        IGRAPH_FINALLY(igraph_free, seen);          for (i = 0; i < k; i++) {             j = (long int) VECTOR(*pairs)[i];@@ -474,7 +471,7 @@             }         } -        free(seen);+        igraph_Free(seen);         IGRAPH_FINALLY_CLEAN(1);     } 
igraph/src/cohesive_blocks.c view
@@ -27,13 +27,12 @@ #include "igraph_flow.h" #include "igraph_separators.h" #include "igraph_structural.h"-#include "igraph_components.h" #include "igraph_dqueue.h" #include "igraph_constructors.h" #include "igraph_interrupt_internal.h" #include "igraph_statusbar.h" -void igraph_i_cohesive_blocks_free(igraph_vector_ptr_t *ptr) {+static void igraph_i_cohesive_blocks_free(igraph_vector_ptr_t *ptr) {     long int i, n = igraph_vector_ptr_size(ptr);      for (i = 0; i < n; i++) {@@ -45,7 +44,7 @@     } } -void igraph_i_cohesive_blocks_free2(igraph_vector_ptr_t *ptr) {+static void igraph_i_cohesive_blocks_free2(igraph_vector_ptr_t *ptr) {     long int i, n = igraph_vector_ptr_size(ptr);      for (i = 0; i < n; i++) {@@ -57,7 +56,7 @@     } } -void igraph_i_cohesive_blocks_free3(igraph_vector_ptr_t *ptr) {+static void igraph_i_cohesive_blocks_free3(igraph_vector_ptr_t *ptr) {     long int i, n = igraph_vector_ptr_size(ptr);      for (i = 0; i < n; i++) {@@ -75,14 +74,14 @@  * all neighboring components.  */ -int igraph_i_cb_components(igraph_t *graph,-                           const igraph_vector_bool_t *excluded,-                           igraph_vector_long_t *components,-                           long int *no,-                           /* working area follows */-                           igraph_vector_long_t *compid,-                           igraph_dqueue_t *Q,-                           igraph_vector_t *neis) {+static int igraph_i_cb_components(igraph_t *graph,+                                  const igraph_vector_bool_t *excluded,+                                  igraph_vector_long_t *components,+                                  long int *no,+                                  /* working area follows */+                                  igraph_vector_long_t *compid,+                                  igraph_dqueue_t *Q,+                                  igraph_vector_t *neis) {      long int no_of_nodes = igraph_vcount(graph);     long int i;@@ -137,8 +136,8 @@     return 0; } -igraph_bool_t igraph_i_cb_isin(const igraph_vector_t *needle,-                               const igraph_vector_t *haystack) {+static igraph_bool_t igraph_i_cb_isin(const igraph_vector_t *needle,+                                      const igraph_vector_t *haystack) {     long int nlen = igraph_vector_size(needle);     long int hlen = igraph_vector_size(haystack);     long int np = 0, hp = 0;
igraph/src/coloring.c view
@@ -1,4 +1,23 @@+/*+  Heuristic graph coloring algorithms.+  Copyright (C) 2017 Szabolcs Horvat <szhorvat@gmail.com> +  This program is free software; you can redistribute it and/or modify+  it under the terms of the GNU General Public License as published by+  the Free Software Foundation; either version 2 of the License, or+  (at your option) any later version.++  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License for more details.++  You should have received a copy of the GNU General Public License+  along with this program; if not, write to the Free Software+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA+  02110-1301 USA+*/+ #include "igraph_coloring.h" #include "igraph_interface.h" #include "igraph_adjlist.h"@@ -6,7 +25,7 @@ #include "igraph_types_internal.h"  -int igraph_i_vertex_coloring_greedy_cn(const igraph_t *graph, igraph_vector_int_t *colors) {+static int igraph_i_vertex_coloring_greedy_cn(const igraph_t *graph, igraph_vector_int_t *colors) {     long i, vertex, maxdeg;     long vc = igraph_vcount(graph);     igraph_2wheap_t cn; /* indexed heap storing number of already coloured neighbours */@@ -115,7 +134,7 @@  * \brief Computes a vertex coloring using a greedy algorithm.  *  * </para><para>- * This function assigns a "color"---represented as a non-negative integer---to+ * This function assigns a "color"—represented as a non-negative integer—to  * each vertex of the graph in such a way that neighboring vertices never have  * the same color. The obtained coloring is not necessarily minimal.  *
igraph/src/community.c view
@@ -27,7 +27,6 @@ #include "igraph_memory.h" #include "igraph_random.h" #include "igraph_arpack.h"-#include "igraph_arpack_internal.h" #include "igraph_adjlist.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h"@@ -50,7 +49,7 @@     #include <R.h> #endif -int igraph_i_rewrite_membership_vector(igraph_vector_t *membership) {+static int igraph_i_rewrite_membership_vector(igraph_vector_t *membership) {     long int no = (long int) igraph_vector_max(membership) + 1;     igraph_vector_t idx;     long int realno = 0;@@ -73,13 +72,13 @@     return 0; } -int igraph_i_community_eb_get_merges2(const igraph_t *graph,-                                      const igraph_vector_t *edges,-                                      const igraph_vector_t *weights,-                                      igraph_matrix_t *res,-                                      igraph_vector_t *bridges,-                                      igraph_vector_t *modularity,-                                      igraph_vector_t *membership) {+static int igraph_i_community_eb_get_merges2(const igraph_t *graph,+                                             const igraph_vector_t *edges,+                                             const igraph_vector_t *weights,+                                             igraph_matrix_t *res,+                                             igraph_vector_t *bridges,+                                             igraph_vector_t *modularity,+                                             igraph_vector_t *membership) {      igraph_vector_t mymembership;     long int no_of_nodes = igraph_vcount(graph);@@ -177,7 +176,7 @@  /**  * \function igraph_community_eb_get_merges- * \brief Calculating the merges, ie. the dendrogram for an edge betweenness community structure+ * \brief Calculating the merges, i.e. the dendrogram for an edge betweenness community structure  *  * </para><para>  * This function is handy if you have a sequence of edge which are@@ -293,8 +292,8 @@ }  /* Find the smallest active element in the vector */-long int igraph_i_vector_which_max_not_null(const igraph_vector_t *v,-        const char *passive) {+static long int igraph_i_vector_which_max_not_null(const igraph_vector_t *v,+                                                   const char *passive) {     long int which, i = 0, size = igraph_vector_size(v);     igraph_real_t max;     while (passive[i]) {@@ -358,7 +357,7 @@  * \param membership If not a null pointer, then the membership vector,  *     corresponding to the highest modularity value, is stored here.  * \param directed Logical constant, whether to calculate directed- *    betweenness (ie. directed paths) for directed graphs. It is+ *    betweenness (i.e. directed paths) for directed graphs. It is  *    ignored for undirected graphs.  * \param weights An optional vector containing edge weights. If null,  *     the unweighted edge betweenness scores will be calculated and@@ -482,7 +481,9 @@     IGRAPH_CHECK(igraph_vector_resize(result, no_of_edges));     if (edge_betweenness) {         IGRAPH_CHECK(igraph_vector_resize(edge_betweenness, no_of_edges));-        VECTOR(*edge_betweenness)[no_of_edges - 1] = 0;+        if (no_of_edges > 0) {+            VECTOR(*edge_betweenness)[no_of_edges - 1] = 0;+        }     }      IGRAPH_VECTOR_INIT_FINALLY(&eb, no_of_edges);@@ -719,7 +720,7 @@      if (result_owned) {         igraph_vector_destroy(result);-        free(result);+        igraph_Free(result);         IGRAPH_FINALLY_CLEAN(2);     } @@ -890,7 +891,7 @@  * \param graph The input graph. It must be undirected; directed graphs are  *     not supported yet.  * \param membership Numeric vector which gives the type of each- *     vertex, ie. the component to which it belongs.+ *     vertex, i.e. the component to which it belongs.  *     It does not have to be consecutive, i.e. empty communities are  *     allowed.  * \param modularity Pointer to a real number, the result will be@@ -1052,7 +1053,7 @@  * range 0, ..., n - 1.  *  * \param  membership  Numeric vector which gives the type of each- *                     vertex, ie. the component to which it belongs.+ *                     vertex, i.e. the component to which it belongs.  *                     The vector will be altered in-place.  * \param  new_to_old  Pointer to a vector which will contain the  *                     old component ID for each new one, or NULL,@@ -1176,9 +1177,9 @@     igraph_real_t sumweights; } igraph_i_community_leading_eigenvector_data_t; -int igraph_i_community_leading_eigenvector(igraph_real_t *to,-        const igraph_real_t *from,-        int n, void *extra) {+static int igraph_i_community_leading_eigenvector(igraph_real_t *to,+                                                  const igraph_real_t *from,+                                                  int n, void *extra) {      igraph_i_community_leading_eigenvector_data_t *data = extra;     long int j, k, nlen, size = n;@@ -1237,9 +1238,9 @@     return 0; } -int igraph_i_community_leading_eigenvector2(igraph_real_t *to,-        const igraph_real_t *from,-        int n, void *extra) {+static int igraph_i_community_leading_eigenvector2(igraph_real_t *to,+                                                   const igraph_real_t *from,+                                                   int n, void *extra) {      igraph_i_community_leading_eigenvector_data_t *data = extra;     long int j, k, nlen, size = n;@@ -1303,9 +1304,9 @@     return 0; } -int igraph_i_community_leading_eigenvector_weighted(igraph_real_t *to,-        const igraph_real_t *from,-        int n, void *extra) {+static int igraph_i_community_leading_eigenvector_weighted(igraph_real_t *to,+                                                           const igraph_real_t *from,+                                                           int n, void *extra) {      igraph_i_community_leading_eigenvector_data_t *data = extra;     long int j, k, nlen, size = n;@@ -1367,9 +1368,9 @@     return 0; } -int igraph_i_community_leading_eigenvector2_weighted(igraph_real_t *to,-        const igraph_real_t *from,-        int n, void *extra) {+static int igraph_i_community_leading_eigenvector2_weighted(igraph_real_t *to,+                                                            const igraph_real_t *from,+                                                            int n, void *extra) {      igraph_i_community_leading_eigenvector_data_t *data = extra;     long int j, k, nlen, size = n;@@ -1436,7 +1437,7 @@     return 0; } -void igraph_i_levc_free(igraph_vector_ptr_t *ptr) {+static void igraph_i_levc_free(igraph_vector_ptr_t *ptr) {     long int i, n = igraph_vector_ptr_size(ptr);     for (i = 0; i < n; i++) {         igraph_vector_t *v = VECTOR(*ptr)[i];@@ -1447,8 +1448,8 @@     } } -void igraph_i_error_handler_none(const char *reason, const char *file,-                                 int line, int igraph_errno) {+static void igraph_i_error_handler_none(const char *reason, const char *file,+                                        int line, int igraph_errno) {     IGRAPH_UNUSED(reason);     IGRAPH_UNUSED(file);     IGRAPH_UNUSED(line);@@ -1514,7 +1515,7 @@  *    \ref igraph_vector_t object. The user is responsible of  *    deallocating the memory that belongs to the individual vectors,  *    by calling first \ref igraph_vector_destroy(), and then- *    <code>free()</code> on them.+ *    \ref igraph_free() on them.  * \param history Pointer to an initialized vector or a null pointer.  *    If not a null pointer, then a trace of the algorithm is stored  *    here, encoded numerically. The various operations:@@ -2682,7 +2683,7 @@ } igraph_i_multilevel_community_list;  /* Computes the modularity of a community partitioning */-igraph_real_t igraph_i_multilevel_community_modularity(+static igraph_real_t igraph_i_multilevel_community_modularity(     const igraph_i_multilevel_community_list *communities) {     igraph_real_t result = 0;     long int i;@@ -2703,7 +2704,7 @@     long int id; } igraph_i_multilevel_link; -int igraph_i_multilevel_link_cmp(const void *a, const void *b) {+static int igraph_i_multilevel_link_cmp(const void *a, const void *b) {     long int r = (((igraph_i_multilevel_link*)a)->from -                   ((igraph_i_multilevel_link*)b)->from);     if (r != 0) {@@ -2715,7 +2716,7 @@ }  /* removes multiple edges and returns new edge id's for each edge in |E|log|E| */-int igraph_i_multilevel_simplify_multiple(igraph_t *graph, igraph_vector_t *eids) {+static int igraph_i_multilevel_simplify_multiple(igraph_t *graph, igraph_vector_t *eids) {     long int ecount = igraph_ecount(graph);     long int i, l = -1, last_from = -1, last_to = -1;     igraph_bool_t directed = igraph_is_directed(graph);@@ -2730,7 +2731,7 @@     if (links == 0) {         IGRAPH_ERROR("multi-level community structure detection failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, links);+    IGRAPH_FINALLY(igraph_free, links);      for (i = 0; i < ecount; i++) {         igraph_edge(graph, (igraph_integer_t) i, &from, &to);@@ -2760,7 +2761,7 @@         VECTOR(*eids)[links[i].id] = l;     } -    free(links);+    igraph_Free(links);     IGRAPH_FINALLY_CLEAN(1);      igraph_destroy(graph);@@ -2777,7 +2778,7 @@     igraph_real_t weight; } igraph_i_multilevel_community_link; -int igraph_i_multilevel_community_link_cmp(const void *a, const void *b) {+static int igraph_i_multilevel_community_link_cmp(const void *a, const void *b) {     return (int) (((igraph_i_multilevel_community_link*)a)->community -                   ((igraph_i_multilevel_community_link*)b)->community); }@@ -2795,11 +2796,12 @@  *   communities incident on this vertex and the total weight of edges  *   pointing to these communities  */-int igraph_i_multilevel_community_links(const igraph_t *graph,-                                        const igraph_i_multilevel_community_list *communities,-                                        igraph_integer_t vertex, igraph_vector_t *edges,-                                        igraph_real_t *weight_all, igraph_real_t *weight_inside, igraph_real_t *weight_loop,-                                        igraph_vector_t *links_community, igraph_vector_t *links_weight) {+static int igraph_i_multilevel_community_links(+        const igraph_t *graph,+        const igraph_i_multilevel_community_list *communities,+        igraph_integer_t vertex, igraph_vector_t *edges,+        igraph_real_t *weight_all, igraph_real_t *weight_inside, igraph_real_t *weight_loop,+        igraph_vector_t *links_community, igraph_vector_t *links_weight) {      long int i, n, last = -1, c = -1;     igraph_real_t weight = 1;@@ -2869,10 +2871,10 @@     return 0; } -igraph_real_t igraph_i_multilevel_community_modularity_gain(-    const igraph_i_multilevel_community_list *communities,-    igraph_integer_t community, igraph_integer_t vertex,-    igraph_real_t weight_all, igraph_real_t weight_inside) {+static igraph_real_t igraph_i_multilevel_community_modularity_gain(+        const igraph_i_multilevel_community_list *communities,+        igraph_integer_t community, igraph_integer_t vertex,+        igraph_real_t weight_all, igraph_real_t weight_inside) {     IGRAPH_UNUSED(vertex);     return weight_inside -            communities->item[(long int)community].weight_all * weight_all / communities->weight_sum;@@ -2884,7 +2886,7 @@  * detection where a copy of the original graph is used anyway.  * The membership vector will also be rewritten by the underlying  * igraph_membership_reindex call */-int igraph_i_multilevel_shrink(igraph_t *graph, igraph_vector_t *membership) {+static int igraph_i_multilevel_shrink(igraph_t *graph, igraph_vector_t *membership) {     igraph_vector_t edges;     long int no_of_nodes = igraph_vcount(graph);     long int no_of_edges = igraph_ecount(graph);@@ -2955,9 +2957,11 @@  *  * Time complexity: in average near linear on sparse graphs.  */-int igraph_i_community_multilevel_step(igraph_t *graph,-                                       igraph_vector_t *weights, igraph_vector_t *membership,-                                       igraph_real_t *modularity) {+static int igraph_i_community_multilevel_step(+        igraph_t *graph,+        igraph_vector_t *weights,+        igraph_vector_t *membership,+        igraph_real_t *modularity) {      long int i, j;     long int vcount = igraph_vcount(graph);@@ -3316,15 +3320,15 @@ }  -int igraph_i_compare_communities_vi(const igraph_vector_t *v1,-                                    const igraph_vector_t *v2, igraph_real_t* result);-int igraph_i_compare_communities_nmi(const igraph_vector_t *v1,-                                     const igraph_vector_t *v2, igraph_real_t* result);-int igraph_i_compare_communities_rand(const igraph_vector_t *v1,-                                      const igraph_vector_t *v2, igraph_real_t* result, igraph_bool_t adjust);-int igraph_i_split_join_distance(const igraph_vector_t *v1,-                                 const igraph_vector_t *v2, igraph_integer_t* distance12,-                                 igraph_integer_t* distance21);+static int igraph_i_compare_communities_vi(const igraph_vector_t *v1,+                                           const igraph_vector_t *v2, igraph_real_t* result);+static int igraph_i_compare_communities_nmi(const igraph_vector_t *v1,+                                            const igraph_vector_t *v2, igraph_real_t* result);+static int igraph_i_compare_communities_rand(const igraph_vector_t *v1,+                                             const igraph_vector_t *v2, igraph_real_t* result, igraph_bool_t adjust);+static int igraph_i_split_join_distance(const igraph_vector_t *v1,+                                        const igraph_vector_t *v2, igraph_integer_t* distance12,+                                        igraph_integer_t* distance21);  /**  * \ingroup communities@@ -3518,7 +3522,7 @@  * membership vectors v1 and v2. This is needed by both Meila's and Danon's  * community comparison measure.  */-int igraph_i_entropy_and_mutual_information(const igraph_vector_t* v1,+static int igraph_i_entropy_and_mutual_information(const igraph_vector_t* v1,         const igraph_vector_t* v2, double* h1, double* h2, double* mut_inf) {     long int i, n = igraph_vector_size(v1);     long int k1 = (long int)igraph_vector_max(v1) + 1;@@ -3531,12 +3535,12 @@     if (p1 == 0) {         IGRAPH_ERROR("igraph_i_entropy_and_mutual_information failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, p1);+    IGRAPH_FINALLY(igraph_free, p1);     p2 = igraph_Calloc(k2, double);     if (p2 == 0) {         IGRAPH_ERROR("igraph_i_entropy_and_mutual_information failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, p2);+    IGRAPH_FINALLY(igraph_free, p2);      /* Calculate the entropy of v1 */     *h1 = 0.0;@@ -3584,7 +3588,7 @@      igraph_spmatrix_iter_destroy(&mit);     igraph_spmatrix_destroy(&m);-    free(p1); free(p2);+    igraph_Free(p1); igraph_Free(p2);      IGRAPH_FINALLY_CLEAN(4); @@ -3603,7 +3607,7 @@  * </para><para>  * Time complexity: O(n log(n))  */-int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, const igraph_vector_t *v2,+static int igraph_i_compare_communities_nmi(const igraph_vector_t *v1, const igraph_vector_t *v2,                                      igraph_real_t* result) {     double h1, h2, mut_inf; @@ -3633,7 +3637,7 @@  * </para><para>  * Time complexity: O(n log(n))  */-int igraph_i_compare_communities_vi(const igraph_vector_t *v1, const igraph_vector_t *v2,+static int igraph_i_compare_communities_vi(const igraph_vector_t *v1, const igraph_vector_t *v2,                                     igraph_real_t* result) {     double h1, h2, mut_inf; @@ -3654,7 +3658,7 @@  * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1  * and k2 are the number of clusters in each of the clusterings.  */-int igraph_i_confusion_matrix(const igraph_vector_t *v1, const igraph_vector_t *v2,+static int igraph_i_confusion_matrix(const igraph_vector_t *v1, const igraph_vector_t *v2,                               igraph_spmatrix_t *m) {     long int k1 = (long int)igraph_vector_max(v1) + 1;     long int k2 = (long int)igraph_vector_max(v2) + 1;@@ -3685,7 +3689,7 @@  * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1  * and k2 are the number of clusters in each of the clusterings.  */-int igraph_i_split_join_distance(const igraph_vector_t *v1, const igraph_vector_t *v2,+static int igraph_i_split_join_distance(const igraph_vector_t *v1, const igraph_vector_t *v2,                                  igraph_integer_t* distance12, igraph_integer_t* distance21) {     long int n = igraph_vector_size(v1);     igraph_vector_t rowmax, colmax;@@ -3750,8 +3754,9 @@  * Time complexity: O(n log(max(k1, k2))), where n is the number of vertices, k1  * and k2 are the number of clusters in each of the clusterings.  */-int igraph_i_compare_communities_rand(const igraph_vector_t *v1,-                                      const igraph_vector_t *v2, igraph_real_t *result, igraph_bool_t adjust) {+static int igraph_i_compare_communities_rand(+        const igraph_vector_t *v1, const igraph_vector_t *v2,+        igraph_real_t *result, igraph_bool_t adjust) {     igraph_spmatrix_t m;     igraph_spmatrix_iter_t mit;     igraph_vector_t rowsums, colsums;
igraph/src/community_leiden.c view
@@ -46,7 +46,8 @@  * and is updated in-place.  *  */-int igraph_i_community_leiden_fastmovenodes(const igraph_t *graph,+static int igraph_i_community_leiden_fastmovenodes(+        const igraph_t *graph,         const igraph_inclist_t *edges_per_node,         const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,         const igraph_real_t resolution_parameter,@@ -121,7 +122,7 @@         VECTOR(cluster_weights)[current_cluster] -= VECTOR(*node_weights)[v];         VECTOR(nb_nodes_per_cluster)[current_cluster]--;         if (VECTOR(nb_nodes_per_cluster)[current_cluster] == 0) {-            igraph_stack_push(&empty_clusters, current_cluster);+            IGRAPH_CHECK(igraph_stack_push(&empty_clusters, current_cluster));         }          /* Find out neighboring clusters */@@ -136,12 +137,14 @@         for (i = 0; i < degree; i++) {             long int e = VECTOR(*edges)[i];             long int u = (long int)IGRAPH_OTHER(graph, e, v);-            c = VECTOR(*membership)[u];-            if (!VECTOR(neighbor_cluster_added)[c]) {-                VECTOR(neighbor_cluster_added)[c] = 1;-                VECTOR(neighbor_clusters)[nb_neigh_clusters++] = c;+            if (u != v) {+                c = VECTOR(*membership)[u];+                if (!VECTOR(neighbor_cluster_added)[c]) {+                    VECTOR(neighbor_cluster_added)[c] = 1;+                    VECTOR(neighbor_clusters)[nb_neigh_clusters++] = c;+                }+                VECTOR(edge_weights_per_cluster)[c] += VECTOR(*edge_weights)[e];             }-            VECTOR(edge_weights_per_cluster)[c] += VECTOR(*edge_weights)[e];         }          /* Calculate maximum diff */@@ -176,7 +179,7 @@                 long int e = VECTOR(*edges)[i];                 long int u = (long int)IGRAPH_OTHER(graph, e, v);                 if (VECTOR(node_is_stable)[u] && VECTOR(*membership)[u] != best_cluster) {-                    igraph_dqueue_push(&unstable_nodes, u);+                    IGRAPH_CHECK(igraph_dqueue_push(&unstable_nodes, u));                     VECTOR(node_is_stable)[u] = 0;                 }             }@@ -215,7 +218,10 @@  * resulting \c nb_refined_clusters, then nodes in \c node_subset are numbered  * C, C + 1, ..., C' - 1.  */-int igraph_i_community_leiden_clean_refined_membership(const igraph_vector_t* node_subset, igraph_vector_t *refined_membership, igraph_integer_t* nb_refined_clusters) {+static int igraph_i_community_leiden_clean_refined_membership(+        const igraph_vector_t* node_subset,+        igraph_vector_t *refined_membership,+        igraph_integer_t* nb_refined_clusters) {     long int i, n = igraph_vector_size(node_subset);     igraph_vector_t new_cluster; @@ -280,7 +286,8 @@  * igraph_i_community_leiden_clean_refined_membership for more information about  * this aspect.  */-int igraph_i_community_leiden_mergenodes(const igraph_t *graph,+static int igraph_i_community_leiden_mergenodes(+        const igraph_t *graph,         const igraph_inclist_t *edges_per_node,         const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,         const igraph_vector_t *node_subset,@@ -324,7 +331,7 @@         for (j = 0; j < degree; j++) {             long int e = VECTOR(*edges)[j];             long int u = (long int)IGRAPH_OTHER(graph, e, v);-            if (VECTOR(*membership)[u] == cluster_subset) {+            if (u != v && VECTOR(*membership)[u] == cluster_subset) {                 VECTOR(external_edge_weight_per_cluster_in_subset)[i] += VECTOR(*edge_weights)[e];             }         }@@ -378,7 +385,7 @@             for (j = 0; j < degree; j++) {                 long int e = (long int)VECTOR(*edges)[j];                 long int u = (long int)IGRAPH_OTHER(graph, e, v);-                if (VECTOR(*membership)[u] == cluster_subset) {+                if (u != v && VECTOR(*membership)[u] == cluster_subset) {                     long int c = VECTOR(*refined_membership)[u];                     if (!VECTOR(neighbor_cluster_added)[c]) {                         VECTOR(neighbor_cluster_added)[c] = 1;@@ -420,7 +427,7 @@             if (total_cum_trans_diff < IGRAPH_INFINITY) {                 igraph_real_t r = igraph_rng_get_unif(igraph_rng_default(), 0, total_cum_trans_diff);                 long int chosen_idx;-                igraph_i_vector_binsearch_slice(&cum_trans_diff, r, &chosen_idx, 0, nb_neigh_clusters);+                igraph_vector_binsearch_slice(&cum_trans_diff, r, &chosen_idx, 0, nb_neigh_clusters);                 chosen_cluster = VECTOR(neighbor_clusters)[chosen_idx];             } else {                 chosen_cluster = best_cluster;@@ -479,7 +486,7 @@  * should be ensured that all clusters are always properly empty (or  * non-existing) before calling this function.  */-int igraph_i_community_get_clusters(const igraph_vector_t *membership, igraph_vector_ptr_t *clusters) {+static int igraph_i_community_get_clusters(const igraph_vector_t *membership, igraph_vector_ptr_t *clusters) {     long int i, c, n = igraph_vector_size(membership);     igraph_vector_t *cluster;     for (i = 0; i < n; i++) {@@ -498,7 +505,7 @@         }          /* Add node i to cluster vector */-        igraph_vector_push_back(cluster, i);+        IGRAPH_CHECK(igraph_vector_push_back(cluster, i));     }      return IGRAPH_SUCCESS;@@ -518,7 +525,7 @@  * aggregated_membership are all expected to be initialized.  *  */-int igraph_i_community_leiden_aggregate(+static int igraph_i_community_leiden_aggregate(     const igraph_t *graph, const igraph_inclist_t *edges_per_node, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,     const igraph_vector_t *membership, const igraph_vector_t *refined_membership, const igraph_integer_t nb_refined_clusters,     igraph_t *aggregated_graph, igraph_vector_t *aggregated_edge_weights, igraph_vector_t *aggregated_node_weights, igraph_vector_t *aggregated_membership) {@@ -531,7 +538,7 @@      /* Get refined clusters */     IGRAPH_CHECK(igraph_vector_ptr_init(&refined_clusters, nb_refined_clusters));-    igraph_vector_ptr_set_item_destructor(&refined_clusters, igraph_vector_destroy);+    IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&refined_clusters, igraph_vector_destroy);     IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &refined_clusters);     IGRAPH_CHECK(igraph_i_community_get_clusters(refined_membership, &refined_clusters)); @@ -591,10 +598,11 @@             long int c2 = VECTOR(neighbor_clusters)[i];              /* Add edge */-            igraph_vector_push_back(&aggregated_edges, c); igraph_vector_push_back(&aggregated_edges, c2);+            IGRAPH_CHECK(igraph_vector_push_back(&aggregated_edges, c));+            IGRAPH_CHECK(igraph_vector_push_back(&aggregated_edges, c2));              /* Add edge weight */-            igraph_vector_push_back(aggregated_edge_weights, VECTOR(edge_weight_to_cluster)[c2]);+            IGRAPH_CHECK(igraph_vector_push_back(aggregated_edge_weights, VECTOR(edge_weight_to_cluster)[c2]));              VECTOR(edge_weight_to_cluster)[c2] = 0.0;             VECTOR(neighbor_cluster_added)[c2] = 0;@@ -604,17 +612,21 @@      } -    IGRAPH_CHECK(igraph_create(aggregated_graph, &aggregated_edges, nb_refined_clusters,-                               IGRAPH_UNDIRECTED));-     igraph_vector_destroy(&neighbor_clusters);     igraph_vector_bool_destroy(&neighbor_cluster_added);     igraph_vector_destroy(&edge_weight_to_cluster);-    igraph_vector_destroy(&aggregated_edges);     igraph_vector_ptr_destroy_all(&refined_clusters); -    IGRAPH_FINALLY_CLEAN(5);+    IGRAPH_FINALLY_CLEAN(4); +    igraph_destroy(aggregated_graph);+    IGRAPH_CHECK(igraph_create(aggregated_graph, &aggregated_edges, nb_refined_clusters,+                               IGRAPH_UNDIRECTED));++    igraph_vector_destroy(&aggregated_edges);++    IGRAPH_FINALLY_CLEAN(1);+     return IGRAPH_SUCCESS; } @@ -641,9 +653,10 @@  * weights inside cluster c. This is how the quality is calculated in practice.  *  */-int igraph_i_community_leiden_quality(const igraph_t *graph, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,-                                      const igraph_vector_t *membership, const igraph_integer_t nb_comms, const igraph_real_t resolution_parameter,-                                      igraph_real_t *quality) {+static int igraph_i_community_leiden_quality(+        const igraph_t *graph, const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,+        const igraph_vector_t *membership, const igraph_integer_t nb_comms, const igraph_real_t resolution_parameter,+        igraph_real_t *quality) {     igraph_vector_t cluster_weights;     igraph_real_t total_edge_weight = 0.0;     igraph_eit_t eit;@@ -697,13 +710,14 @@  * partition for the aggregate network.  */ int igraph_i_community_leiden(const igraph_t *graph,-                              const igraph_vector_t *edge_weights, const igraph_vector_t *node_weights,+                              igraph_vector_t *edge_weights, igraph_vector_t *node_weights,                               const igraph_real_t resolution_parameter, const igraph_real_t beta,                               igraph_vector_t *membership, igraph_integer_t *nb_clusters, igraph_real_t *quality) {     igraph_integer_t nb_refined_clusters;     long int i, c, n = igraph_vcount(graph);-    igraph_t *aggregated_graph, *tmp_graph;-    igraph_vector_t *aggregated_edge_weights, *aggregated_node_weights, *aggregated_membership;+    igraph_t aggregated_graph, *i_graph;+    igraph_vector_t aggregated_edge_weights, aggregated_node_weights, aggregated_membership;+    igraph_vector_t *i_edge_weights, *i_node_weights, *i_membership;     igraph_vector_t tmp_edge_weights, tmp_node_weights, tmp_membership;     igraph_vector_t refined_membership;     igraph_vector_int_t aggregate_node;@@ -722,8 +736,9 @@      /* Initialize clusters */     IGRAPH_CHECK(igraph_vector_ptr_init(&clusters, n));-    igraph_vector_ptr_set_item_destructor(&clusters, igraph_vector_destroy);+    IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&clusters, igraph_vector_destroy);     IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &clusters);+     /* Initialize aggregate nodes, which initially is identical to simply the      * nodes in the graph. */     IGRAPH_CHECK(igraph_vector_int_init(&aggregate_node, n));@@ -732,18 +747,36 @@         VECTOR(aggregate_node)[i] = i;     } +    /* Initialize refined membership */     IGRAPH_CHECK(igraph_vector_init(&refined_membership, 0));     IGRAPH_FINALLY(igraph_vector_destroy, &refined_membership); -    /* Initialize aggregated graph, weights and membership. */-    aggregated_graph = graph;-    aggregated_edge_weights = edge_weights;-    aggregated_node_weights = node_weights;-    aggregated_membership = membership;+    /* Initialize aggregated graph */+    IGRAPH_CHECK(igraph_empty(&aggregated_graph, 0, IGRAPH_UNDIRECTED));+    IGRAPH_FINALLY(igraph_destroy, &aggregated_graph); +    /* Initialize aggregated edge weights */+    IGRAPH_CHECK(igraph_vector_init(&aggregated_edge_weights, 0));+    IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_edge_weights);++    /* Initialize aggregated node weights */+    IGRAPH_CHECK(igraph_vector_init(&aggregated_node_weights, 0));+    IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_node_weights);++    /* Initialize aggregated membership */+    IGRAPH_CHECK(igraph_vector_init(&aggregated_membership, 0));+    IGRAPH_FINALLY(igraph_vector_destroy, &aggregated_membership);++    /* Set actual graph, weights and membership to be used. */+    i_graph = (igraph_t*)graph;+    i_edge_weights = edge_weights;+    i_node_weights = node_weights;+    i_membership = membership;+     /* Clean membership and count number of *clusters */-    IGRAPH_CHECK(igraph_reindex_membership(aggregated_membership, NULL, nb_clusters)); +    IGRAPH_CHECK(igraph_reindex_membership(i_membership, NULL, nb_clusters));+     if (*nb_clusters > n) {         IGRAPH_ERROR("Too many communities in membership vector", IGRAPH_EINVAL);     }@@ -751,45 +784,45 @@     do {          /* Get incidence list for fast iteration */-        IGRAPH_CHECK(igraph_inclist_init(aggregated_graph, &edges_per_node, IGRAPH_ALL));+        IGRAPH_CHECK(igraph_inclist_init( i_graph, &edges_per_node, IGRAPH_ALL));         IGRAPH_FINALLY(igraph_inclist_destroy, &edges_per_node);          /* Move around the nodes in order to increase the quality */-        IGRAPH_CHECK(igraph_i_community_leiden_fastmovenodes(aggregated_graph,+        IGRAPH_CHECK(igraph_i_community_leiden_fastmovenodes(i_graph,                      &edges_per_node,-                     aggregated_edge_weights, aggregated_node_weights,+                     i_edge_weights, i_node_weights,                      resolution_parameter,                      nb_clusters,-                     aggregated_membership));+                     i_membership));          /* We only continue clustering if not all clusters are represented by a          * single node yet          */-        continue_clustering = (*nb_clusters < igraph_vcount(aggregated_graph));+        continue_clustering = (*nb_clusters < igraph_vcount(i_graph));          if (continue_clustering) {             /* Set original membership */             if (level > 0) {                 for (i = 0; i < n; i++) {                     long int v_aggregate = VECTOR(aggregate_node)[i];-                    VECTOR(*membership)[i] = VECTOR(*aggregated_membership)[v_aggregate];+                    VECTOR(*membership)[i] = VECTOR(*i_membership)[v_aggregate];                 }             }              /* Get node sets for each cluster. */-            IGRAPH_CHECK(igraph_i_community_get_clusters(aggregated_membership, &clusters));+            IGRAPH_CHECK(igraph_i_community_get_clusters(i_membership, &clusters));              /* Ensure refined membership is correct size */-            IGRAPH_CHECK(igraph_vector_resize(&refined_membership, igraph_vcount(aggregated_graph)));+            IGRAPH_CHECK(igraph_vector_resize(&refined_membership, igraph_vcount(i_graph)));              /* Refine each cluster */             nb_refined_clusters = 0;             for (c = 0; c < *nb_clusters; c++) {                 igraph_vector_t* cluster = (igraph_vector_t*)VECTOR(clusters)[c];-                IGRAPH_CHECK(igraph_i_community_leiden_mergenodes(aggregated_graph,+                IGRAPH_CHECK(igraph_i_community_leiden_mergenodes(i_graph,                              &edges_per_node,-                             aggregated_edge_weights, aggregated_node_weights,-                             cluster, aggregated_membership, c,+                             i_edge_weights, i_node_weights,+                             cluster, i_membership, c,                              resolution_parameter, beta,                              &nb_refined_clusters, &refined_membership));                 /* Empty cluster */@@ -798,8 +831,9 @@              /* If refinement didn't aggregate anything, we aggregate on the basis of              * the actual clustering */-            if (nb_refined_clusters >= igraph_vcount(aggregated_graph)) {-                igraph_vector_update(&refined_membership, aggregated_membership);+            if (nb_refined_clusters >= igraph_vcount(i_graph)) {+                igraph_vector_update(&refined_membership, i_membership);+                nb_refined_clusters = *nb_clusters;             }              /* Keep track of aggregate node. */@@ -810,70 +844,27 @@                 VECTOR(aggregate_node)[i] = (igraph_integer_t)VECTOR(refined_membership)[v_aggregate];             } -            /* Allocate temporary graph */-            tmp_graph = igraph_Calloc(1, igraph_t);-            if (tmp_graph == 0) {-                IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate graph", IGRAPH_ENOMEM);-            }-            IGRAPH_FINALLY(free, tmp_graph);-             IGRAPH_CHECK(igraph_i_community_leiden_aggregate(-                             aggregated_graph, &edges_per_node, aggregated_edge_weights, aggregated_node_weights,-                             aggregated_membership, &refined_membership, nb_refined_clusters,-                             tmp_graph, &tmp_edge_weights, &tmp_node_weights, &tmp_membership));--            /* Graph has been created by aggregation, ensure it is properly destroyed if-             * an error occurs. */-            IGRAPH_FINALLY(igraph_destroy, tmp_graph);--            if (level >= 1) {-                /* Destroy previously allocated graph (note that aggregated_graph points to-                 * the previously allocated tmp_graph). */-                igraph_destroy(aggregated_graph);-                igraph_Free(aggregated_graph);-                IGRAPH_FINALLY_CLEAN(2);-            }+                             i_graph, &edges_per_node, i_edge_weights, i_node_weights,+                             i_membership, &refined_membership, nb_refined_clusters,+                             &aggregated_graph, &tmp_edge_weights, &tmp_node_weights, &tmp_membership));              /* On the lowest level, the actual graph and node and edge weights and-             * membership are used. On higher levels, we will have to use a new graph-             * and node and edge weights to represent them. We perform the allocation-             * of memory here. We only allocate the memory once, and simply update-             * them in any subsequent rounds.+             * membership are used. On higher levels, we will use the aggregated graph+             * and associated vectors.              */             if (level == 0) {-                aggregated_edge_weights = igraph_Calloc(1, igraph_vector_t);-                if (aggregated_edge_weights == 0) {-                    IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate edge weights", IGRAPH_ENOMEM);-                }-                IGRAPH_FINALLY(free, aggregated_edge_weights);-                IGRAPH_CHECK(igraph_vector_init(aggregated_edge_weights, 0));-                IGRAPH_FINALLY(igraph_vector_destroy, aggregated_edge_weights);--                aggregated_node_weights = igraph_Calloc(1, igraph_vector_t);-                if (aggregated_node_weights == 0) {-                    IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate node weights", IGRAPH_ENOMEM);-                }-                IGRAPH_FINALLY(free, aggregated_node_weights);-                IGRAPH_CHECK(igraph_vector_init(aggregated_node_weights, 0));-                IGRAPH_FINALLY(igraph_vector_destroy, aggregated_node_weights);--                aggregated_membership = igraph_Calloc(1, igraph_vector_t);-                if (aggregated_membership == 0) {-                    IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for aggregate membership", IGRAPH_ENOMEM);-                }-                IGRAPH_FINALLY(free, aggregated_membership);-                IGRAPH_CHECK(igraph_vector_init(aggregated_membership, 0));-                IGRAPH_FINALLY(igraph_vector_destroy, aggregated_membership);+                /* Set actual graph, weights and membership to be used. */+                i_graph = &aggregated_graph;+                i_edge_weights = &aggregated_edge_weights;+                i_node_weights = &aggregated_node_weights;+                i_membership = &aggregated_membership;             } -            /* Set the aggregated graph correctly */-            aggregated_graph = tmp_graph;--            /* Update the aggregated administration. This does not allocate memory,-             * it will always fit in existing memory allocated previously. */-            igraph_vector_update(aggregated_edge_weights, &tmp_edge_weights);-            igraph_vector_update(aggregated_node_weights, &tmp_node_weights);-            igraph_vector_update(aggregated_membership, &tmp_membership);+            /* Update the aggregated administration. */+            IGRAPH_CHECK(igraph_vector_update(i_edge_weights, &tmp_edge_weights));+            IGRAPH_CHECK(igraph_vector_update(i_node_weights, &tmp_node_weights));+            IGRAPH_CHECK(igraph_vector_update(i_membership, &tmp_membership));              level += 1;         }@@ -883,21 +874,12 @@         IGRAPH_FINALLY_CLEAN(1);     } while (continue_clustering); -    /* If memory was allocated to represent the aggregated administration we need-     * to make sure it is properly freed. This is only done if we have at least-     * passed on to the next level of aggregation.-     */-    if (level > 0) {-        igraph_destroy(aggregated_graph);-        igraph_Free(aggregated_graph);-        igraph_vector_destroy(aggregated_membership);-        igraph_Free(aggregated_membership);-        igraph_vector_destroy(aggregated_node_weights);-        igraph_Free(aggregated_node_weights);-        igraph_vector_destroy(aggregated_edge_weights);-        igraph_Free(aggregated_edge_weights);-        IGRAPH_FINALLY_CLEAN(8);-    }+    /* Free aggregated graph and associated vectors */+    igraph_vector_destroy(&aggregated_membership);+    igraph_vector_destroy(&aggregated_node_weights);+    igraph_vector_destroy(&aggregated_edge_weights);+    igraph_destroy(&aggregated_graph);+    IGRAPH_FINALLY_CLEAN(4);      /* Free remaining memory */     igraph_vector_destroy(&refined_membership);@@ -910,7 +892,7 @@      /* Calculate quality */     if (quality) {-        igraph_i_community_leiden_quality(graph, edge_weights, node_weights, membership, *nb_clusters, resolution_parameter, quality);+        IGRAPH_CHECK(igraph_i_community_leiden_quality(graph, edge_weights, node_weights, membership, *nb_clusters, resolution_parameter, quality));     }      return IGRAPH_SUCCESS;@@ -924,7 +906,7 @@  * This function implements the Leiden algorithm for finding community  * structure, see Traag, V. A., Waltman, L., &amp; van Eck, N. J. (2019). From  * Louvain to Leiden: guaranteeing well-connected communities. Scientific- * reports, 9(1), 5233.  http://dx.doi.org/10.1038/s41598-019-41695-z.+ * reports, 9(1), 5233. http://dx.doi.org/10.1038/s41598-019-41695-z  *  * </para><para>  * It is similar to the multilevel algorithm, often called the Louvain@@ -1002,7 +984,6 @@                             const igraph_real_t resolution_parameter, const igraph_real_t beta, const igraph_bool_t start,                             igraph_vector_t *membership, igraph_integer_t *nb_clusters, igraph_real_t *quality) {     igraph_vector_t *i_edge_weights, *i_node_weights;-    int ret;     igraph_integer_t n = igraph_vcount(graph);      if (start) {@@ -1036,12 +1017,12 @@         if (i_edge_weights == 0) {             IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for edge weights", IGRAPH_ENOMEM);         }+        IGRAPH_FINALLY(igraph_free, i_edge_weights);         IGRAPH_CHECK(igraph_vector_init(i_edge_weights, igraph_ecount(graph)));-        IGRAPH_FINALLY(free, i_edge_weights);         IGRAPH_FINALLY(igraph_vector_destroy, i_edge_weights);         igraph_vector_fill(i_edge_weights, 1);     } else {-        i_edge_weights = edge_weights;+        i_edge_weights = (igraph_vector_t*)edge_weights;     }      /* Check edge weights to possibly use default */@@ -1050,18 +1031,18 @@         if (i_node_weights == 0) {             IGRAPH_ERROR("Leiden algorithm failed, could not allocate memory for node weights", IGRAPH_ENOMEM);         }+        IGRAPH_FINALLY(igraph_free, i_node_weights);         IGRAPH_CHECK(igraph_vector_init(i_node_weights, n));-        IGRAPH_FINALLY(free, i_node_weights);         IGRAPH_FINALLY(igraph_vector_destroy, i_node_weights);         igraph_vector_fill(i_node_weights, 1);     } else {-        i_node_weights = node_weights;+        i_node_weights = (igraph_vector_t*)node_weights;     }      /* Perform actual Leiden algorithm */-    ret = igraph_i_community_leiden(graph, i_edge_weights, i_node_weights,-                                    resolution_parameter, beta,-                                    membership, nb_clusters, quality);+    IGRAPH_CHECK(igraph_i_community_leiden(graph, i_edge_weights, i_node_weights,+                                           resolution_parameter, beta,+                                           membership, nb_clusters, quality));      if (!edge_weights) {         igraph_vector_destroy(i_edge_weights);@@ -1075,5 +1056,5 @@         IGRAPH_FINALLY_CLEAN(2);     } -    return ret;+    return IGRAPH_SUCCESS; }
igraph/src/components.c view
@@ -32,7 +32,6 @@ #include "igraph_stack.h" #include "igraph_vector.h" #include "config.h"-#include <string.h> #include <limits.h>  static int igraph_i_clusters_weak(const igraph_t *graph, igraph_vector_t *membership,@@ -410,7 +409,7 @@     if (already_added == 0) {         IGRAPH_ERROR("is connected (weak) failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, already_added); /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, already_added);      IGRAPH_DQUEUE_INIT_FINALLY(&q, 10);     IGRAPH_VECTOR_INIT_FINALLY(&neis, 0);@@ -616,7 +615,7 @@     igraph_vector_destroy(&neis);     igraph_vector_destroy(&verts);     igraph_dqueue_destroy(&q);-    igraph_free(already_added);+    igraph_Free(already_added);     IGRAPH_FINALLY_CLEAN(5);  /* + components */      return 0;@@ -877,7 +876,7 @@  * components.  *  * </para><para>- * Somewhat arbitrarily, igraph does not consider comppnents containing+ * Somewhat arbitrarily, igraph does not consider components containing  * a single vertex only as being biconnected. Isolated vertices will  * not be part of any of the biconnected components.  *@@ -889,7 +888,7 @@  *     a spanning tree of the biconnected component is returned.  *     Note you'll have to  *     destroy each vector first by calling \ref igraph_vector_destroy()- *     and then <code>free()</code> on it, plus you need to call+ *     and then \ref igraph_free() on it, plus you need to call  *     \ref igraph_vector_ptr_destroy() on the list to regain all  *     allocated memory.  * \param component_edges If not a NULL pointer, then the edges of the@@ -1146,9 +1145,15 @@   /* igraph_bridges -- find all bridges in the graph */-/* based on https://www.geeksforgeeks.org/bridge-in-a-graph/ */+/* The algorithm is based on https://www.geeksforgeeks.org/bridge-in-a-graph/+   but instead of keeping track of the parent of each vertex in the DFS tree+   we keep track of its incoming edge. This is necessary to support multigraphs. */ -static int igraph_i_bridges_rec(const igraph_t *graph, const igraph_inclist_t *il, igraph_integer_t u, igraph_integer_t *time, igraph_vector_t *bridges, igraph_vector_bool_t *visited, igraph_vector_int_t *disc, igraph_vector_int_t *low, igraph_vector_int_t *parent) {+static int igraph_i_bridges_rec(+        const igraph_t *graph, const igraph_inclist_t *il, igraph_integer_t u,+        igraph_integer_t *time, igraph_vector_t *bridges, igraph_vector_bool_t *visited,+        igraph_vector_int_t *disc, igraph_vector_int_t *low, igraph_vector_int_t *incoming_edge)+{     igraph_vector_int_t *incedges;     long nc; /* neighbour count */     long i;@@ -1167,15 +1172,15 @@         igraph_integer_t v = IGRAPH_TO(graph, edge) == u ? IGRAPH_FROM(graph, edge) : IGRAPH_TO(graph, edge);          if (! VECTOR(*visited)[v]) {-            VECTOR(*parent)[v] = u;-            IGRAPH_CHECK(igraph_i_bridges_rec(graph, il, v, time, bridges, visited, disc, low, parent));+            VECTOR(*incoming_edge)[v] = edge;+            IGRAPH_CHECK(igraph_i_bridges_rec(graph, il, v, time, bridges, visited, disc, low, incoming_edge));              VECTOR(*low)[u] = VECTOR(*low)[u] < VECTOR(*low)[v] ? VECTOR(*low)[u] : VECTOR(*low)[v];              if (VECTOR(*low)[v] > VECTOR(*disc)[u]) {                 IGRAPH_CHECK(igraph_vector_push_back(bridges, edge));             }-        } else if (v != VECTOR(*parent)[u]) {+        } else if (edge != VECTOR(*incoming_edge)[u]) {             VECTOR(*low)[u] = VECTOR(*low)[u] < VECTOR(*disc)[v] ? VECTOR(*low)[u] : VECTOR(*disc)[v];         }     }@@ -1204,7 +1209,7 @@     igraph_inclist_t il;     igraph_vector_bool_t visited;     igraph_vector_int_t disc, low;-    igraph_vector_int_t parent;+    igraph_vector_int_t incoming_edge;     long n;     long i;     igraph_integer_t time;@@ -1223,10 +1228,10 @@     IGRAPH_CHECK(igraph_vector_int_init(&low, n));     IGRAPH_FINALLY(igraph_vector_int_destroy, &low); -    IGRAPH_CHECK(igraph_vector_int_init(&parent, n));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &parent);+    IGRAPH_CHECK(igraph_vector_int_init(&incoming_edge, n));+    IGRAPH_FINALLY(igraph_vector_int_destroy, &incoming_edge);     for (i = 0; i < n; ++i) {-        VECTOR(parent)[i] = -1;+        VECTOR(incoming_edge)[i] = -1;     }      igraph_vector_clear(bridges);@@ -1234,10 +1239,10 @@     time = 0;     for (i = 0; i < n; ++i)         if (! VECTOR(visited)[i]) {-            IGRAPH_CHECK(igraph_i_bridges_rec(graph, &il, i, &time, bridges, &visited, &disc, &low, &parent));+            IGRAPH_CHECK(igraph_i_bridges_rec(graph, &il, i, &time, bridges, &visited, &disc, &low, &incoming_edge));         } -    igraph_vector_int_destroy(&parent);+    igraph_vector_int_destroy(&incoming_edge);     igraph_vector_int_destroy(&low);     igraph_vector_int_destroy(&disc);     igraph_vector_bool_destroy(&visited);
igraph/src/conversion.c view
@@ -37,8 +37,8 @@  * \brief Returns the adjacency matrix of a graph  *  * </para><para>- * The result is an incidence matrix, it contains numbers greater- * than one if there are multiple edges in the graph.+ * The result is an adjacency matrix. Entry i, j of the matrix+ * contains the number of edges connecting vertex i to vertex j.  * \param graph Pointer to the graph to convert  * \param res Pointer to an initialized matrix object, it will be  *        resized if needed.@@ -172,8 +172,8 @@  * \brief Returns the adjacency matrix of a graph in sparse matrix format  *  * </para><para>- * The result is an incidence matrix, it contains numbers greater- * than one if there are multiple edges in the graph.+ * The result is an adjacency matrix. Entry i, j of the matrix+ * contains the number of edges connecting vertex i to vertex j.  * \param graph Pointer to the graph to convert  * \param res Pointer to an initialized sparse matrix object, it will be  *        resized if needed.@@ -782,8 +782,6 @@      return 0; }-int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat,-                                 igraph_bool_t column_wise);   int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat,
igraph/src/defs.cc view
@@ -1,5 +1,6 @@ #include <cstdlib> #include <cstdio>+#include <stdexcept> #include "defs.hh"  /*@@ -23,20 +24,17 @@  namespace bliss { -#ifndef USING_R- void fatal_error(const char* fmt, ...) {+  char buffer[1024];   va_list ap;   va_start(ap, fmt);-  fprintf(stderr,"Bliss fatal error: ");-  vfprintf(stderr, fmt, ap);-  fprintf(stderr, "\nAborting!\n");+  sprintf(buffer, "Bliss fatal error: ");+  vsprintf(buffer, fmt, ap);+  throw std::runtime_error(buffer);   va_end(ap);   exit(1); }--#endif  }
igraph/src/degree_sequence.cpp view
@@ -1,6 +1,6 @@ /*   Constructing realizations of degree sequences and bi-degree sequences.-  Copyright (C) 2018 Szabolcs Horvat <szhorvat@gmail.com>+  Copyright (C) 2018-2020 Szabolcs Horvat <szhorvat@gmail.com>    This program is free software; you can redistribute it and/or modify   it under the terms of the GNU General Public License as published by@@ -82,10 +82,6 @@         vd_pair vd = vertices.back();         vertices.pop_back(); -        if (vd.degree < 0) {-            IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL);-        }-         if (vd.degree == 0) {             continue;         }@@ -148,10 +144,6 @@         vd_pair vd = **pt;         vertices.erase(*pt); -        if (vd.degree < 0) {-            IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL);-        }-         if (vd.degree == 0) {             continue;         }@@ -226,12 +218,8 @@         }  -        if (vdp->degree.first < 0 || vdp->degree.second < 0) {-            IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL);-        }-         // are there a sufficient number of other vertices to connect to?-        if (vertices.size() < vdp->degree.second - 1) {+        if (vertices.size() - 1 < vdp->degree.second) {             goto fail;         } @@ -294,10 +282,6 @@             continue;         } -        if (vd.degree.first < 0 || vd.degree.second < 0) {-            IGRAPH_ERROR("Vertex degrees must be positive", IGRAPH_EINVAL);-        }-         int k = 0;         vlist::iterator it;         for (it = vertices.begin();@@ -342,6 +326,10 @@         IGRAPH_ERROR("The sum of degrees must be even for an undirected graph", IGRAPH_EINVAL);     } +    if (igraph_vector_min(deg) < 0) {+        IGRAPH_ERROR("Vertex degrees must be non-negative", IGRAPH_EINVAL);+    }+     igraph_vector_t edges;     IGRAPH_CHECK(igraph_vector_init(&edges, deg_sum));     IGRAPH_FINALLY(igraph_vector_destroy, &edges);@@ -384,6 +372,10 @@         IGRAPH_ERROR("In- and out-degree sequences do not sum to the same value", IGRAPH_EINVAL);     } +    if (igraph_vector_min(outdeg) < 0 || igraph_vector_min(indeg) < 0) {+        IGRAPH_ERROR("Vertex degrees must be non-negative", IGRAPH_EINVAL);+    }+     igraph_vector_t edges;     IGRAPH_CHECK(igraph_vector_init(&edges, 2 * edge_count));     IGRAPH_FINALLY(igraph_vector_destroy, &edges);@@ -426,6 +418,32 @@  *  * The \c method parameter controls the order in which the vertices to be connected are chosen.  *+ * </para><para>+ * References:+ *+ * </para><para>+ * V. Havel,+ * Poznámka o existenci konečných grafů (A remark on the existence of finite graphs),+ * Časopis pro pěstování matematiky 80, 477-480 (1955).+ * http://eudml.org/doc/19050+ *+ * </para><para>+ * S. L. Hakimi,+ * On Realizability of a Set of Integers as Degrees of the Vertices of a Linear Graph,+ * Journal of the SIAM 10, 3 (1962).+ * https://www.jstor.org/stable/2098746+ *+ * </para><para>+ * D. J. Kleitman and D. L. Wang,+ * Algorithms for Constructing Graphs and Digraphs with Given Valences and Factors,+ * Discrete Mathematics 6, 1 (1973).+ * https://doi.org/10.1016/0012-365X%2873%2990037-X+ *+ * </para><para>+ * Sz. Horvát and C. D. Modes,+ * Connectivity matters: Construction and exact random sampling of connected graphs (2020).+ * https://arxiv.org/abs/2009.03747+ *  * \param graph Pointer to an uninitialized graph object.  * \param outdeg The degree sequence for a simple undirected graph  *        (if \p indeg is NULL or of length zero), or the out-degree sequence of@@ -438,8 +456,8 @@  *          The vertex with smallest remaining degree is selected first. The result is usually  *          a graph with high negative degree assortativity. In the undirected case, this method  *          is guaranteed to generate a connected graph, provided that a connected realization exists.- *          See http://szhorvat.net/pelican/hh-connected-graphs.html for a proof.- *          In the directed case it tends to generate weakly connected graphs, but this is not+ *          See Horvát and Modes (2020) as well as http://szhorvat.net/pelican/hh-connected-graphs.html + *          for a proof. In the directed case it tends to generate weakly connected graphs, but this is not  *          guaranteed.  *          \cli IGRAPH_REALIZE_DEGSEQ_LARGEST  *          The vertex with the largest remaining degree is selected first. The result
igraph/src/distances.c view
@@ -22,6 +22,7 @@  */ +#include "igraph_paths.h" #include "igraph_datatype.h" #include "igraph_dqueue.h" #include "igraph_iterators.h"@@ -30,11 +31,11 @@ #include "igraph_interface.h" #include "igraph_adjlist.h" -int igraph_i_eccentricity(const igraph_t *graph,-                          igraph_vector_t *res,-                          igraph_vs_t vids,-                          igraph_neimode_t mode,-                          const igraph_adjlist_t *adjlist) {+static int igraph_i_eccentricity(const igraph_t *graph,+                                 igraph_vector_t *res,+                                 igraph_vs_t vids,+                                 igraph_neimode_t mode,+                                 const igraph_adjlist_t *adjlist) {      int no_of_nodes = igraph_vcount(graph);     igraph_dqueue_long_t q;
igraph/src/dotproduct.c view
@@ -24,7 +24,7 @@ #include "igraph_games.h" #include "igraph_random.h" #include "igraph_constructors.h"-#include "igraph_lapack.h"+#include "igraph_blas.h"  /**  * \function igraph_dot_product_game@@ -80,7 +80,7 @@                 continue;             }             igraph_vector_view(&v2, &MATRIX(*vecs, 0, j), nrow);-            igraph_lapack_ddot(&v1, &v2, &prob);+            igraph_blas_ddot(&v1, &v2, &prob);             if (prob < 0 && ! warned_neg) {                 warned_neg = 1;                 IGRAPH_WARNING("Negative connection probability in "
igraph/src/drl_graph.cpp view
@@ -32,13 +32,10 @@  */ // This file contains the member definitions of the master class -#include <iostream>-#include <fstream>+ #include <map> #include <vector>-#include <cstdlib> #include <cmath>-#include <cstring>  using namespace std; 
igraph/src/drl_graph_3d.cpp view
@@ -32,13 +32,9 @@  */ // This file contains the member definitions of the master class -#include <iostream>-#include <fstream> #include <map> #include <vector>-#include <cstdlib> #include <cmath>-#include <cstring>  using namespace std; 
igraph/src/drl_layout.cpp view
@@ -45,12 +45,7 @@ // 5/6/2005  // C++ library routines-#include <iostream>-#include <fstream> #include <map>-#include <set>-#include <string>-#include <deque> #include <vector>  using namespace std;@@ -70,6 +65,8 @@ #include "igraph_random.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h"+ namespace drl {  // int main(int argc, char **argv) {@@ -460,17 +457,19 @@                       const igraph_vector_t *weights,                       const igraph_vector_bool_t *fixed) { -    RNG_BEGIN();+    IGRAPH_HANDLE_EXCEPTIONS(+        RNG_BEGIN(); -    drl::graph neighbors(graph, options, weights);-    neighbors.init_parms(options);-    if (use_seed) {-        IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 2));-        neighbors.read_real(res, fixed);-    }-    neighbors.draw_graph(res);+        drl::graph neighbors(graph, options, weights);+        neighbors.init_parms(options);+        if (use_seed) {+            IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 2));+            neighbors.read_real(res, fixed);+        }+        neighbors.draw_graph(res); -    RNG_END();+        RNG_END();+    );      return 0; }
igraph/src/drl_layout_3d.cpp view
@@ -45,12 +45,7 @@ // 5/6/2005  // C++ library routines-#include <iostream>-#include <fstream> #include <map>-#include <set>-#include <string>-#include <deque> #include <vector>  using namespace std;@@ -70,6 +65,8 @@ #include "igraph_random.h" #include "igraph_interface.h" +#include "igraph_handle_exceptions.h"+ /**  * \function igraph_layout_drl_3d  * The DrL layout generator, 3d version.@@ -106,18 +103,19 @@                          igraph_layout_drl_options_t *options,                          const igraph_vector_t *weights,                          const igraph_vector_bool_t *fixed) {--    RNG_BEGIN();+    IGRAPH_HANDLE_EXCEPTIONS(+        RNG_BEGIN(); -    drl3d::graph neighbors(graph, options, weights);-    neighbors.init_parms(options);-    if (use_seed) {-        IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 3));-        neighbors.read_real(res, fixed);-    }-    neighbors.draw_graph(res);+        drl3d::graph neighbors(graph, options, weights);+        neighbors.init_parms(options);+        if (use_seed) {+            IGRAPH_CHECK(igraph_matrix_resize(res, igraph_vcount(graph), 3));+            neighbors.read_real(res, fixed);+        }+        neighbors.draw_graph(res); -    RNG_END();+        RNG_END();+    );      return 0; }
igraph/src/drl_parse.cpp view
@@ -32,14 +32,6 @@  */ // This file contains the methods for the parse.h class -#include <string>-#include <iostream>-#include <map>-#include <cstdlib>-#include <cstdio>--using namespace std;- #include "drl_layout.h" #include "drl_parse.h" 
igraph/src/eigen.c view
@@ -30,7 +30,7 @@ #include <math.h> #include <float.h> -int igraph_i_eigen_arpackfun_to_mat(igraph_arpack_function_t *fun,+static int igraph_i_eigen_arpackfun_to_mat(igraph_arpack_function_t *fun,                                     int n, void *extra,                                     igraph_matrix_t *res) { @@ -55,7 +55,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_lm(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_lm(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -133,7 +133,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sm(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_sm(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -209,7 +209,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_la(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_la(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -226,7 +226,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sa(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_sa(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -242,7 +242,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_be(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_be(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -321,7 +321,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_all(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_all(const igraph_matrix_t *A,         igraph_vector_t *values,         igraph_matrix_t *vectors) { @@ -334,7 +334,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_iv(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_iv(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -349,7 +349,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack_sel(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack_sel(const igraph_matrix_t *A,         const igraph_eigen_which_t *which,         igraph_vector_t *values,         igraph_matrix_t *vectors) {@@ -363,7 +363,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_lapack(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_lapack(const igraph_matrix_t *A,         const igraph_sparsemat_t *sA,         igraph_arpack_function_t *fun,         int n, void *extra,@@ -444,7 +444,7 @@     const igraph_sparsemat_t *sA; } igraph_i_eigen_matrix_sym_arpack_data_t; -int igraph_i_eigen_matrix_sym_arpack_cb(igraph_real_t *to,+static int igraph_i_eigen_matrix_sym_arpack_cb(igraph_real_t *to,                                         const igraph_real_t *from,                                         int n, void *extra) { @@ -457,14 +457,14 @@     } else { /* data->sA */         igraph_vector_t vto, vfrom;         igraph_vector_view(&vto, to, n);-        igraph_vector_view(&vfrom, to, n);+        igraph_vector_view(&vfrom, from, n);         igraph_vector_null(&vto);         igraph_sparsemat_gaxpy(data->sA, &vfrom, &vto);     }     return 0; } -int igraph_i_eigen_matrix_symmetric_arpack_be(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_arpack_be(const igraph_matrix_t *A,         const igraph_sparsemat_t *sA,         igraph_arpack_function_t *fun,         int n, void *extra,@@ -535,7 +535,7 @@     return 0; } -int igraph_i_eigen_matrix_symmetric_arpack(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_symmetric_arpack(const igraph_matrix_t *A,         const igraph_sparsemat_t *sA,         igraph_arpack_function_t *fun,         int n, void *extra,@@ -637,7 +637,7 @@    3 Larger real part    4 Larger imaginary part */ -int igraph_i_eigen_matrix_lapack_cmp_lm(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_lm(void *extra, const void *a,                                         const void *b) {     igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;     int *aa = (int*) a, *bb = (int*) b;@@ -682,7 +682,7 @@    4 Smaller imaginary part    This ensures that lm has exactly the opposite order to sm */ -int igraph_i_eigen_matrix_lapack_cmp_sm(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_sm(void *extra, const void *a,                                         const void *b) {     igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;     int *aa = (int*) a, *bb = (int*) b;@@ -725,7 +725,7 @@    2 Real eigenvalues come before complex ones    3 Larger complex part */ -int igraph_i_eigen_matrix_lapack_cmp_lr(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_lr(void *extra, const void *a,                                         const void *b) {      igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;@@ -764,7 +764,7 @@    This is opposite to LR */ -int igraph_i_eigen_matrix_lapack_cmp_sr(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_sr(void *extra, const void *a,                                         const void *b) {      igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;@@ -801,7 +801,7 @@    2 Real eigenvalues before complex ones    3 Larger real part */ -int igraph_i_eigen_matrix_lapack_cmp_li(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_li(void *extra, const void *a,                                         const void *b) {      igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;@@ -839,7 +839,7 @@    3 Smaller real part    Order is opposite to LI */ -int igraph_i_eigen_matrix_lapack_cmp_si(void *extra, const void *a,+static int igraph_i_eigen_matrix_lapack_cmp_si(void *extra, const void *a,                                         const void *b) {      igraph_i_eml_cmp_t *myextra = (igraph_i_eml_cmp_t *) extra;@@ -888,7 +888,7 @@         }                                   \     } while (0) -int igraph_i_eigen_matrix_lapack_reorder(const igraph_vector_t *real,+static int igraph_i_eigen_matrix_lapack_reorder(const igraph_vector_t *real,         const igraph_vector_t *imag,         const igraph_matrix_t *compressed,         const igraph_eigen_which_t *which,@@ -1006,7 +1006,7 @@     return 0; } -int igraph_i_eigen_matrix_lapack_common(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_common(const igraph_matrix_t *A,                                         const igraph_eigen_which_t *which,                                         igraph_vector_complex_t *values,                                         igraph_matrix_complex_t *vectors) {@@ -1042,21 +1042,21 @@  } -int igraph_i_eigen_matrix_lapack_lm(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_lm(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_sm(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_sm(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_lr(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_lr(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {@@ -1064,42 +1064,42 @@ }  -int igraph_i_eigen_matrix_lapack_sr(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_sr(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_li(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_li(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_si(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_si(const igraph_matrix_t *A,                                     const igraph_eigen_which_t *which,                                     igraph_vector_complex_t *values,                                     igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_select(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_select(const igraph_matrix_t *A,                                         const igraph_eigen_which_t *which,                                         igraph_vector_complex_t *values,                                         igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack_all(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack_all(const igraph_matrix_t *A,                                      const igraph_eigen_which_t *which,                                      igraph_vector_complex_t *values,                                      igraph_matrix_complex_t *vectors) {     return igraph_i_eigen_matrix_lapack_common(A, which, values, vectors); } -int igraph_i_eigen_matrix_lapack(const igraph_matrix_t *A,+static int igraph_i_eigen_matrix_lapack(const igraph_matrix_t *A,                                  const igraph_sparsemat_t *sA,                                  igraph_arpack_function_t *fun,                                  int n, void *extra,@@ -1172,7 +1172,7 @@     return 0; } -int igraph_i_eigen_checks(const igraph_matrix_t *A,+static int igraph_i_eigen_checks(const igraph_matrix_t *A,                           const igraph_sparsemat_t *sA,                           igraph_arpack_function_t *fun, int n) { @@ -1322,7 +1322,7 @@     return 0; } -int igraph_i_eigen_adjacency_arpack_sym_cb(igraph_real_t *to,+static int igraph_i_eigen_adjacency_arpack_sym_cb(igraph_real_t *to,         const igraph_real_t *from,         int n, void *extra) {     igraph_adjlist_t *adjlist = (igraph_adjlist_t *) extra;@@ -1342,7 +1342,7 @@     return 0; } -int igraph_i_eigen_adjacency_arpack(const igraph_t *graph,+static int igraph_i_eigen_adjacency_arpack(const igraph_t *graph,                                     const igraph_eigen_which_t *which,                                     igraph_arpack_options_t *options,                                     igraph_arpack_storage_t* storage,
igraph/src/embedding.c view
@@ -24,7 +24,6 @@ #include "igraph_embedding.h" #include "igraph_interface.h" #include "igraph_adjlist.h"-#include "igraph_random.h" #include "igraph_centrality.h" #include "igraph_blas.h" @@ -40,7 +39,7 @@  /* Adjacency matrix, unweighted, undirected.    Eigendecomposition is used */-int igraph_i_asembeddingu(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembeddingu(igraph_real_t *to, const igraph_real_t *from,                           int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_adjlist_t *outlist = data->outlist;@@ -65,7 +64,7 @@  /* Adjacency matrix, weighted, undirected.    Eigendecomposition is used. */-int igraph_i_asembeddinguw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembeddinguw(igraph_real_t *to, const igraph_real_t *from,                            int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_inclist_t *outlist = data->eoutlist;@@ -93,7 +92,7 @@ }  /* Adjacency matrix, unweighted, directed. SVD. */-int igraph_i_asembedding(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembedding(igraph_real_t *to, const igraph_real_t *from,                          int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_adjlist_t *outlist = data->outlist;@@ -131,7 +130,7 @@ }  /* Adjacency matrix, unweighted, directed. SVD, right eigenvectors */-int igraph_i_asembedding_right(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembedding_right(igraph_real_t *to, const igraph_real_t *from,                                int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_adjlist_t *inlist = data->inlist;@@ -155,7 +154,7 @@ }  /* Adjacency matrix, weighted, directed. SVD. */-int igraph_i_asembeddingw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembeddingw(igraph_real_t *to, const igraph_real_t *from,                           int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_inclist_t *outlist = data->eoutlist;@@ -199,7 +198,7 @@ }  /* Adjacency matrix, weighted, directed. SVD, right eigenvectors. */-int igraph_i_asembeddingw_right(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_asembeddingw_right(igraph_real_t *to, const igraph_real_t *from,                                 int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_inclist_t *inlist = data->einlist;@@ -227,7 +226,7 @@ }  /* Laplacian D-A, unweighted, undirected. Eigendecomposition. */-int igraph_i_lsembedding_da(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_da(igraph_real_t *to, const igraph_real_t *from,                             int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_adjlist_t *outlist = data->outlist;@@ -251,7 +250,7 @@ }  /* Laplacian D-A, weighted, undirected. Eigendecomposition. */-int igraph_i_lsembedding_daw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_daw(igraph_real_t *to, const igraph_real_t *from,                              int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;     igraph_inclist_t *outlist = data->eoutlist;@@ -279,7 +278,7 @@ }  /* Laplacian DAD, unweighted, undirected. Eigendecomposition. */-int igraph_i_lsembedding_dad(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_dad(igraph_real_t *to, const igraph_real_t *from,                              int n, void *extra) {      igraph_i_asembedding_data_t *data = extra;@@ -313,7 +312,7 @@     return 0; } -int igraph_i_lsembedding_dadw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_dadw(igraph_real_t *to, const igraph_real_t *from,                               int n, void *extra) {      igraph_i_asembedding_data_t *data = extra;@@ -370,7 +369,7 @@ }  /* Laplacian I-DAD, unweighted, undirected. Eigendecomposition. */-int igraph_i_lsembedding_idad(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_idad(igraph_real_t *to, const igraph_real_t *from,                               int n, void *extra) {      int i;@@ -383,7 +382,7 @@     return 0; } -int igraph_i_lsembedding_idadw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lsembedding_idadw(igraph_real_t *to, const igraph_real_t *from,                                int n, void *extra) {     int i; @@ -396,7 +395,7 @@ }  /* Laplacian OAP, unweighted, directed. SVD. */-int igraph_i_lseembedding_oap(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lseembedding_oap(igraph_real_t *to, const igraph_real_t *from,                               int n, void *extra) {      igraph_i_asembedding_data_t *data = extra;@@ -454,7 +453,7 @@ }  /* Laplacian OAP, unweighted, directed. SVD, right eigenvectors. */-int igraph_i_lseembedding_oap_right(igraph_real_t *to,+static int igraph_i_lseembedding_oap_right(igraph_real_t *to,                                     const igraph_real_t *from,                                     int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;@@ -490,7 +489,7 @@ }  /* Laplacian OAP, weighted, directed. SVD. */-int igraph_i_lseembedding_oapw(igraph_real_t *to, const igraph_real_t *from,+static int igraph_i_lseembedding_oapw(igraph_real_t *to, const igraph_real_t *from,                                int n, void *extra) {      igraph_i_asembedding_data_t *data = extra;@@ -554,7 +553,7 @@ }  /* Laplacian OAP, weighted, directed. SVD, right eigenvectors. */-int igraph_i_lseembedding_oapw_right(igraph_real_t *to,+static int igraph_i_lseembedding_oapw_right(igraph_real_t *to,                                      const igraph_real_t *from,                                      int n, void *extra) {     igraph_i_asembedding_data_t *data = extra;@@ -593,7 +592,7 @@     return 0; } -int igraph_i_spectral_embedding(const igraph_t *graph,+static int igraph_i_spectral_embedding(const igraph_t *graph,                                 igraph_integer_t no,                                 const igraph_vector_t *weights,                                 igraph_eigen_which_position_t which,@@ -785,29 +784,29 @@  * Adjacency spectral embedding  *  * Spectral decomposition of the adjacency matrices of graphs.- * This function computes a \code{no}-dimensional Euclidean+ * This function computes an <code>n</code>-dimensional Euclidean  * representation of the graph based on its adjacency  * matrix, A. This representation is computed via the singular value- * decomposition of the adjacency matrix, A=UDV^T. In the case,+ * decomposition of the adjacency matrix, A=U D V^T. In the case,  * where the graph is a random dot product graph generated using latent- * position vectors in R^no for each vertex, the embedding will+ * position vectors in R^n for each vertex, the embedding will  * provide an estimate of these latent vectors.  *  * </para><para>- * For undirected graphs the latent positions are calculated as- * X=U^no D^(1/2) where U^no equals to the first no columns of U, and+ * For undirected graphs, the latent positions are calculated as+ * X = U^n D^(1/2) where U^n equals to the first no columns of U, and  * D^(1/2) is a diagonal matrix containing the square root of the selected  * singular values on the diagonal.  *  * </para><para>- * For directed graphs the embedding is defined as the pair- * X=U^no D^(1/2), Y=V^no D^(1/2). (For undirected graphs U=V,- * so it is enough to keep one of them.)+ * For directed graphs, the embedding is defined as the pair+ * X = U^n D^(1/2), Y = V^n D^(1/2).+ * (For undirected graphs U=V, so it is sufficient to keep one of them.)  *  * \param graph The input graph, can be directed or undirected.- * \param no An integer scalar. This value is the embedding dimension of+ * \param n An integer scalar. This value is the embedding dimension of  *        the spectral embedding. Should be smaller than the number of- *        vertices. The largest no-dimensional non-zero+ *        vertices. The largest n-dimensional non-zero  *        singular values are used for the spectral embedding.  * \param weights Optional edge weights. Supply a null pointer for  *        unweighted graphs.@@ -824,7 +823,7 @@  *        For directed graphs, <code>IGRAPH_EIGEN_LM</code> and  *        <code>IGRAPH_EIGEN_LA</code> are the same because singular  *        values are used for the ordering instead of eigenvalues.- * \param scaled Whether to return X and Y (if scaled is non-zero), or+ * \param scaled Whether to return X and Y (if \c scaled is true), or  *        U and V.  * \param X Initialized matrix, the estimated latent positions are  *        stored here.@@ -847,7 +846,7 @@  */  int igraph_adjacency_spectral_embedding(const igraph_t *graph,-                                        igraph_integer_t no,+                                        igraph_integer_t n,                                         const igraph_vector_t *weights,                                         igraph_eigen_which_position_t which,                                         igraph_bool_t scaled,@@ -869,14 +868,14 @@         callback_right = 0;     } -    return igraph_i_spectral_embedding(graph, no, weights, which, scaled,+    return igraph_i_spectral_embedding(graph, n, weights, which, scaled,                                        X, Y, D, cvec, /* deg2=*/ 0,                                        options, callback, callback_right,                                        /*symmetric=*/ !directed,                                        /*eigen=*/ !directed, /*zapsmall=*/ 1); } -int igraph_i_lse_und(const igraph_t *graph,+static int igraph_i_lse_und(const igraph_t *graph,                      igraph_integer_t no,                      const igraph_vector_t *weights,                      igraph_eigen_which_position_t which,@@ -937,7 +936,7 @@     return 0; } -int igraph_i_lse_dir(const igraph_t *graph,+static int igraph_i_lse_dir(const igraph_t *graph,                      igraph_integer_t no,                      const igraph_vector_t *weights,                      igraph_eigen_which_position_t which,@@ -994,7 +993,7 @@  * \ref igraph_adjacency_spectral_embedding, but works on the Laplacian  * of the graph, instead of the adjacency matrix.  * \param graph The input graph.- * \param no The number of eigenvectors (or singular vectors if the graph+ * \param n The number of eigenvectors (or singular vectors if the graph  *        is directed) to use for the embedding.  * \param weights Optional edge weights. Supply a null pointer for  *        unweighted graphs.@@ -1025,7 +1024,7 @@  *          means I - Di A Di, where I  *          is the identity matrix.  *        \endclist- * \param scaled Whether to return X and Y (if scaled is non-zero), or+ * \param scaled Whether to return X and Y (if \c scaled is true), or  *        U and V.  * \param X Initialized matrix, the estimated latent positions are  *        stored here.@@ -1047,7 +1046,7 @@  */  int igraph_laplacian_spectral_embedding(const igraph_t *graph,-                                        igraph_integer_t no,+                                        igraph_integer_t n,                                         const igraph_vector_t *weights,                                         igraph_eigen_which_position_t which,                                         igraph_neimode_t degmode,@@ -1059,10 +1058,10 @@                                         igraph_arpack_options_t *options) {      if (igraph_is_directed(graph)) {-        return igraph_i_lse_dir(graph, no, weights, which, degmode, type, scaled,+        return igraph_i_lse_dir(graph, n, weights, which, degmode, type, scaled,                                 X, Y, D, options);     } else {-        return igraph_i_lse_und(graph, no, weights, which, degmode, type, scaled,+        return igraph_i_lse_und(graph, n, weights, which, degmode, type, scaled,                                 X, Y, D, options);     } }@@ -1090,7 +1089,7 @@  * </para><para>  * This function can also be used for the general separation problem,  * where we assume that the left and the right of the vector are coming- * from two Normal distributions, with different means, and we want+ * from two normal distributions, with different means, and we want  * to know their border.  *  * \param sv A numeric vector, the ordered singular values.
igraph/src/error.c view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -20,6 +20,7 @@ #include <stdio.h> #include <stdlib.h> #include "error.h"+#include "platform.h"  static char *plfit_i_error_strings[] = {     "No error",@@ -69,6 +70,6 @@ } #endif -void plfit_error_handler_ignore(const char *reason, const char *file, int line,-        int plfit_errno) {+void plfit_error_handler_ignore(const char* reason, const char* file, int line,+		int plfit_errno) { }
igraph/src/fast_community.c view
@@ -109,8 +109,8 @@ /* Scans the community neighborhood list for the new maximal dq value.  * Returns 1 if the maximum is different from the previous one,  * 0 otherwise. */-int igraph_i_fastgreedy_community_rescan_max(-    igraph_i_fastgreedy_community* comm) {+static int igraph_i_fastgreedy_community_rescan_max(+        igraph_i_fastgreedy_community* comm) {     long int i, n;     igraph_i_fastgreedy_commpair *p, *best;     igraph_real_t bestdq, currdq;@@ -141,24 +141,24 @@ }  /* Destroys the global community list object */-void igraph_i_fastgreedy_community_list_destroy(-    igraph_i_fastgreedy_community_list* list) {+static void igraph_i_fastgreedy_community_list_destroy(+        igraph_i_fastgreedy_community_list* list) {     long int i;     for (i = 0; i < list->n; i++) {         igraph_vector_ptr_destroy(&list->e[i].neis);     }-    free(list->e);+    igraph_Free(list->e);     if (list->heapindex != 0) {-        free(list->heapindex);+        igraph_Free(list->heapindex);     }     if (list->heap != 0) {-        free(list->heap);+        igraph_Free(list->heap);     } }  /* Community list heap maintenance: sift down */-void igraph_i_fastgreedy_community_list_sift_down(-    igraph_i_fastgreedy_community_list* list, long int idx) {+static void igraph_i_fastgreedy_community_list_sift_down(+        igraph_i_fastgreedy_community_list* list, long int idx) {     long int root, child, c1, c2;     igraph_i_fastgreedy_community* dummy;     igraph_integer_t dummy2;@@ -192,8 +192,8 @@ }  /* Community list heap maintenance: sift up */-void igraph_i_fastgreedy_community_list_sift_up(-    igraph_i_fastgreedy_community_list* list, long int idx) {+static void igraph_i_fastgreedy_community_list_sift_up(+        igraph_i_fastgreedy_community_list* list, long int idx) {     long int root, parent, c1, c2;     igraph_i_fastgreedy_community* dummy;     igraph_integer_t dummy2;@@ -223,8 +223,8 @@ }  /* Builds the community heap for the first time */-void igraph_i_fastgreedy_community_list_build_heap(-    igraph_i_fastgreedy_community_list* list) {+static void igraph_i_fastgreedy_community_list_build_heap(+        igraph_i_fastgreedy_community_list* list) {     long int i;     for (i = list->no_of_communities / 2 - 1; i >= 0; i--) {         igraph_i_fastgreedy_community_list_sift_down(list, i);@@ -236,8 +236,8 @@ #define igraph_i_fastgreedy_community_list_find_in_heap(list, idx) (list)->heapindex[idx]  /* Dumps the heap - for debugging purposes */-void igraph_i_fastgreedy_community_list_dump_heap(-    igraph_i_fastgreedy_community_list* list) {+static void igraph_i_fastgreedy_community_list_dump_heap(+        igraph_i_fastgreedy_community_list* list) {     long int i;     debug("Heap:\n");     for (i = 0; i < list->no_of_communities; i++) {@@ -258,8 +258,8 @@  /* Checks if the community heap satisfies the heap property.  * Only useful for debugging. */-void igraph_i_fastgreedy_community_list_check_heap(-    igraph_i_fastgreedy_community_list* list) {+static void igraph_i_fastgreedy_community_list_check_heap(+        igraph_i_fastgreedy_community_list* list) {     long int i;     for (i = 0; i < list->no_of_communities / 2; i++) {         if ((2 * i + 1 < list->no_of_communities && *list->heap[i]->maxdq->dq < *list->heap[2 * i + 1]->maxdq->dq) ||@@ -272,8 +272,8 @@ }  /* Removes a given element from the heap */-void igraph_i_fastgreedy_community_list_remove(-    igraph_i_fastgreedy_community_list* list, long int idx) {+static void igraph_i_fastgreedy_community_list_remove(+        igraph_i_fastgreedy_community_list* list, long int idx) {     igraph_real_t old;     long int commidx; @@ -298,8 +298,8 @@  /* Removes a given element from the heap when there are no more neighbors  * for it (comm->maxdq is NULL) */-void igraph_i_fastgreedy_community_list_remove2(-    igraph_i_fastgreedy_community_list* list, long int idx, long int comm) {+static void igraph_i_fastgreedy_community_list_remove2(+        igraph_i_fastgreedy_community_list* list, long int idx, long int comm) {     long int i;      if (idx == list->no_of_communities - 1) {@@ -327,8 +327,8 @@  /* Removes the pair belonging to community k from the neighborhood list  * of community c (that is, clist[c]) and recalculates maxdq */-void igraph_i_fastgreedy_community_remove_nei(-    igraph_i_fastgreedy_community_list* list, long int c, long int k) {+static void igraph_i_fastgreedy_community_remove_nei(+        igraph_i_fastgreedy_community_list* list, long int c, long int k) {     long int i, n;     igraph_bool_t rescan = 0;     igraph_i_fastgreedy_commpair *p;@@ -371,7 +371,7 @@  /* Auxiliary function to sort a community pair list with respect to the  * `second` field */-int igraph_i_fastgreedy_commpair_cmp(const void* p1, const void* p2) {+static int igraph_i_fastgreedy_commpair_cmp(const void* p1, const void* p2) {     igraph_i_fastgreedy_commpair *cp1, *cp2;     cp1 = *(igraph_i_fastgreedy_commpair**)p1;     cp2 = *(igraph_i_fastgreedy_commpair**)p2;@@ -381,9 +381,9 @@ /* Sorts the neighbor list of the community with the given index, optionally  * optimizing the process if we know that the list is nearly sorted and only  * a given pair is in the wrong place. */-void igraph_i_fastgreedy_community_sort_neighbors_of(-    igraph_i_fastgreedy_community_list* list, long int index,-    igraph_i_fastgreedy_commpair* changed_pair) {+static void igraph_i_fastgreedy_community_sort_neighbors_of(+        igraph_i_fastgreedy_community_list* list, long int index,+        igraph_i_fastgreedy_commpair* changed_pair) {     igraph_vector_ptr_t* vec;     long int i, n;     igraph_bool_t can_skip_sort = 0;@@ -453,9 +453,9 @@  * of the community list clist to newdq and restores the heap property  * in community c if necessary. Returns 1 if the maximum in the row had  * to be updated, zero otherwise */-int igraph_i_fastgreedy_community_update_dq(-    igraph_i_fastgreedy_community_list* list,-    igraph_i_fastgreedy_commpair* p, igraph_real_t newdq) {+static int igraph_i_fastgreedy_community_update_dq(+        igraph_i_fastgreedy_community_list* list,+        igraph_i_fastgreedy_commpair* p, igraph_real_t newdq) {     long int i, j, to, from;     igraph_real_t olddq;     igraph_i_fastgreedy_community *comm_to, *comm_from;@@ -698,12 +698,12 @@     if (communities.e == 0) {         IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, communities.e);+    IGRAPH_FINALLY(igraph_free, communities.e);     communities.heap = (igraph_i_fastgreedy_community**)calloc((size_t) no_of_nodes, sizeof(igraph_i_fastgreedy_community*));     if (communities.heap == 0) {         IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, communities.heap);+    IGRAPH_FINALLY(igraph_free, communities.heap);     communities.heapindex = (igraph_integer_t*)calloc((size_t)no_of_nodes, sizeof(igraph_integer_t));     if (communities.heapindex == 0) {         IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);@@ -722,7 +722,7 @@     if (dq == 0) {         IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, dq);+    IGRAPH_FINALLY(igraph_free, dq);     debug("Creating community pair list\n");     IGRAPH_CHECK(igraph_eit_create(graph, igraph_ess_all(0), &edgeit));     IGRAPH_FINALLY(igraph_eit_destroy, &edgeit);@@ -730,7 +730,7 @@     if (pairs == 0) {         IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, pairs);+    IGRAPH_FINALLY(igraph_free, pairs);     loop_weight_sum = 0;     for (i = 0, j = 0; !IGRAPH_EIT_END(edgeit); i += 2, j++, IGRAPH_EIT_NEXT(edgeit)) {         long int eidx = IGRAPH_EIT_GET(edgeit);@@ -1022,12 +1022,12 @@         if (ivec == 0) {             IGRAPH_ERROR("can't run fast greedy community detection", IGRAPH_ENOMEM);         }-        IGRAPH_FINALLY(free, ivec);+        IGRAPH_FINALLY(igraph_free, ivec);         for (i = 0; i < no_of_joins; i++) {             ivec[i] = i + 1;         }         igraph_matrix_permdelete_rows(merges, ivec, total_joins - no_of_joins);-        free(ivec);+        igraph_Free(ivec);         IGRAPH_FINALLY_CLEAN(1);     }     IGRAPH_PROGRESS("fast greedy community detection", 100.0, 0);@@ -1038,8 +1038,8 @@     }      debug("Freeing memory\n");-    free(pairs);-    free(dq);+    igraph_Free(pairs);+    igraph_Free(dq);     igraph_i_fastgreedy_community_list_destroy(&communities);     igraph_vector_destroy(&a);     IGRAPH_FINALLY_CLEAN(4);
igraph/src/feedback_arc_set.c view
@@ -475,7 +475,7 @@         if (vptr == 0) {             IGRAPH_ERROR("cannot calculate feedback arc set using IP", IGRAPH_ENOMEM);         }-        IGRAPH_FINALLY(free, vptr);+        IGRAPH_FINALLY(igraph_free, vptr);         IGRAPH_CHECK(igraph_vector_init(vptr, 0));         IGRAPH_FINALLY_CLEAN(1);         VECTOR(vertices_by_components)[i] = vptr;@@ -487,7 +487,7 @@         if (vptr == 0) {             IGRAPH_ERROR("cannot calculate feedback arc set using IP", IGRAPH_ENOMEM);         }-        IGRAPH_FINALLY(free, vptr);+        IGRAPH_FINALLY(igraph_free, vptr);         IGRAPH_CHECK(igraph_vector_init(vptr, 0));         IGRAPH_FINALLY_CLEAN(1);         VECTOR(edges_by_components)[i] = vptr;
igraph/src/flow.c view
@@ -33,15 +33,12 @@ #include "igraph_structural.h" #include "igraph_components.h" #include "igraph_types_internal.h"-#include "config.h" #include "igraph_math.h" #include "igraph_dqueue.h"-#include "igraph_visitor.h" #include "igraph_interrupt_internal.h" #include "igraph_topology.h"+#include "config.h" -#include <limits.h>-#include <stdio.h>  /*  * Some general remarks about the functions in this file.@@ -156,16 +153,16 @@  * undirected edge.  */ -int igraph_i_maxflow_undirected(const igraph_t *graph,-                                igraph_real_t *value,-                                igraph_vector_t *flow,-                                igraph_vector_t *cut,-                                igraph_vector_t *partition,-                                igraph_vector_t *partition2,-                                igraph_integer_t source,-                                igraph_integer_t target,-                                const igraph_vector_t *capacity,-                                igraph_maxflow_stats_t *stats) {+static int igraph_i_maxflow_undirected(const igraph_t *graph,+                                       igraph_real_t *value,+                                       igraph_vector_t *flow,+                                       igraph_vector_t *cut,+                                       igraph_vector_t *partition,+                                       igraph_vector_t *partition2,+                                       igraph_integer_t source,+                                       igraph_integer_t target,+                                       const igraph_vector_t *capacity,+                                       igraph_maxflow_stats_t *stats) {     igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph);     igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph);     igraph_vector_t edges;@@ -253,10 +250,10 @@                                         &first, &current, &to, &excess,       \                                         &rescap, &rev)) -void igraph_i_mf_gap(long int b, igraph_maxflow_stats_t *stats,-                     igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets,-                     long int no_of_nodes,-                     igraph_vector_long_t *distance) {+static void igraph_i_mf_gap(long int b, igraph_maxflow_stats_t *stats,+                            igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets,+                            long int no_of_nodes,+                            igraph_vector_long_t *distance) {      long int bo;     (stats->nogap)++;@@ -269,12 +266,12 @@     } } -void igraph_i_mf_relabel(long int v, long int no_of_nodes,-                         igraph_vector_long_t *distance,-                         igraph_vector_long_t *first,-                         igraph_vector_t *rescap, igraph_vector_long_t *to,-                         igraph_vector_long_t *current,-                         igraph_maxflow_stats_t *stats, int *nrelabelsince) {+static void igraph_i_mf_relabel(long int v, long int no_of_nodes,+                                igraph_vector_long_t *distance,+                                igraph_vector_long_t *first,+                                igraph_vector_t *rescap, igraph_vector_long_t *to,+                                igraph_vector_long_t *current,+                                igraph_maxflow_stats_t *stats, int *nrelabelsince) {      long int min = no_of_nodes;     long int k, l, min_edge = 0;@@ -293,14 +290,14 @@     } } -void igraph_i_mf_push(long int v, long int e, long int n,-                      igraph_vector_long_t *current,-                      igraph_vector_t *rescap, igraph_vector_t *excess,-                      long int target, long int source,-                      igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets,-                      igraph_vector_long_t *distance,-                      igraph_vector_long_t *rev, igraph_maxflow_stats_t *stats,-                      int *npushsince) {+static void igraph_i_mf_push(long int v, long int e, long int n,+                             igraph_vector_long_t *current,+                             igraph_vector_t *rescap, igraph_vector_t *excess,+                             long int target, long int source,+                             igraph_buckets_t *buckets, igraph_dbuckets_t *ibuckets,+                             igraph_vector_long_t *distance,+                             igraph_vector_long_t *rev, igraph_maxflow_stats_t *stats,+                             int *npushsince) {     igraph_real_t delta =         RESCAP(e) < EXCESS(v) ? RESCAP(e) : EXCESS(v);     (stats->nopush)++; (*npushsince)++;@@ -314,19 +311,19 @@     EXCESS(v) -= delta; } -void igraph_i_mf_discharge(long int v,-                           igraph_vector_long_t *current,-                           igraph_vector_long_t *first,-                           igraph_vector_t *rescap,-                           igraph_vector_long_t *to,-                           igraph_vector_long_t *distance,-                           igraph_vector_t *excess,-                           long int no_of_nodes, long int source,-                           long int target, igraph_buckets_t *buckets,-                           igraph_dbuckets_t *ibuckets,-                           igraph_vector_long_t *rev,-                           igraph_maxflow_stats_t *stats,-                           int *npushsince, int *nrelabelsince) {+static void igraph_i_mf_discharge(long int v,+                                  igraph_vector_long_t *current,+                                  igraph_vector_long_t *first,+                                  igraph_vector_t *rescap,+                                  igraph_vector_long_t *to,+                                  igraph_vector_long_t *distance,+                                  igraph_vector_t *excess,+                                  long int no_of_nodes, long int source,+                                  long int target, igraph_buckets_t *buckets,+                                  igraph_dbuckets_t *ibuckets,+                                  igraph_vector_long_t *rev,+                                  igraph_maxflow_stats_t *stats,+                                  int *npushsince, int *nrelabelsince) {     do {         long int i;         long int start = (long int) CURRENT(v);@@ -360,14 +357,14 @@     } while (1); } -void igraph_i_mf_bfs(igraph_dqueue_long_t *bfsq,-                     long int source, long int target,-                     long int no_of_nodes, igraph_buckets_t *buckets,-                     igraph_dbuckets_t *ibuckets,-                     igraph_vector_long_t *distance,-                     igraph_vector_long_t *first, igraph_vector_long_t *current,-                     igraph_vector_long_t *to, igraph_vector_t *excess,-                     igraph_vector_t *rescap, igraph_vector_long_t *rev) {+static void igraph_i_mf_bfs(igraph_dqueue_long_t *bfsq,+                            long int source, long int target,+                            long int no_of_nodes, igraph_buckets_t *buckets,+                            igraph_dbuckets_t *ibuckets,+                            igraph_vector_long_t *distance,+                            igraph_vector_long_t *first, igraph_vector_long_t *current,+                            igraph_vector_long_t *to, igraph_vector_t *excess,+                            igraph_vector_t *rescap, igraph_vector_long_t *rev) {      long int k, l; @@ -414,8 +411,8 @@  * assigning positive real numbers to the edges and satisfying two  * requirements: (1) the flow value is less than the capacity of the  * edge and (2) at each vertex except the source and the target, the- * incoming flow (ie. the sum of the flow on the incoming edges) is- * the same as the outgoing flow (ie. the sum of the flow on the+ * incoming flow (i.e. the sum of the flow on the incoming edges) is+ * the same as the outgoing flow (i.e. the sum of the flow on the  * outgoing edges). The value of the flow is the incoming flow at the  * target vertex. The maximum flow is the flow with the maximum  * value.@@ -745,7 +742,7 @@         IGRAPH_CHECK(igraph_vector_int_init(&added, no_of_nodes));         IGRAPH_FINALLY(igraph_vector_int_destroy, &added);         IGRAPH_CHECK(igraph_dqueue_init(&Q, 100));-        IGRAPH_FINALLY(igraph_dqueue_destroy, &added);+        IGRAPH_FINALLY(igraph_dqueue_destroy, &Q);          igraph_dqueue_push(&Q, source);         igraph_dqueue_push(&Q, 0);@@ -1031,8 +1028,8 @@  * assigning positive real numbers to the edges and satisfying two  * requirements: (1) the flow value is less than the capacity of the  * edge and (2) at each vertex except the source and the target, the- * incoming flow (ie. the sum of the flow on the incoming edges) is- * the same as the outgoing flow (ie. the sum of the flow on the+ * incoming flow (i.e. the sum of the flow on the incoming edges) is+ * the same as the outgoing flow (i.e. the sum of the flow on the  * outgoing edges). The value of the flow is the incoming flow at the  * target vertex. The maximum flow is the flow with the maximum  * value. </para>@@ -1212,12 +1209,12 @@  * It can also calculate the cut itself, not just the cut value.  */ -int igraph_i_mincut_undirected(const igraph_t *graph,-                               igraph_real_t *res,-                               igraph_vector_t *partition,-                               igraph_vector_t *partition2,-                               igraph_vector_t *cut,-                               const igraph_vector_t *capacity) {+static int igraph_i_mincut_undirected(const igraph_t *graph,+                                      igraph_real_t *res,+                                      igraph_vector_t *partition,+                                      igraph_vector_t *partition2,+                                      igraph_vector_t *cut,+                                      const igraph_vector_t *capacity) {      igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph);     igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph);@@ -1479,12 +1476,12 @@     return 0; } -int igraph_i_mincut_directed(const igraph_t *graph,-                             igraph_real_t *value,-                             igraph_vector_t *partition,-                             igraph_vector_t *partition2,-                             igraph_vector_t *cut,-                             const igraph_vector_t *capacity) {+static int igraph_i_mincut_directed(const igraph_t *graph,+                                    igraph_real_t *value,+                                    igraph_vector_t *partition,+                                    igraph_vector_t *partition2,+                                    igraph_vector_t *cut,+                                    const igraph_vector_t *capacity) {     long int i;     long int no_of_nodes = igraph_vcount(graph);     igraph_real_t flow;@@ -1665,9 +1662,9 @@ }  -int igraph_i_mincut_value_undirected(const igraph_t *graph,-                                     igraph_real_t *res,-                                     const igraph_vector_t *capacity) {+static int igraph_i_mincut_value_undirected(const igraph_t *graph,+                                            igraph_real_t *res,+                                            const igraph_vector_t *capacity) {     return igraph_i_mincut_undirected(graph, res, 0, 0, 0, capacity); } @@ -1747,11 +1744,11 @@     return 0; } -int igraph_i_st_vertex_connectivity_directed(const igraph_t *graph,-        igraph_integer_t *res,-        igraph_integer_t source,-        igraph_integer_t target,-        igraph_vconn_nei_t neighbors) {+static int igraph_i_st_vertex_connectivity_directed(const igraph_t *graph,+                                                    igraph_integer_t *res,+                                                    igraph_integer_t source,+                                                    igraph_integer_t target,+                                                    igraph_vconn_nei_t neighbors) {      igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph);     igraph_integer_t no_of_edges = (igraph_integer_t) igraph_ecount(graph);@@ -1835,11 +1832,11 @@     return 0; } -int igraph_i_st_vertex_connectivity_undirected(const igraph_t *graph,-        igraph_integer_t *res,-        igraph_integer_t source,-        igraph_integer_t target,-        igraph_vconn_nei_t neighbors) {+static int igraph_i_st_vertex_connectivity_undirected(const igraph_t *graph,+                                                      igraph_integer_t *res,+                                                      igraph_integer_t source,+                                                      igraph_integer_t target,+                                                      igraph_vconn_nei_t neighbors) {      igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph);     igraph_t newgraph;@@ -1902,7 +1899,7 @@  * target. Directed paths are considered in directed graphs.</para>  *  * <para>The vertex connectivity of a pair is the same as the number- * of different (ie. node-independent) paths from source to+ * of different (i.e. node-independent) paths from source to  * target.</para>  *  * <para>The current implementation uses maximum flow calculations to@@ -1953,8 +1950,8 @@     return 0; } -int igraph_i_vertex_connectivity_directed(const igraph_t *graph,-        igraph_integer_t *res) {+static int igraph_i_vertex_connectivity_directed(const igraph_t *graph,+                                                 igraph_integer_t *res) {      igraph_integer_t no_of_nodes = (igraph_integer_t) igraph_vcount(graph);     long int i, j;@@ -1991,8 +1988,8 @@     return 0; } -int igraph_i_vertex_connectivity_undirected(const igraph_t *graph,-        igraph_integer_t *res) {+static int igraph_i_vertex_connectivity_undirected(const igraph_t *graph,+                                                   igraph_integer_t *res) {     igraph_t newgraph;      IGRAPH_CHECK(igraph_copy(&newgraph, graph));@@ -2008,9 +2005,9 @@ }  /* Use that vertex.connectivity(G) <= edge.connectivity(G) <= min(degree(G)) */-int igraph_i_connectivity_checks(const igraph_t *graph,-                                 igraph_integer_t *res,-                                 igraph_bool_t *found) {+static int igraph_i_connectivity_checks(const igraph_t *graph,+                                        igraph_integer_t *res,+                                        igraph_bool_t *found) {     igraph_bool_t conn;     *found = 0; @@ -2529,4 +2526,3 @@      return IGRAPH_SUCCESS; }-
igraph/src/foreign-dl-lexer.c view
@@ -590,16 +590,16 @@ #include "foreign-dl-parser.h" #define YY_EXTRA_TYPE igraph_i_dl_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno;-/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1)-#endif+#define YY_FATAL_ERROR(msg)                                     \+  igraph_error("Fatal error in DL parser: " # msg, __FILE__,    \+               __LINE__, IGRAPH_PARSEERROR); #ifdef stdout  #  undef stdout #endif #define stdout 0-#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \-				__LINE__, IGRAPH_PARSEERROR);+#endif #define YY_NO_INPUT 1  #line 606 "foreign-dl-lexer.c"
igraph/src/foreign-gml-lexer.c view
@@ -499,16 +499,16 @@ #include "foreign-gml-parser.h" #define YY_EXTRA_TYPE igraph_i_gml_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno;-/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1)-#endif+#define YY_FATAL_ERROR(msg)                                      \+  igraph_error("Fatal error in GML parser: " # msg, __FILE__,    \+               __LINE__, IGRAPH_PARSEERROR); #ifdef stdout  #  undef stdout #endif #define stdout 0-#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \-				__LINE__, IGRAPH_PARSEERROR);+#endif #define YY_NO_INPUT 1 #line 514 "foreign-gml-lexer.c" 
igraph/src/foreign-graphml.c view
@@ -133,8 +133,8 @@                     "attribute specifications", file, line, 0, target); } -igraph_real_t igraph_i_graphml_parse_numeric(const char* char_data,-        igraph_real_t default_value) {+static igraph_real_t igraph_i_graphml_parse_numeric(const char* char_data,+                                                    igraph_real_t default_value) {     double result;      if (char_data == 0) {@@ -148,8 +148,8 @@     return result; } -igraph_bool_t igraph_i_graphml_parse_boolean(const char* char_data,-        igraph_bool_t default_value) {+static igraph_bool_t igraph_i_graphml_parse_boolean(const char* char_data,+                                                    igraph_bool_t default_value) {     int value;     if (char_data == 0) {         return default_value;@@ -172,7 +172,7 @@     return value != 0; } -void igraph_i_graphml_attribute_record_destroy(igraph_i_graphml_attribute_record_t* rec) {+static void igraph_i_graphml_attribute_record_destroy(igraph_i_graphml_attribute_record_t* rec) {     if (rec->record.type == IGRAPH_ATTRIBUTE_NUMERIC) {         if (rec->record.value != 0) {             igraph_vector_destroy((igraph_vector_t*)rec->record.value);@@ -200,7 +200,7 @@     } } -void igraph_i_graphml_destroy_state(struct igraph_i_graphml_parser_state* state) {+static void igraph_i_graphml_destroy_state(struct igraph_i_graphml_parser_state* state) {     if (state->destroyed) {         return;     }@@ -231,7 +231,7 @@     IGRAPH_FINALLY_CLEAN(1); } -void igraph_i_graphml_sax_handler_error(void *state0, const char* msg, ...) {+static void igraph_i_graphml_sax_handler_error(void *state0, const char* msg, ...) {     struct igraph_i_graphml_parser_state *state =         (struct igraph_i_graphml_parser_state*)state0;     va_list ap;@@ -249,7 +249,7 @@     va_end(ap); } -xmlEntityPtr igraph_i_graphml_sax_handler_get_entity(void *state0,+static xmlEntityPtr igraph_i_graphml_sax_handler_get_entity(void *state0,         const xmlChar* name) {     xmlEntityPtr predef = xmlGetPredefinedEntity(name);     IGRAPH_UNUSED(state0);@@ -260,7 +260,7 @@     return blankEntity; } -void igraph_i_graphml_handle_unknown_start_tag(struct igraph_i_graphml_parser_state *state) {+static void igraph_i_graphml_handle_unknown_start_tag(struct igraph_i_graphml_parser_state *state) {     if (state->st != UNKNOWN) {         igraph_vector_int_push_back(&state->prev_state_stack, state->st);         state->st = UNKNOWN;@@ -270,7 +270,7 @@     } } -void igraph_i_graphml_sax_handler_start_document(void *state0) {+static void igraph_i_graphml_sax_handler_start_document(void *state0) {     struct igraph_i_graphml_parser_state *state =         (struct igraph_i_graphml_parser_state*)state0;     int ret;@@ -359,7 +359,7 @@     IGRAPH_FINALLY(igraph_i_graphml_destroy_state, state); } -void igraph_i_graphml_sax_handler_end_document(void *state0) {+static void igraph_i_graphml_sax_handler_end_document(void *state0) {     struct igraph_i_graphml_parser_state *state =         (struct igraph_i_graphml_parser_state*)state0;     long i, l;@@ -559,9 +559,9 @@ #define XML_ATTR_VALUE_END(it) (*(it+4)) #define XML_ATTR_VALUE(it) *(it+3), (*(it+4))-(*(it+3)) -igraph_i_graphml_attribute_record_t* igraph_i_graphml_add_attribute_key(-    const xmlChar** attrs, int nb_attrs,-    struct igraph_i_graphml_parser_state *state) {+static igraph_i_graphml_attribute_record_t* igraph_i_graphml_add_attribute_key(+        const xmlChar** attrs, int nb_attrs,+        struct igraph_i_graphml_parser_state *state) {     xmlChar **it;     xmlChar *localname;     igraph_trie_t *trie = 0;@@ -749,10 +749,10 @@     return rec; } -void igraph_i_graphml_attribute_data_setup(struct igraph_i_graphml_parser_state *state,-        const xmlChar **attrs,-        int nb_attrs,-        igraph_attribute_elemtype_t type) {+static void igraph_i_graphml_attribute_data_setup(struct igraph_i_graphml_parser_state *state,+                                                  const xmlChar **attrs,+                                                  int nb_attrs,+                                                  igraph_attribute_elemtype_t type) {     xmlChar **it;     int i; @@ -782,8 +782,8 @@     } } -void igraph_i_graphml_append_to_data_char(struct igraph_i_graphml_parser_state *state,-        const xmlChar *data, int len) {+static void igraph_i_graphml_append_to_data_char(struct igraph_i_graphml_parser_state *state,+                                                 const xmlChar *data, int len) {     long int data_char_new_start = 0;      if (!state->successful) {@@ -805,7 +805,7 @@     state->data_char[data_char_new_start + len] = '\0'; } -void igraph_i_graphml_attribute_data_finish(struct igraph_i_graphml_parser_state *state) {+static void igraph_i_graphml_attribute_data_finish(struct igraph_i_graphml_parser_state *state) {     const char *key = fromXmlChar(state->data_key);     igraph_attribute_elemtype_t type = state->data_type;     igraph_trie_t *trie = 0;@@ -930,8 +930,8 @@     } } -void igraph_i_graphml_attribute_default_value_finish(-    struct igraph_i_graphml_parser_state *state) {+static void igraph_i_graphml_attribute_default_value_finish(+        struct igraph_i_graphml_parser_state *state) {     igraph_i_graphml_attribute_record_t *graphmlrec = state->current_attr_record;      if (graphmlrec == 0) {@@ -971,10 +971,10 @@     } } -void igraph_i_graphml_sax_handler_start_element_ns(-    void *state0, const xmlChar* localname, const xmlChar* prefix,-    const xmlChar* uri, int nb_namespaces, const xmlChar** namespaces,-    int nb_attributes, int nb_defaulted, const xmlChar** attributes) {+static void igraph_i_graphml_sax_handler_start_element_ns(+        void *state0, const xmlChar* localname, const xmlChar* prefix,+        const xmlChar* uri, int nb_namespaces, const xmlChar** namespaces,+        int nb_attributes, int nb_defaulted, const xmlChar** attributes) {     struct igraph_i_graphml_parser_state *state =         (struct igraph_i_graphml_parser_state*)state0;     xmlChar** it;@@ -1174,7 +1174,8 @@     } } -void igraph_i_graphml_sax_handler_end_element_ns(void *state0,+static void igraph_i_graphml_sax_handler_end_element_ns(+        void *state0,         const xmlChar* localname, const xmlChar* prefix,         const xmlChar* uri) {     struct igraph_i_graphml_parser_state *state =@@ -1232,7 +1233,7 @@     } } -void igraph_i_graphml_sax_handler_chars(void* state0, const xmlChar* ch, int len) {+static void igraph_i_graphml_sax_handler_chars(void* state0, const xmlChar* ch, int len) {     struct igraph_i_graphml_parser_state *state =         (struct igraph_i_graphml_parser_state*)state0; @@ -1294,7 +1295,7 @@  #define IS_FORBIDDEN_CONTROL_CHAR(x) ((x) < ' ' && (x) != '\t' && (x) != '\r' && (x) != '\n') -int igraph_i_xml_escape(char* src, char** dest) {+static int igraph_i_xml_escape(char* src, char** dest) {     long int destlen = 0;     char *s, *d;     unsigned char ch;@@ -1353,13 +1354,13 @@  * graphs. Currently only the most basic import functionality is implemented  * in igraph: it can read GraphML files without nested graphs and hyperedges.  * Attributes of the graph are loaded only if an attribute interface- * is attached, ie. if you use igraph from R or Python.+ * is attached, i.e. if you use igraph from R or Python.  *  * </para><para>- * Graph attribute names are taken from the \c attr.name attributes of the- * \c key tags in the GraphML file. Since \c attr.name is not mandatory,+ * Graph attribute names are taken from the <code>attr.name</code> attributes of the+ * \c key tags in the GraphML file. Since <code>attr.name</code> is not mandatory,  * igraph will fall back to the \c id attribute of the \c key tag if- * \c attr.name is missing.+ * <code>attr.name</code> is missing.  *  * \param graph Pointer to an uninitialized graph object.  * \param instream A stream, it should be readable.
igraph/src/foreign-lgl-lexer.c view
@@ -485,16 +485,16 @@ #include "foreign-lgl-parser.h" #define YY_EXTRA_TYPE igraph_i_lgl_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno;-/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1)-#endif+#define YY_FATAL_ERROR(msg)                                      \+  igraph_error("Fatal error in LGL parser: " # msg, __FILE__,    \+               __LINE__, IGRAPH_PARSEERROR); #ifdef stdout  #  undef stdout #endif #define stdout 0-#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \-				__LINE__, IGRAPH_PARSEERROR);+#endif #define YY_NO_INPUT 1 #line 500 "foreign-lgl-lexer.c" 
igraph/src/foreign-ncol-lexer.c view
@@ -485,16 +485,16 @@ #include "foreign-ncol-parser.h" #define YY_EXTRA_TYPE igraph_i_ncol_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno;-/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1)-#endif+#define YY_FATAL_ERROR(msg)                                       \+  igraph_error("Fatal error in NCOL parser: " # msg, __FILE__,    \+               __LINE__, IGRAPH_PARSEERROR); #ifdef stdout  #  undef stdout #endif #define stdout 0-#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \-				__LINE__, IGRAPH_PARSEERROR);+#endif #define YY_NO_INPUT 1 #line 500 "foreign-ncol-lexer.c" 
igraph/src/foreign-pajek-lexer.c view
@@ -604,16 +604,16 @@ #include "foreign-pajek-parser.h" #define YY_EXTRA_TYPE igraph_i_pajek_parsedata_t* #define YY_USER_ACTION yylloc->first_line = yylineno;-/* We assume that 'file' is 'stderr' here. */ #ifdef USING_R #define fprintf(file, msg, ...) (1)-#endif+#define YY_FATAL_ERROR(msg)                                        \+  igraph_error("Fatal error in PAJEK parser: " # msg, __FILE__,    \+               __LINE__, IGRAPH_PARSEERROR); #ifdef stdout  #  undef stdout #endif #define stdout 0-#define exit(code) igraph_error("Fatal error in DL parser", __FILE__, \-				__LINE__, IGRAPH_PARSEERROR);+#endif #define YY_NO_INPUT 1 #line 619 "foreign-pajek-lexer.c" 
igraph/src/foreign-pajek-parser.c view
@@ -2690,7 +2690,7 @@   if (tmp==0) {     IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM);   }-  IGRAPH_FINALLY(free, tmp);+  IGRAPH_FINALLY(igraph_free, tmp);   strncpy(tmp, value, len);   tmp[len]='\0'; @@ -2717,7 +2717,7 @@   if (tmp==0) {     IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM);   }-  IGRAPH_FINALLY(free, tmp);+  IGRAPH_FINALLY(igraph_free, tmp);   strncpy(tmp, value, len);   tmp[len]='\0';   
igraph/src/foreign.c view
@@ -22,7 +22,6 @@ */  #include "igraph_foreign.h"-#include "config.h" #include "igraph_math.h" #include "igraph_gml_tree.h" #include "igraph_memory.h"@@ -31,6 +30,7 @@ #include "igraph_interrupt_internal.h" #include "igraph_constructors.h" #include "igraph_types_internal.h"+#include "config.h"  #include <ctype.h>      /* isspace */ #include <string.h>@@ -53,10 +53,10 @@  * \brief Reads an edge list from a file and creates a graph.  *  * </para><para>- * This format is simply a series of even number integers separated by- * whitespace. The one edge (ie. two integers) per line format is thus- * not required (but recommended for readability). Edges of directed- * graphs are assumed to be in from, to order.+ * This format is simply a series of an even number of non-negative integers separated by+ * whitespace. The integers represent vertex IDs. Placing each edge (i.e. pair of integers) + * on a separate line is not required, but it is recommended for readability. + * Edges of directed graphs are assumed to be in "from, to" order.  * \param graph Pointer to an uninitialized graph object.  * \param instream Pointer to a stream, it should be readable.  * \param n The number of vertices in the graph. If smaller than the@@ -485,7 +485,7 @@  * project files (<filename>.paj</filename>) are not. These might be  * supported in the future if there is need for it.  * \oli Time events networks are not supported.- * \oli Hypergraphs (ie. graphs with non-binary edges) are not+ * \oli Hypergraphs (i.e. graphs with non-binary edges) are not  * supported.  * \oli Graphs with both directed and non-directed edges are not  * supported, are they cannot be represented in@@ -499,35 +499,35 @@  * If there are attribute handlers installed,  * <command>igraph</command> also reads the vertex and edge attributes  * from the file. Most attributes are renamed to be more informative:- * `\c color' instead of `\c c', `\c xfact' instead of `\c x_fact',- * `\c yfact' instead of `y_fact', `\c labeldist' instead of `\c lr',- * `\c labeldegree2' instead of `\c lphi', `\c framewidth' instead of `\c bw',- * `\c fontsize'- * instead of `\c fos', `\c rotation' instead of `\c phi', `\c radius' instead- * of `\c r',- * `\c diamondratio' instead of `\c q', `\c labeldegree' instead of `\c la',- * `\c vertexsize'- * instead of `\c size', `\c color' instead of `\c ic', `\c framecolor' instead of- * `\c bc', `\c labelcolor' instead of `\c lc', these belong to vertices.+ * \c color instead of \c c, \c xfact instead of \c x_fact,+ * \c yfact instead of y_fact, \c labeldist instead of \c lr,+ * \c labeldegree2 instead of \c lphi, \c framewidth instead of \c bw,+ * \c fontsize+ * instead of \c fos, \c rotation instead of \c phi, \c radius instead+ * of \c r,+ * \c diamondratio instead of \c q, \c labeldegree instead of \c la,+ * \c vertexsize+ * instead of \c size, \c color instead of \c ic, \c framecolor instead of+ * \c bc, \c labelcolor instead of \c lc, these belong to vertices.  *  * </para><para>- * Edge attributes are also renamed, `\c s' to `\c arrowsize', `\c w'- * to `\c edgewidth', `\c h1' to `\c hook1', `\c h2' to `\c hook2',- * `\c a1' to `\c angle1', `\c a2' to `\c angle2', `\c k1' to- * `\c velocity1', `\c k2' to `\c velocity2', `\c ap' to `\c- * arrowpos', `\c lp' to `\c labelpos', `\c lr' to- * `\c labelangle', `\c lphi' to `\c labelangle2', `\c la' to `\c- * labeldegree', `\c fos' to- * `\c fontsize', `\c a' to `\c arrowtype', `\c p' to `\c- * linepattern', `\c l' to `\c label', `\c lc' to- * `\c labelcolor', `\c c' to `\c color'.+ * Edge attributes are also renamed, \c s to \c arrowsize, \c w+ * to \c edgewidth, \c h1 to \c hook1, \c h2 to \c hook2,+ * \c a1 to \c angle1, \c a2 to \c angle2, \c k1 to+ * \c velocity1, \c k2 to \c velocity2, \c ap to \c+ * arrowpos, \c lp to \c labelpos, \c lr to+ * \c labelangle, \c lphi to \c labelangle2, \c la to \c+ * labeldegree, \c fos to+ * \c fontsize, \c a to \c arrowtype, \c p to \c+ * linepattern, \c l to \c label, \c lc to+ * \c labelcolor, \c c to \c color.  *  * </para><para>- * In addition the following vertex attributes might be added: `\c id'- * if there are vertex ids in the file, `\c x' and `\c y' or `\c x'- * and `\c y' and `\c z' if there are vertex coordinates in the file.+ * In addition the following vertex attributes might be added: \c id+ * if there are vertex ids in the file, \c x and \c y or \c x+ * and \c y and \c z if there are vertex coordinates in the file.  *- * </para><para>The `\c weight' edge attribute might be+ * </para><para>The \c weight edge attribute might be  * added if there are edge weights present.  *  * </para><para>@@ -878,7 +878,7 @@     return 0; } -int igraph_i_read_graph_graphdb_getword(FILE *instream) {+static int igraph_i_read_graph_graphdb_getword(FILE *instream) {     int b1, b2;     unsigned char c1, c2;     b1 = fgetc(instream);@@ -977,7 +977,7 @@ int igraph_gml_yyparse (igraph_i_gml_parsedata_t* context); void igraph_gml_yyset_in  (FILE * in_str, void* yyscanner ); -void igraph_i_gml_destroy_attrs(igraph_vector_ptr_t **ptr) {+static void igraph_i_gml_destroy_attrs(igraph_vector_ptr_t **ptr) {     long int i;     igraph_vector_ptr_t *vec;     for (i = 0; i < 3; i++) {@@ -1005,7 +1005,7 @@     } } -igraph_real_t igraph_i_gml_toreal(igraph_gml_tree_t *node, long int pos) {+static igraph_real_t igraph_i_gml_toreal(igraph_gml_tree_t *node, long int pos) {      igraph_real_t value = 0.0;     int type = igraph_gml_tree_type(node, pos);@@ -1025,10 +1025,10 @@     return value; } -const char *igraph_i_gml_tostring(igraph_gml_tree_t *node, long int pos) {+static const char *igraph_i_gml_tostring(igraph_gml_tree_t *node, long int pos) {      int type = igraph_gml_tree_type(node, pos);-    char tmp[256];+    static char tmp[256];     const char *p = tmp;     long int i;     igraph_real_t d;@@ -1155,7 +1155,7 @@     }     gtree = igraph_gml_tree_get_tree(context.tree, gidx); -    IGRAPH_FINALLY(igraph_i_gml_destroy_attrs, &attrs);+    IGRAPH_FINALLY(igraph_i_gml_destroy_attrs, attrs);     igraph_vector_ptr_init(&gattrs, 0);     igraph_vector_ptr_init(&vattrs, 0);     igraph_vector_ptr_init(&eattrs, 0);@@ -1942,7 +1942,7 @@ #define E_COLOR            22 #define E_LAST             23 -int igraph_i_pajek_escape(char* src, char** dest) {+static int igraph_i_pajek_escape(char* src, char** dest) {     long int destlen = 0;     igraph_bool_t need_escape = 0; @@ -2010,18 +2010,30 @@  * the attributes of the vertices and edges, of course this requires  * an attribute handler to be installed. The names of the  * corresponding vertex and edge attributes are listed at \ref- * igraph_read_graph_pajek(), eg. the `\c color' vertex attributes- * determines the color (`\c c' in Pajek) parameter.+ * igraph_read_graph_pajek(), eg. the \c color vertex attributes+ * determines the color (\c c in Pajek) parameter.  *  * </para><para>  * As of version 0.6.1 igraph writes bipartite graphs into Pajek files  * correctly, i.e. they will be also bipartite when read into Pajek.- * As Pajek is less flexible for bipartite graphs (the numeric ids of+ * As Pajek is less flexible for bipartite graphs (the numeric IDs of  * the vertices must be sorted according to vertex type), igraph might  * need to reorder the vertices when writing a bipartite Pajek file.- * This effectively means that numeric vertex ids usually change when+ * This effectively means that numeric vertex IDs usually change when  * a bipartite graph is written to a Pajek file, and then read back  * into igraph.+ *+ * </para><para>+ * Early versions of Pajek supported only Windows-style line endings+ * in Pajek files, but recent versions support both Windows and Unix+ * line endings. igraph therefore uses the platform-native line endings+ * when the input file is opened in text mode, and uses Unix-style+ * line endings when the input file is opened in binary mode. If you+ * are using an old version of Pajek, you are on Unix and you are having+ * problems reading files written by igraph on a Windows machine, convert the+ * line endings manually with a text editor or with \c unix2dos or \c iconv+ * from the command line).+ *  * \param graph The graph object to write.  * \param outstream The file to write to. It should be opened and  * writable. Make sure that you open the file in binary format if you use MS Windows,@@ -2091,7 +2103,10 @@                               };     const char *estrnames2[] = { "a", "p", "l", "lc", "c" }; -    const char *newline = "\x0d\x0a";+    /* Newer Pajek versions support both Unix and Windows-style line endings,+     * so we just use Unix style. This will get converted to CRLF on Windows+     * when the file is opened in text mode */+    const char *newline = "\n";      igraph_es_t es;     igraph_eit_t eit;@@ -2466,7 +2481,7 @@     return 0; } -int igraph_i_gml_convert_to_key(const char *orig, char **key) {+static int igraph_i_gml_convert_to_key(const char *orig, char **key) {     int no = 1;     char strno[50];     size_t i, len = strlen(orig), newlen = 0, plen = 0;@@ -2741,7 +2756,7 @@     return 0; } -int igraph_i_dot_escape(const char *orig, char **result) {+static int igraph_i_dot_escape(const char *orig, char **result) {     /* do we have to escape the string at all? */     long int i, j, len = (long int) strlen(orig), newlen = 0;     igraph_bool_t need_quote = 0, is_number = 1;@@ -3386,5 +3401,3 @@ }  #undef CHECK--
igraph/src/forestfire.c view
@@ -38,7 +38,7 @@ } igraph_i_forest_fire_data_t;  -void igraph_i_forest_fire_free(igraph_i_forest_fire_data_t *data) {+static void igraph_i_forest_fire_free(igraph_i_forest_fire_data_t *data) {     long int i;     for (i = 0; i < data->no_of_nodes; i++) {         igraph_vector_destroy(data->inneis + i);@@ -117,21 +117,20 @@     igraph_real_t param_geom_out = 1 - fw_prob;     igraph_real_t param_geom_in = 1 - fw_prob * bw_factor; -    if (fw_prob < 0) {-        IGRAPH_ERROR("Forest fire model: 'fw_prob' should be between non-negative",+    if (fw_prob < 0 || fw_prob >= 1) {+        IGRAPH_ERROR("Forest fire model: 'fw_prob' must satisfy 0 <= fw_prob < 1.",                      IGRAPH_EINVAL);     }-    if (bw_factor < 0) {-        IGRAPH_ERROR("Forest fire model: 'bw_factor' should be non-negative",+    if (bw_factor * fw_prob < 0 || bw_factor * fw_prob >= 1) {+        IGRAPH_ERROR("Forest fire model: 'bw_factor' must satisfy 0 <= bw_factor * fw_prob < 1.",                      IGRAPH_EINVAL);     }     if (ambs < 0) {-        IGRAPH_ERROR("Number of ambassadors ('ambs') should be non-negative",+        IGRAPH_ERROR("Forest fire model: Number of ambassadors must not be negative.",                      IGRAPH_EINVAL);     } -    if (fw_prob == 0 || ambs == 0) {-        IGRAPH_WARNING("'fw_prob or ambs is zero, creating empty graph");+    if (ambs == 0) {         IGRAPH_CHECK(igraph_empty(graph, nodes, directed));         return 0;     }
igraph/src/fortran_intrinsics.c view
@@ -23,31 +23,31 @@  #include <float.h> -double digitsdbl_(double x) {+double digitsdbl_(double *x) {     return (double) DBL_MANT_DIG; } -double epsilondbl_(double x) {+double epsilondbl_(double *x) {     return DBL_EPSILON; } -double hugedbl_(double x) {+double hugedbl_(double *x) {     return DBL_MAX; } -double tinydbl_(double x) {+double tinydbl_(double *x) {     return DBL_MIN; } -int maxexponentdbl_(double x) {+int maxexponentdbl_(double *x) {     return DBL_MAX_EXP; } -int minexponentdbl_(double x) {+int minexponentdbl_(double *x) {     return DBL_MIN_EXP; } -double radixdbl_(double x) {+double radixdbl_(double *x) {     return (double) FLT_RADIX; } 
igraph/src/games.c view
@@ -47,8 +47,8 @@     igraph_psumtree_t *sumtrees; } igraph_i_citing_cited_type_game_struct_t; -void igraph_i_citing_cited_type_game_free (-    igraph_i_citing_cited_type_game_struct_t *s);+static void igraph_i_citing_cited_type_game_free (+        igraph_i_citing_cited_type_game_struct_t *s); /**  * \section about_games  *@@ -56,39 +56,39 @@  * they generate a different graph every time you call them. </para>  */ -int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n,-                               igraph_integer_t m,-                               const igraph_vector_t *outseq,-                               igraph_bool_t outpref,-                               igraph_bool_t directed,-                               const igraph_t *start_from);+static int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n,+                                      igraph_integer_t m,+                                      const igraph_vector_t *outseq,+                                      igraph_bool_t outpref,+                                      igraph_bool_t directed,+                                      const igraph_t *start_from); -int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph,-        igraph_integer_t n,-        igraph_real_t power,-        igraph_integer_t m,-        const igraph_vector_t *outseq,-        igraph_bool_t outpref,-        igraph_real_t A,-        igraph_bool_t directed,-        const igraph_t *start_from);+static int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph,+                                                    igraph_integer_t n,+                                                    igraph_real_t power,+                                                    igraph_integer_t m,+                                                    const igraph_vector_t *outseq,+                                                    igraph_bool_t outpref,+                                                    igraph_real_t A,+                                                    igraph_bool_t directed,+                                                    const igraph_t *start_from); -int igraph_i_barabasi_game_psumtree(igraph_t *graph,-                                    igraph_integer_t n,-                                    igraph_real_t power,-                                    igraph_integer_t m,-                                    const igraph_vector_t *outseq,-                                    igraph_bool_t outpref,-                                    igraph_real_t A,-                                    igraph_bool_t directed,-                                    const igraph_t *start_from);+static int igraph_i_barabasi_game_psumtree(igraph_t *graph,+                                           igraph_integer_t n,+                                           igraph_real_t power,+                                           igraph_integer_t m,+                                           const igraph_vector_t *outseq,+                                           igraph_bool_t outpref,+                                           igraph_real_t A,+                                           igraph_bool_t directed,+                                           const igraph_t *start_from); -int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n,-                               igraph_integer_t m,-                               const igraph_vector_t *outseq,-                               igraph_bool_t outpref,-                               igraph_bool_t directed,-                               const igraph_t *start_from) {+static int igraph_i_barabasi_game_bag(igraph_t *graph, igraph_integer_t n,+                                      igraph_integer_t m,+                                      const igraph_vector_t *outseq,+                                      igraph_bool_t outpref,+                                      igraph_bool_t directed,+                                      const igraph_t *start_from) {      long int no_of_nodes = n;     long int no_of_neighbors = m;@@ -124,7 +124,7 @@     if (bag == 0) {         IGRAPH_ERROR("barabasi_game failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, bag);    /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, bag);      /* The first node(s) in the bag */     if (start_from) {@@ -190,15 +190,15 @@     return 0; } -int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph,-        igraph_integer_t n,-        igraph_real_t power,-        igraph_integer_t m,-        const igraph_vector_t *outseq,-        igraph_bool_t outpref,-        igraph_real_t A,-        igraph_bool_t directed,-        const igraph_t *start_from) {+static int igraph_i_barabasi_game_psumtree_multiple(igraph_t *graph,+                                                    igraph_integer_t n,+                                                    igraph_real_t power,+                                                    igraph_integer_t m,+                                                    const igraph_vector_t *outseq,+                                                    igraph_bool_t outpref,+                                                    igraph_real_t A,+                                                    igraph_bool_t directed,+                                                    const igraph_t *start_from) {      long int no_of_nodes = n;     long int no_of_neighbors = m;@@ -296,15 +296,15 @@     return 0; } -int igraph_i_barabasi_game_psumtree(igraph_t *graph,-                                    igraph_integer_t n,-                                    igraph_real_t power,-                                    igraph_integer_t m,-                                    const igraph_vector_t *outseq,-                                    igraph_bool_t outpref,-                                    igraph_real_t A,-                                    igraph_bool_t directed,-                                    const igraph_t *start_from) {+static int igraph_i_barabasi_game_psumtree(igraph_t *graph,+                                           igraph_integer_t n,+                                           igraph_real_t power,+                                           igraph_integer_t m,+                                           const igraph_vector_t *outseq,+                                           igraph_bool_t outpref,+                                           igraph_real_t A,+                                           igraph_bool_t directed,+                                           const igraph_t *start_from) {      long int no_of_nodes = n;     long int no_of_neighbors = m;@@ -437,7 +437,7 @@  *        no outgoing edges, so the first number in this vector is  *        ignored.  * \param outpref Boolean, if true not only the in- but also the out-degree- *        of a vertex increases its citation probability. Ie. the+ *        of a vertex increases its citation probability. I.e., the  *        citation probability is determined by the total degree of  *        the vertices. Ignored and assumed to be true if the graph  *        being generated is undirected.@@ -860,7 +860,7 @@     if (bag1 == 0) {         IGRAPH_ERROR("degree sequence game (simple)", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, bag1);   /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, bag1);      for (i = 0; i < no_of_nodes; i++) {         for (j = 0; j < VECTOR(*out_seq)[i]; j++) {@@ -872,7 +872,7 @@         if (bag2 == 0) {             IGRAPH_ERROR("degree sequence game (simple)", IGRAPH_ENOMEM);         }-        IGRAPH_FINALLY(free, bag2);+        IGRAPH_FINALLY(igraph_free, bag2);         for (i = 0; i < no_of_nodes; i++) {             for (j = 0; j < VECTOR(*in_seq)[i]; j++) {                 bag2[bagp2++] = i;@@ -965,6 +965,8 @@      * until it finally succeeds. */     finished = 0;     while (!finished) {+        IGRAPH_ALLOW_INTERRUPTION();+         /* Be optimistic :) */         failed = 0; @@ -1111,6 +1113,8 @@      * until it finally succeeds. */     finished = 0;     while (!finished) {+        IGRAPH_ALLOW_INTERRUPTION();+         /* Be optimistic :) */         failed = 0; @@ -1210,15 +1214,24 @@     return IGRAPH_SUCCESS; } +/* swap two elements of a vector_int */+#define SWAP_INT_ELEM(vec, i, j) \+    { \+        igraph_integer_t temp; \+        temp = VECTOR(vec)[i]; \+        VECTOR(vec)[i] = VECTOR(vec)[j]; \+        VECTOR(vec)[j] = temp; \+    }+ int igraph_degree_sequence_game_no_multiple_undirected_uniform(igraph_t *graph, const igraph_vector_t *degseq) {     igraph_vector_int_t stubs;     igraph_vector_t edges;     igraph_bool_t degseq_ok;     igraph_vector_ptr_t adjlist;-    long i, j, k;+    long i, j;     long vcount, ecount, stub_count; -    IGRAPH_CHECK(igraph_is_graphical_degree_sequence(degseq, 0, &degseq_ok));+    IGRAPH_CHECK(igraph_is_graphical_degree_sequence(degseq, NULL, &degseq_ok));     if (!degseq_ok) {         IGRAPH_ERROR("No simple undirected graph can realize the given degree sequence", IGRAPH_EINVAL);     }@@ -1230,16 +1243,21 @@     IGRAPH_VECTOR_INT_INIT_FINALLY(&stubs, stub_count);     IGRAPH_VECTOR_INIT_FINALLY(&edges, stub_count); -    k = 0;-    for (i = 0; i < vcount; ++i) {-        long deg = (long) VECTOR(*degseq)[i];-        for (j = 0; j < deg; ++j) {-            VECTOR(stubs)[k++] = i;+    /* Fill stubs vector. */+    {+        long k = 0;+        for (i = 0; i < vcount; ++i) {+            long deg = (long) VECTOR(*degseq)[i];+            for (j = 0; j < deg; ++j) {+                VECTOR(stubs)[k++] = i;+            }         }     } +    /* Build an adjacency list in terms of sets; used to check for multi-edges. */     IGRAPH_CHECK(igraph_vector_ptr_init(&adjlist, vcount));     IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&adjlist, igraph_set_destroy);+    IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist);     for (i = 0; i < vcount; ++i) {         igraph_set_t *set = igraph_malloc(sizeof(igraph_set_t));         if (! set) {@@ -1248,21 +1266,28 @@         IGRAPH_CHECK(igraph_set_init(set, 0));         VECTOR(adjlist)[i] = set;         IGRAPH_CHECK(igraph_set_reserve(set, (long) VECTOR(*degseq)[i]));-    }-    IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist);+    }          RNG_BEGIN();      for (;;) {         igraph_bool_t success = 1;-        IGRAPH_CHECK(igraph_vector_int_shuffle(&stubs)); +        /* Shuffle stubs vector with Fisher-Yates and check for self-loops and multi-edges as we go. */         for (i = 0; i < ecount; ++i) {-            igraph_integer_t from = VECTOR(stubs)[2 * i];-            igraph_integer_t to = VECTOR(stubs)[2 * i + 1];+            long k, from, to; -            /* loop edge, fail */-            if (to == from) {+            k = RNG_INTEGER(2*i, stub_count-1);+            SWAP_INT_ELEM(stubs, 2*i, k);++            k = RNG_INTEGER(2*i+1, stub_count-1);+            SWAP_INT_ELEM(stubs, 2*i+1, k);++            from = VECTOR(stubs)[2*i];+            to   = VECTOR(stubs)[2*i+1];++            /* self-loop, fail */+            if (from == to) {                 success = 0;                 break;             }@@ -1286,11 +1311,12 @@             break;         } -        IGRAPH_ALLOW_INTERRUPTION();-+        /* Clear adjacency list. */         for (j = 0; j < vcount; ++j) {             igraph_set_clear((igraph_set_t *) VECTOR(adjlist)[j]);         }++        IGRAPH_ALLOW_INTERRUPTION();     }      RNG_END();@@ -1307,13 +1333,14 @@     return IGRAPH_SUCCESS; } + int igraph_degree_sequence_game_no_multiple_directed_uniform(     igraph_t *graph, const igraph_vector_t *out_deg, const igraph_vector_t *in_deg) {     igraph_vector_int_t out_stubs, in_stubs;     igraph_vector_t edges;     igraph_bool_t degseq_ok;     igraph_vector_ptr_t adjlist;-    long i, j, k, l;+    long i, j;     long vcount, ecount;      IGRAPH_CHECK(igraph_is_graphical_degree_sequence(out_deg, in_deg, &degseq_ok));@@ -1328,23 +1355,28 @@     IGRAPH_VECTOR_INT_INIT_FINALLY(&in_stubs, ecount);     IGRAPH_VECTOR_INIT_FINALLY(&edges, 2 * ecount); -    k = 0; l = 0;-    for (i = 0; i < vcount; ++i) {-        long dout, din;+    /* Fill in- and out-stubs vectors. */+    {+        long k = 0, l = 0;+        for (i = 0; i < vcount; ++i) {+            long dout, din; -        dout = (long) VECTOR(*out_deg)[i];-        for (j = 0; j < dout; ++j) {-            VECTOR(out_stubs)[k++] = i;-        }+            dout = (long) VECTOR(*out_deg)[i];+            for (j = 0; j < dout; ++j) {+                VECTOR(out_stubs)[k++] = i;+            } -        din  = (long) VECTOR(*in_deg)[i];-        for (j = 0; j < din; ++j) {-            VECTOR(in_stubs)[l++] = i;+            din  = (long) VECTOR(*in_deg)[i];+            for (j = 0; j < din; ++j) {+                VECTOR(in_stubs)[l++] = i;+            }         }     } +    /* Build an adjacency list in terms of sets; used to check for multi-edges. */     IGRAPH_CHECK(igraph_vector_ptr_init(&adjlist, vcount));     IGRAPH_VECTOR_PTR_SET_ITEM_DESTRUCTOR(&adjlist, igraph_set_destroy);+    IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist);     for (i = 0; i < vcount; ++i) {         igraph_set_t *set = igraph_malloc(sizeof(igraph_set_t));         if (! set) {@@ -1353,21 +1385,25 @@         IGRAPH_CHECK(igraph_set_init(set, 0));         VECTOR(adjlist)[i] = set;         IGRAPH_CHECK(igraph_set_reserve(set, (long) VECTOR(*out_deg)[i]));-    }-    IGRAPH_FINALLY(igraph_vector_ptr_destroy_all, &adjlist);+    }          RNG_BEGIN();      for (;;) {         igraph_bool_t success = 1;-        IGRAPH_CHECK(igraph_vector_int_shuffle(&out_stubs)); +        /* Shuffle out-stubs vector with Fisher-Yates and check for self-loops and multi-edges as we go. */         for (i = 0; i < ecount; ++i) {-            igraph_integer_t from = VECTOR(out_stubs)[i];-            igraph_integer_t to = VECTOR(in_stubs)[i];+            long k, from, to;             igraph_set_t *set; -            /* loop edge, fail */+            k = RNG_INTEGER(i, ecount-1);+            SWAP_INT_ELEM(out_stubs, i, k);++            from = VECTOR(out_stubs)[i];+            to   = VECTOR(in_stubs)[i];++            /* self-loop, fail */             if (to == from) {                 success = 0;                 break;@@ -1392,11 +1428,12 @@             break;         } -        IGRAPH_ALLOW_INTERRUPTION();-+        /* Clear adjacency list. */         for (j = 0; j < vcount; ++j) {             igraph_set_clear((igraph_set_t *) VECTOR(adjlist)[j]);         }++        IGRAPH_ALLOW_INTERRUPTION();     }      RNG_END();@@ -1414,6 +1451,9 @@     return IGRAPH_SUCCESS; } +#undef SWAP_INT_ELEM++ /* This is in gengraph_mr-connected.cpp */  int igraph_degree_sequence_game_vl(igraph_t *graph,@@ -1426,9 +1466,9 @@  *  * \param graph Pointer to an uninitialized graph object.  * \param out_deg The degree sequence for an undirected graph (if- *        \p in_seq is of length zero), or the out-degree+ *        \p in_seq is \c NULL or of length zero), or the out-degree  *        sequence of a directed graph (if \p in_deq is not- *        of length zero.+ *        of length zero).  * \param in_deg It is either a zero-length vector or  *        \c NULL (if an undirected  *        graph is generated), or the in-degree sequence.@@ -1439,34 +1479,36 @@  *          For undirected graphs, it puts all vertex IDs in a bag  *          such that the multiplicity of a vertex in the bag is the same as  *          its degree. Then it draws pairs from the bag until the bag becomes- *          empty. This method can generate both loop (self) edges and multiple+ *          empty. This method may generate both loop (self) edges and multiple  *          edges. For directed graphs, the algorithm is basically the same,  *          but two separate bags are used for the in- and out-degrees.  *          Undirected graphs are generated with probability proportional to  *          <code>(\prod_{i&lt;j} A_{ij} ! \prod_i A_{ii} !!)^{-1}</code>,  *          where \c A denotes the adjacency matrix and <code>!!</code> denotes- *          the double factorial.- *          The corresponding  expression for directed ones is+ *          the double factorial. Here \c A is assumed to have twice the number of+ *          self-loops on its diagonal.+ *          The corresponding  expression for directed graphs is  *          <code>(\prod_{i,j} A_{ij}!)^{-1}</code>.  *          Thus the probability of all simple graphs (which only have 0s and 1s  *          in the adjacency matrix) is the same, while that of- *          non-simple ones depends on their structure.+ *          non-simple ones depends on their edge and self-loop multiplicities.  *          \cli IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE- *          This method is similar to \c IGRAPH_DEGSEQ_SIMPLE+ *          This method generates simple graphs.+ *          It is similar to \c IGRAPH_DEGSEQ_SIMPLE  *          but tries to avoid multiple and loop edges and restarts the- *          generation from scratch if it gets stuck. It is not guaranteed- *          to sample uniformly from the space of all possible graphs with- *          the given sequence, but it is relatively fast and it will+ *          generation from scratch if it gets stuck. It can generate all simple+ *          realizations of a degree sequence, but it is not guaranteed+ *          to sample them uniformly. This method is relatively fast and it will  *          eventually succeed if the provided degree sequence is graphical,  *          but there is no upper bound on the number of iterations.  *          \cli IGRAPH_DEGSEQ_SIMPLE_NO_MULTIPLE_UNIFORM  *          This method is identical to \c IGRAPH_DEGSEQ_SIMPLE, but if the  *          generated graph is not simple, it rejects it and re-starts the- *          generation. It samples all simple graphs with the same probability.+ *          generation. It generates all simple graphs with the same probability.  *          \cli IGRAPH_DEGSEQ_VL- *          This method is a much more sophisticated generator than the- *          previous ones. It can sample undirected, connected simple graphs- *          uniformly and uses Monte-Carlo methods to randomize the graphs.+ *          This method samples undirected connected graphs approximately+ *          uniformly. It is a Monte Carlo method based on degree-preserving+ *          edge swaps.  *          This generator should be favoured if undirected and connected  *          graphs are to be generated and execution time is not a concern.  *          igraph uses the original implementation of Fabien Viger; for the algorithm,@@ -1540,7 +1582,7 @@  * growing) random graphs.  * \param graph Uninitialized graph object.  * \param n The number of vertices in the graph.- * \param m The number of edges to add in a time step (ie. after+ * \param m The number of edges to add in a time step (i.e. after  *        adding a vertex).  * \param directed Boolean, whether to generate a directed graph.  * \param citation Boolean, if \c TRUE, the edges always@@ -2268,7 +2310,7 @@  * \param nodes The number of vertices in the graph.  * \param radius The radius within which the vertices will be connected.  * \param torus Logical constant, if true periodic boundary conditions- *        will be used, ie. the vertices are assumed to be on a torus+ *        will be used, i.e. the vertices are assumed to be on a torus  *        instead of a square.  * \return Error code.  *@@ -2382,9 +2424,7 @@ }  -void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs);--void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs) {+static void igraph_i_preference_game_free_vids_by_type(igraph_vector_ptr_t *vecs) {     int i = 0, n;     igraph_vector_t *v; @@ -2926,13 +2966,9 @@     return 0; } -int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob,-                                      igraph_bool_t loops,-                                      igraph_vector_t *edges);--int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob,-                                      igraph_bool_t loops,-                                      igraph_vector_t *edges) {+static int igraph_i_rewire_edges_no_multiple(igraph_t *graph, igraph_real_t prob,+                                             igraph_bool_t loops,+                                             igraph_vector_t *edges) {      int no_verts = igraph_vcount(graph);     int no_edges = igraph_ecount(graph);@@ -3386,7 +3422,7 @@  *  * </para><para>  * The \p preference argument specifies the preferences for the- * citation lags, ie. its first elements contains the attractivity+ * citation lags, i.e. its first elements contains the attractivity  * of the very recently cited vertices, etc. The last element is  * special, it contains the attractivity of the vertices which were  * never cited. This element should be bigger than zero.@@ -3627,7 +3663,7 @@     return 0; } -void igraph_i_citing_cited_type_game_free(igraph_i_citing_cited_type_game_struct_t *s) {+static void igraph_i_citing_cited_type_game_free(igraph_i_citing_cited_type_game_struct_t *s) {     long int i;     if (!s->sumtrees) {         return;@@ -3651,7 +3687,7 @@  * category of both the citing and the cited vertex and is given in  * the \p pref matrix. The categories of the citing vertex correspond  * to the rows, the categories of the cited vertex to the columns of- * this matrix. Ie. the element in row \c i and column \c j gives the+ * this matrix. I.e. the element in row \c i and column \c j gives the  * probability that a \c j vertex is cited, if the category of the  * citing vertex is \c i.  *@@ -3783,16 +3819,15 @@  *  */ int igraph_simple_interconnected_islands_game(-    igraph_t        *graph,-    igraph_integer_t    islands_n,-    igraph_integer_t    islands_size,-    igraph_real_t       islands_pin,-    igraph_integer_t    n_inter) {+        igraph_t *graph,+        igraph_integer_t islands_n,+        igraph_integer_t islands_size,+        igraph_real_t islands_pin,+        igraph_integer_t n_inter) {       igraph_vector_t edges = IGRAPH_VECTOR_NULL;     igraph_vector_t s = IGRAPH_VECTOR_NULL;-    int retval = 0;     int nbNodes;     double maxpossibleedgesPerIsland;     double maxedgesPerIsland;@@ -3816,73 +3851,63 @@         IGRAPH_ERROR("Invalid number of inter-islands links", IGRAPH_EINVAL);     } -    // how much memory ?+    /* how much memory ? */     nbNodes = islands_n * islands_size;     maxpossibleedgesPerIsland = ((double)islands_size * ((double)islands_size - (double)1)) / (double)2;     maxedgesPerIsland = islands_pin * maxpossibleedgesPerIsland;     nbEdgesInterIslands = n_inter * (islands_n * (islands_n - 1)) / 2;-    maxedges = maxedgesPerIsland * islands_n + nbEdgesInterIslands;--    // debug&tests : printf("total nodes %d, maxedgesperisland %f, maxedgesinterislands %d, maxedges %f\n", nbNodes, maxedgesPerIsland, nbEdgesInterIslands, maxedges);+    maxedges = maxedgesPerIsland * islands_n + nbEdgesInterIslands;     -    // reserve enough place for all the edges, thanks !+    /* reserve enough space for all the edges */     IGRAPH_VECTOR_INIT_FINALLY(&edges, 0);     IGRAPH_CHECK(igraph_vector_reserve(&edges, (long int) maxedges));      RNG_BEGIN(); -    // first create all the islands-    for (is = 1; is <= islands_n; is++) { // for each island+    /* first create all the islands */+    for (is = 1; is <= islands_n; is++) { /* for each island */ -        // index for start and end of nodes in this island+        /* index for start and end of nodes in this island */         startIsland = islands_size * (is - 1);         endIsland = startIsland + islands_size - 1; --        // debug&tests : printf("start %d,end %d\n", startIsland, endIsland);--        // create the random numbers to be used (into s)+        /* create the random numbers to be used (into s) */         IGRAPH_VECTOR_INIT_FINALLY(&s, 0);         IGRAPH_CHECK(igraph_vector_reserve(&s, (long int) maxedgesPerIsland));          last = RNG_GEOM(islands_pin);-        // debug&tests : printf("last=%f \n", last);-        while (last < maxpossibleedgesPerIsland) { // maxedgesPerIsland+        while (last < maxpossibleedgesPerIsland) { /* maxedgesPerIsland */             IGRAPH_CHECK(igraph_vector_push_back(&s, last));             myrand = RNG_GEOM(islands_pin);-            last += myrand; //RNG_GEOM(islands_pin);-            //printf("myrand=%f , last=%f \n", myrand, last);+            last += myrand; /* RNG_GEOM(islands_pin); */             last += 1;         }   -        // change this to edges !+        /* change this to edges ! */         for (i = 0; i < igraph_vector_size(&s); i++) {-             long int to = (long int) floor((sqrt(8 * VECTOR(s)[i] + 1) + 1) / 2);             long int from = (long int) (VECTOR(s)[i] - (((igraph_real_t)to) * (to - 1)) / 2);             to += startIsland;             from += startIsland;-            // debug&tests : printf("from %d to %d\n", from, to);+             igraph_vector_push_back(&edges, from);             igraph_vector_push_back(&edges, to);         } -        // clear the memory used for random number for this island+        /* clear the memory used for random number for this island */         igraph_vector_destroy(&s);         IGRAPH_FINALLY_CLEAN(1);  -        // create the links with other islands-        for (i = is + 1; i <= islands_n; i++) { // for each other island (not the previous ones)--            // debug&tests : printf("link islands %d and %d\n", is, i);-            for (j = 0; j < n_inter; j++) { // for each link between islands+        /* create the links with other islands */+        for (i = is + 1; i <= islands_n; i++) { /* for each other island (not the previous ones) */ +            for (j = 0; j < n_inter; j++) { /* for each link between islands */                 long int from = (long int) RNG_UNIF(startIsland, endIsland);                 long int to = (long int) RNG_UNIF((i - 1) * islands_size, i * islands_size);-                //printf("from %d to %d\n", from, to);+                 igraph_vector_push_back(&edges, from);                 igraph_vector_push_back(&edges, to);             }@@ -3892,14 +3917,14 @@      RNG_END(); -    // actually fill the graph object-    IGRAPH_CHECK(retval = igraph_create(graph, &edges, nbNodes, 0));+    /* actually fill the graph object */+    IGRAPH_CHECK(igraph_create(graph, &edges, nbNodes, 0)); -    // an clear remaining things+    /* clean remaining things */     igraph_vector_destroy(&edges);     IGRAPH_FINALLY_CLEAN(1); -    return retval;+    return IGRAPH_SUCCESS; }  @@ -4318,8 +4343,11 @@  * graphs, at least one of k and the number of vertices must be even.  *  * </para><para>- * The game simply uses \ref igraph_degree_sequence_game with appropriately- * constructed degree sequences.+ * Currently, this game simply uses \ref igraph_degree_sequence_game with + * the \c SIMPLE_NO_MULTIPLE method and appropriately constructed degree sequences.+ * Thefore, it does not sample uniformly: while it can generate all k-regular graphs+ * with the given number of vertices, it does not generate each one with the same+ * probability.  *  * \param graph        Pointer to an uninitialized graph object.  * \param no_of_nodes  The number of nodes in the generated graph.@@ -4744,7 +4772,7 @@  * \brief Generates a random tree with the given number of nodes  *  * This function samples uniformly from the set of labelled trees,- * i.e. it can generate each labelled tree with the same probability.+ * i.e. it generates each labelled tree with the same probability.  *  * \param graph Pointer to an uninitialized graph object.  * \param n The number of nodes in the tree.@@ -4752,7 +4780,7 @@  * \param method The algorithm to use to generate the tree. Possible values:  *        \clist  *        \cli IGRAPH_RANDOM_TREE_PRUFER- *          This algorithm samples Pr&uuml;fer sequences unformly, then converts them to trees.+ *          This algorithm samples Pr&uuml;fer sequences uniformly, then converts them to trees.  *          Directed trees are not currently supported.  *        \cli IGRAPH_RANDOM_LERW  *          This algorithm effectively performs a loop-erased random walk on the complete graph
igraph/src/gengraph_box_list.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -24,7 +24,7 @@ namespace gengraph {  void box_list::insert(int v) {-    register int d = deg[v];+    int d = deg[v];     if (d < 1) {         return;     }@@ -41,10 +41,10 @@ }  void box_list::pop(int v) {-    register int p = prev[v];-    register int n = next[v];+    int p = prev[v];+    int n = next[v];     if (p < 0) {-        register int d = deg[v];+        int d = deg[v];         assert(list[d - 1] == v);         list[d - 1] = n;         if (d == dmax && n < 0) do {@@ -90,13 +90,13 @@     int *w = neigh[v];     while (k--) {         int v2 = *(w++);-        register int *w2 = neigh[v2];+        int *w2 = neigh[v2];         while (*w2 != v) {             w2++;         }-        register int *w3 = neigh[v2] + (deg[v2] - 1);+        int *w3 = neigh[v2] + (deg[v2] - 1);         assert(w2 <= w3);-        register int tmp = *w3;+        int tmp = *w3;         *w3 = *w2;         *w2 = tmp;         pop(v2);
igraph/src/gengraph_degree_sequence.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,
igraph/src/gengraph_graph_molloy_hash.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -132,7 +132,7 @@     int *p = hc + 2 + n;     int *l = links;     for (int i = 0; i < n; i++) for (int j = HASH_SIZE(deg[i]); j--; l++) {-            register int d;+            int d;             if ((d = *l) != HASH_NONE && d >= i) {                 *(p++) = d;             }@@ -1168,6 +1168,6 @@ }  //___________________________________________________________________________________-//*/+*/  } // namespace gengraph
igraph/src/gengraph_graph_molloy_optimized.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -34,9 +34,6 @@ #include "igraph_statusbar.h" #include "igraph_progress.h" -#ifndef register-    #define register-#endif  using namespace std; @@ -1051,7 +1048,7 @@             int dv = deg[v];             double f = target[v] / paths[v];             // pick ALL fathers-            register int father;+            int father;             for (int k = 0; k < dv; k++) if (dist[father = ww[k]] == pd) {                     // increase target[] of father                     target[father] += paths[father] * f;@@ -2081,7 +2078,7 @@   //___________________________________________________________________________________-//*/+*/   @@ -2216,6 +2213,6 @@   return b; } -//*/+*/  } // namespace gengraph
igraph/src/gengraph_mr-connected.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -28,16 +28,18 @@ #include "igraph_types.h" #include "igraph_error.h" +#include "igraph_handle_exceptions.h"+ namespace gengraph {  // return negative number if program should exit int parse_options(int &argc, char** &argv);  // options-static const bool MONITOR_TIME = false;+// static const bool MONITOR_TIME = false; static const int  SHUFFLE_TYPE = FINAL_HEURISTICS;-static const bool RAW_DEGREES  = false;-static const FILE *Fdeg = stdin;+// static const bool RAW_DEGREES  = false;+// static const FILE *Fdeg = stdin;  //_________________________________________________________________________ // int main(int argc, char** argv) {@@ -137,48 +139,50 @@     int igraph_degree_sequence_game_vl(igraph_t *graph,                                        const igraph_vector_t *out_seq,                                        const igraph_vector_t *in_seq) {-        long int sum = igraph_vector_sum(out_seq);-        if (sum % 2 != 0) {-            IGRAPH_ERROR("Sum of degrees should be even", IGRAPH_EINVAL);-        }+        IGRAPH_HANDLE_EXCEPTIONS(+            long int sum = igraph_vector_sum(out_seq);+            if (sum % 2 != 0) {+                IGRAPH_ERROR("Sum of degrees should be even", IGRAPH_EINVAL);+            } -        RNG_BEGIN();+            RNG_BEGIN(); -        if (in_seq && igraph_vector_size(in_seq) != 0) {-            RNG_END();-            IGRAPH_ERROR("This generator works with undirected graphs only", IGRAPH_EINVAL);-        }+            if (in_seq && igraph_vector_size(in_seq) != 0) {+                RNG_END();+                IGRAPH_ERROR("This generator works with undirected graphs only", IGRAPH_EINVAL);+            } -        degree_sequence *dd = new degree_sequence(out_seq);+            degree_sequence *dd = new degree_sequence(out_seq); -        graph_molloy_opt *g = new graph_molloy_opt(*dd);-        delete dd;+            graph_molloy_opt *g = new graph_molloy_opt(*dd);+            delete dd; -        if (!g->havelhakimi()) {-            delete g;-            RNG_END();-            IGRAPH_ERROR("Cannot realize the given degree sequence as an undirected, simple graph",-                         IGRAPH_EINVAL);-        }+            if (!g->havelhakimi()) {+                delete g;+                RNG_END();+                IGRAPH_ERROR("Cannot realize the given degree sequence as an undirected, simple graph",+                             IGRAPH_EINVAL);+            } -        if (!g->make_connected()) {-            delete g;-            RNG_END();-            IGRAPH_ERROR("Cannot make a connected graph from the given degree sequence",-                         IGRAPH_EINVAL);-        }+            if (!g->make_connected()) {+                delete g;+                RNG_END();+                IGRAPH_ERROR("Cannot make a connected graph from the given degree sequence",+                             IGRAPH_EINVAL);+            } -        int *hc = g->hard_copy();-        delete g;-        graph_molloy_hash *gh = new graph_molloy_hash(hc);-        delete [] hc;+            int *hc = g->hard_copy();+            delete g;+            graph_molloy_hash *gh = new graph_molloy_hash(hc);+            delete [] hc; -        gh->shuffle(5 * gh->nbarcs(), 100 * gh->nbarcs(), SHUFFLE_TYPE);+            gh->shuffle(5 * gh->nbarcs(), 100 * gh->nbarcs(), SHUFFLE_TYPE); -        IGRAPH_CHECK(gh->print(graph));-        delete gh;+            IGRAPH_CHECK(gh->print(graph));+            delete gh; -        RNG_END();+            RNG_END();+        );          return 0;     }
igraph/src/gengraph_powerlaw.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,
igraph/src/gengraph_random.cpp view
@@ -7,7 +7,7 @@  *  * This program is free software: you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation, either version 3 of the License, or+ * the Free Software Foundation, either version 2 of the License, or  * (at your option) any later version.  *  * This program is distributed in the hope that it will be useful,@@ -28,8 +28,8 @@ // See the header file random.h for a description of the contents of this // file as well as references and credits. -#include <cmath> #include "gengraph_random.h"+#include <cmath>  using namespace std; using namespace KW_RNG;
igraph/src/glet.c view
@@ -75,7 +75,7 @@     int nc; } igraph_i_subclique_next_free_t; -void igraph_i_subclique_next_free(void *ptr) {+static void igraph_i_subclique_next_free(void *ptr) {     igraph_i_subclique_next_free_t *data = ptr;     int i;     if (data->resultids) {@@ -123,15 +123,15 @@  *  */ -int igraph_i_subclique_next(const igraph_t *graph,-                            const igraph_vector_t *weights,-                            const igraph_vector_int_t *ids,-                            const igraph_vector_ptr_t *cliques,-                            igraph_t **result,-                            igraph_vector_t **resultweights,-                            igraph_vector_int_t **resultids,-                            igraph_vector_t *clique_thr,-                            igraph_vector_t *next_thr) {+static int igraph_i_subclique_next(const igraph_t *graph,+                                   const igraph_vector_t *weights,+                                   const igraph_vector_int_t *ids,+                                   const igraph_vector_ptr_t *cliques,+                                   igraph_t **result,+                                   igraph_vector_t **resultweights,+                                   igraph_vector_int_t **resultids,+                                   igraph_vector_t *clique_thr,+                                   igraph_vector_t *next_thr) {      /* The input is a set of cliques, that were found at a previous level.        For each clique, we calculate the next threshold, drop the isolate@@ -173,9 +173,9 @@     igraph_vector_init(&newedges, 100);     IGRAPH_FINALLY(igraph_vector_destroy, &newedges);     igraph_vector_int_init(&mark, no_of_nodes);-    IGRAPH_FINALLY(igraph_vector_destroy, &mark);+    IGRAPH_FINALLY(igraph_vector_int_destroy, &mark);     igraph_vector_int_init(&map, no_of_nodes);-    IGRAPH_FINALLY(igraph_vector_destroy, &map);+    IGRAPH_FINALLY(igraph_vector_int_destroy, &map);     igraph_vector_int_init(&edges, 100);     IGRAPH_FINALLY(igraph_vector_int_destroy, &edges);     igraph_vector_init(&neis, 10);@@ -294,7 +294,7 @@     return 0; } -void igraph_i_graphlets_destroy_vectorlist(igraph_vector_ptr_t *vl) {+static void igraph_i_graphlets_destroy_vectorlist(igraph_vector_ptr_t *vl) {     int i, n = igraph_vector_ptr_size(vl);     for (i = 0; i < n; i++) {         igraph_vector_t *v = (igraph_vector_t*) VECTOR(*vl)[i];@@ -305,12 +305,12 @@     igraph_vector_ptr_destroy(vl); } -int igraph_i_graphlets(const igraph_t *graph,-                       const igraph_vector_t *weights,-                       igraph_vector_ptr_t *cliques,-                       igraph_vector_t *thresholds,-                       const igraph_vector_int_t *ids,-                       igraph_real_t startthr) {+static int igraph_i_graphlets(const igraph_t *graph,+                              const igraph_vector_t *weights,+                              igraph_vector_ptr_t *cliques,+                              igraph_vector_t *thresholds,+                              const igraph_vector_int_t *ids,+                              igraph_real_t startthr) {      /* This version is different from the main function, and is        appropriate to use in recursive calls, because it _adds_ the@@ -401,7 +401,7 @@     const igraph_vector_t *thresholds; } igraph_i_graphlets_filter_t; -int igraph_i_graphlets_filter_cmp(void *data, const void *a, const void *b) {+static int igraph_i_graphlets_filter_cmp(void *data, const void *a, const void *b) {     igraph_i_graphlets_filter_t *ddata = (igraph_i_graphlets_filter_t *) data;     int *aa = (int*) a;     int *bb = (int*) b;@@ -430,8 +430,8 @@     } } -int igraph_i_graphlets_filter(igraph_vector_ptr_t *cliques,-                              igraph_vector_t *thresholds) {+static int igraph_i_graphlets_filter(igraph_vector_ptr_t *cliques,+                                     igraph_vector_t *thresholds) {      /* Filter out non-maximal cliques. Every non-maximal clique is        part of a maximal clique, at the same threshold.@@ -583,6 +583,7 @@     return 0; } +/* TODO: not made static because it is used by the R interface */ int igraph_i_graphlets_project(const igraph_t *graph,                                const igraph_vector_t *weights,                                const igraph_vector_ptr_t *cliques,@@ -794,7 +795,7 @@     const igraph_vector_t *Mu; } igraph_i_graphlets_order_t; -int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b) {+static int igraph_i_graphlets_order_cmp(void *data, const void *a, const void *b) {     igraph_i_graphlets_order_t *ddata = (igraph_i_graphlets_order_t*) data;     int *aa = (int*) a;     int *bb = (int*) b;
igraph/src/glpk_support.c view
@@ -30,7 +30,6 @@ #include "igraph_error.h" #include "igraph_interrupt_internal.h" #include <glpk.h>-#include <memory.h> #include <stdio.h>  void igraph_i_glpk_interruption_hook(glp_tree *tree, void *info) {
igraph/src/graph.cc view
@@ -1,4 +1,5 @@-#include <cstdio>++// #include <cstdio> #include <cassert> #include <climits> #include <set>@@ -15,11 +16,6 @@ #include <ciso646> #endif -#ifdef USING_R-#undef stdout-#define stdout NULL-#endif- /*   Copyright (c) 2003-2015 Tommi Junttila   Released under the GNU Lesser General Public License version 3.@@ -62,6 +58,7 @@   first_path_automorphism = 0;   best_path_automorphism = 0;   in_search = false;+  refine_equal_to_first = false;    /* Default value for using "long prune" */   opt_use_long_prune = true;@@ -72,7 +69,7 @@     verbose_level = 0;-  verbstr = stdout;+  // verbstr = stdout;    report_hook = 0;   report_user_param = 0;@@ -115,7 +112,7 @@ void AbstractGraph::set_verbose_file(FILE* const fp) {-  verbstr = fp;+  // verbstr = fp; }  @@ -811,6 +808,7 @@     root.in_best_path = false;     root.cmp_to_best_path = 0;     root.long_prune_begin = 0;+    root.needs_long_prune = false;      root.failure_recording_ival = 0; @@ -1034,15 +1032,6 @@ 		 */ 		if(index == cell->length and all_same_level == current_level+1) 		  all_same_level = current_level;-		if(verbstr and verbose_level >= 2) {-		  fprintf(verbstr,-			  "Level %u: orbits=%u, index=%u/%u, all_same_level=%u\n",-			  current_level,-			  first_path_orbits.nof_orbits(),-			  index, cell->length,-			  all_same_level);-		  fflush(verbstr);-		} 	      } 	    continue; 	  }@@ -2080,6 +2069,7 @@  *-------------------------------------------------------------------------*/  +#if 0 void Digraph::write_dot(const char* const filename) {@@ -2116,6 +2106,7 @@    fprintf(fp, "}\n"); }+#endif   void@@ -2185,6 +2176,7 @@  *  *-------------------------------------------------------------------------*/ +#if 0 Digraph* Digraph::read_dimacs(FILE* const fp, FILE* const errstr) {@@ -2341,11 +2333,11 @@     delete g;   return 0; }--+#endif   +#if 0 void Digraph::write_dimacs(FILE* const fp) {@@ -2387,7 +2379,7 @@ 	}     } }-+#endif   @@ -3688,12 +3680,6 @@       cr_component_elements += cell->length;     } -  if(verbstr and verbose_level > 2) {-    fprintf(verbstr, "NU-component with %lu cells and %u vertices\n",-	    (long unsigned)cr_component.size(), cr_component_elements);-    fflush(verbstr);-  }-   return true; } @@ -3889,12 +3875,6 @@       component_elements += cell->length;     } -  if(verbstr and verbose_level > 2) {-    fprintf(verbstr, "NU-component with %lu cells and %u vertices\n",-	    (long unsigned)component.size(), component_elements);-    fflush(verbstr);-  }-   return true; } @@ -4034,6 +4014,7 @@  *  *-------------------------------------------------------------------------*/ +#if 0 Graph* Graph::read_dimacs(FILE* const fp, FILE* const errstr) {@@ -4249,7 +4230,7 @@ 	}     } }-+#endif   void@@ -4370,6 +4351,7 @@  *-------------------------------------------------------------------------*/  +#if 0 void Graph::write_dot(const char* const filename) {@@ -4407,8 +4389,7 @@    fprintf(fp, "}\n"); }--+#endif   @@ -5430,12 +5411,6 @@       cr_component_elements += cell->length;     } -  if(verbstr and verbose_level > 2) {-    fprintf(verbstr, "NU-component with %lu cells and %u vertices\n",-	    (long unsigned)cr_component.size(), cr_component_elements);-    fflush(verbstr);-  }-   return true; } @@ -5593,12 +5568,6 @@       component.push_back(cell->first);       component_elements += cell->length;     }--  if(verbstr and verbose_level > 2) {-    fprintf(verbstr, "NU-component with %lu cells and %u vertices\n",-	    (long unsigned)component.size(), component_elements);-    fflush(verbstr);-  }    return true; }
igraph/src/gss.c view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -151,4 +151,3 @@      return successful ? PLFIT_SUCCESS : PLFIT_FAILURE; }-
igraph/src/heap.c view
@@ -24,10 +24,9 @@ #include "igraph_types.h" #include "igraph_types_internal.h" #include "igraph_memory.h"-#include "igraph_random.h" #include "igraph_error.h"-#include "config.h" #include "igraph_math.h"+#include "config.h"  #include <assert.h> #include <string.h>         /* memcpy & co. */@@ -289,12 +288,12 @@     if (tmp1 == 0) {         IGRAPH_ERROR("indheap reserve failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp1);   /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, tmp1);     tmp2 = igraph_Calloc(size, long int);     if (tmp2 == 0) {         IGRAPH_ERROR("indheap reserve failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp2);+    IGRAPH_FINALLY(igraph_free, tmp2);     memcpy(tmp1, h->stor_begin, (size_t) actual_size * sizeof(igraph_real_t));     memcpy(tmp2, h->index_begin, (size_t) actual_size * sizeof(long int));     igraph_Free(h->stor_begin);@@ -575,17 +574,17 @@     if (tmp1 == 0) {         IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp1);   /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, tmp1);     tmp2 = igraph_Calloc(size, long int);     if (tmp2 == 0) {         IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp2);   /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, tmp2);     tmp3 = igraph_Calloc(size, long int);     if (tmp3 == 0) {         IGRAPH_ERROR("d_indheap reserve failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp3);   /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, tmp3);      memcpy(tmp1, h->stor_begin, (size_t) actual_size * sizeof(igraph_real_t));     memcpy(tmp2, h->index_begin, (size_t) actual_size * sizeof(long int));
+ igraph/src/hzeta.c view
@@ -0,0 +1,651 @@+/* vim:set ts=4 sw=2 sts=2 et: */++/* This file was imported from a private scientific library+ * based on GSL coined Home Scientific Libray (HSL) by its author+ * Jerome Benoit; this very material is itself inspired from the+ * material written by G. Jungan and distributed by GSL.+ * Ultimately, some modifications were done in order to render the+ * imported material independent from the rest of GSL.+ */++/* `hsl/specfunc/hzeta.c' C source file+// HSL - Home Scientific Library+// Copyright (C) 2017-2018  Jerome Benoit+//+// HSL is free software; you can redistribute it and/or+// modify it under the terms of the GNU General Public License+// as published by the Free Software Foundation; either version 2+// of the License, or (at your option) any later version.+//+// This program is distributed in the hope that it will be useful,+// but WITHOUT ANY WARRANTY; without even the implied warranty of+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+// GNU General Public License for more details.+//+// You should have received a copy of the GNU General Public License+// along with this program; if not, write to the Free Software+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.+*/++/*+// The material in this file is mainly inspired by the material written by+// G. Jungan and distributed under GPLv2 by the GNU Scientific Library (GSL)+// ( https://www.gnu.org/software/gsl/ [specfunc/zeta.c]), itself inspired by+// the material written by Moshier and distributed in the Cephes Mathematical+// Library ( http://www.moshier.net/ [zeta.c]).+//+// More specifically, hsl_sf_hzeta_e is a slightly modifed clone of+// gsl_sf_hzeta_e as found in GSL 2.4; the remaining is `inspired by'.+// [Sooner or later a _Working_Note_ may be deposited at ResearchGate+// ( https://www.researchgate.net/profile/Jerome_Benoit )]+*/++/* Author:  Jerome G. Benoit < jgmbenoit _at_ rezozer _dot_ net > */++#ifdef _MSC_VER+#define _USE_MATH_DEFINES+#endif++#include <math.h>+#include <stdio.h>+#include "hzeta.h"+#include "error.h"+#include "platform.h"++/* imported from gsl_machine.h */++#define GSL_LOG_DBL_MIN (-7.0839641853226408e+02)+#define GSL_LOG_DBL_MAX 7.0978271289338397e+02+#define GSL_DBL_EPSILON 2.2204460492503131e-16++/* imported from gsl_math.h */++#ifndef M_LOG2E+#define M_LOG2E    1.44269504088896340735992468100      /* log_2 (e) */+#endif++/* imported from gsl_sf_result.h */++struct gsl_sf_result_struct {+  double val;+  double err;+};+typedef struct gsl_sf_result_struct gsl_sf_result;++/* imported and adapted from hsl/specfunc/specfunc_def.h */++#define HSL_SF_EVAL_RESULT(FnE) \+	gsl_sf_result result; \+	FnE ; \+	return (result.val);++#define HSL_SF_EVAL_TUPLE_RESULT(FnET) \+	gsl_sf_result result0; \+	gsl_sf_result result1; \+	FnET ; \+	*tuple1=result1.val; \+	*tuple0=result0.val; \+	return (result0.val);++/* */+++#define HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT 10+#define HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER 32++#define HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX 256++// B_{2j}/(2j)+static+double hsl_sf_hzeta_eulermaclaurin_series_coeffs[HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={+	+1.0,+	+1.0/12.0,+	-1.0/720.0,+	+1.0/30240.0,+	-1.0/1209600.0,+	+1.0/47900160.0,+	-691.0/1307674368000.0,+	+1.0/74724249600.0,+	-3.38968029632258286683019539125e-13,+	+8.58606205627784456413590545043e-15,+	-2.17486869855806187304151642387e-16,+	+5.50900282836022951520265260890e-18,+	-1.39544646858125233407076862641e-19,+	+3.53470703962946747169322997780e-21,+	-8.95351742703754685040261131811e-23,+	+2.26795245233768306031095073887e-24,+	-5.74479066887220244526388198761e-26,+	+1.45517247561486490186626486727e-27,+	-3.68599494066531017818178247991e-29,+	+9.33673425709504467203255515279e-31,+	-2.36502241570062993455963519637e-32,+	+5.99067176248213430465991239682e-34,+	-1.51745488446829026171081313586e-35,+	+3.84375812545418823222944529099e-37,+	-9.73635307264669103526762127925e-39,+	+2.46624704420068095710640028029e-40,+	-6.24707674182074369314875679472e-42,+	+1.58240302446449142975108170683e-43,+	-4.00827368594893596853001219052e-45,+	+1.01530758555695563116307139454e-46,+	-2.57180415824187174992481940976e-48,+	+6.51445603523381493155843485864e-50,+	-1.65013099068965245550609878048e-51+	}; // hsl_sf_hzeta_eulermaclaurin_series_coeffs++// 4\zeta(2j)/(2\pi)^(2j)+static+double hsl_sf_hzeta_eulermaclaurin_series_majorantratios[HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={+	-2.0,+	+1.0/6.0,+	+1.0/360.0,+	+1.0/15120.0,+	+1.0/604800.0,+	+1.0/23950080.0,+	+691.0/653837184000.0,+	+1.0/37362124800.0,+	+3617.0/5335311421440000.0,+	+1.71721241125556891282718109009e-14,+	+4.34973739711612374608303284773e-16,+	+1.10180056567204590304053052178e-17,+	+2.79089293716250466814153725281e-19,+	+7.06941407925893494338645995561e-21,+	+1.79070348540750937008052226362e-22,+	+4.53590490467536612062190147774e-24,+	+1.14895813377444048905277639752e-25,+	+2.91034495122972980373252973454e-27,+	+7.37198988133062035636356495982e-29,+	+1.86734685141900893440651103056e-30,+	+4.73004483140125986911927039274e-32,+	+1.19813435249642686093198247936e-33,+	+3.03490976893658052342162627173e-35,+	+7.68751625090837646445889058198e-37,+	+1.94727061452933820705352425585e-38,+	+4.93249408840136191421280056051e-40,+	+1.24941534836414873862975135893e-41,+	+3.16480604892898285950216341362e-43,+	+8.01654737189787193706002438098e-45,+	+2.03061517111391126232614278906e-46,+	+5.14360831648374349984963881946e-48,+	+1.30289120704676298631168697172e-49,+	+3.30026198137930491101219756091e-51+	}; // hsl_sf_hzeta_eulermaclaurin_series_majorantratios+++extern+int hsl_sf_hzeta_e(const double s, const double q, gsl_sf_result * result) {++	/* CHECK_POINTER(result) */++	if ((s <= 1.0) || (q <= 0.0)) {+		PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL);+		}+	else {+		const double max_bits=54.0; // max_bits=\lceil{s}\rceil with \zeta(s,2)=\zeta(s)-1=GSL_DBL_EPSILON+		const double ln_term0=-s*log(q);+		if (ln_term0 < GSL_LOG_DBL_MIN+1.0) {+			PLFIT_ERROR("underflow", PLFIT_UNDRFLOW);+			}+		else if (GSL_LOG_DBL_MAX-1.0 < ln_term0) {+			PLFIT_ERROR("overflow", PLFIT_OVERFLOW);+			}+#if 1+		else if (((max_bits < s) && (q < 1.0)) || ((0.5*max_bits < s) && (q < 0.25))) {+			result->val=pow(q,-s);+			result->err=2.0*GSL_DBL_EPSILON*fabs(result->val);+			return (PLFIT_SUCCESS);+			}+		else if ((0.5*max_bits < s) && (q < 1.0)) {+			const double a0=pow(q,-s);+			const double p1=pow(q/(1.0+q),s);+			const double p2=pow(q/(2.0+q),s);+			const double ans=a0*(1.0+p1+p2);+			result->val=ans;+			result->err=GSL_DBL_EPSILON*(2.0+0.5*s)*fabs(result->val);+			return (PLFIT_SUCCESS);+			}+#endif+		else { // Euler-Maclaurin summation formula+			const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q;+			const double inv_qshift=1.0/qshift;+			const double sqr_inv_qshift=inv_qshift*inv_qshift;+			const double inv_sm1=1.0/(s-1.0);+			const double pmax=pow(qshift,-s);+			double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN};+			double delta=NAN;+			double tscp=s;+			double scp=tscp;+			double pcp=pmax*inv_qshift;+			double ratio=scp*pcp;+			size_t n=0;+			size_t j=0;+			double ans=0.0;+			double mjr=NAN;++			for(j=0;j<HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT;++j) ans+=(terms[n++]=pow(j+q,-s));+			ans+=(terms[n++]=0.5*pmax);+			ans+=(terms[n++]=pmax*qshift*inv_sm1);+			for(j=1;j<=HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER;++j) {+				delta=hsl_sf_hzeta_eulermaclaurin_series_coeffs[j]*ratio;+				ans+=(terms[n++]=delta);+				scp*=++tscp;+				scp*=++tscp;+				pcp*=sqr_inv_qshift;+				ratio=scp*pcp;+				if ((fabs(delta/ans)) < (0.5*GSL_DBL_EPSILON)) break;+				}++			ans=0.0; while (n) ans+=terms[--n];+			mjr=hsl_sf_hzeta_eulermaclaurin_series_majorantratios[j]*ratio;++			result->val=+ans;+			result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr);+			return (PLFIT_SUCCESS);+			}+		}++	return (PLFIT_SUCCESS); }++extern+double hsl_sf_hzeta(const double s, const double q) {+	HSL_SF_EVAL_RESULT(hsl_sf_hzeta_e(s,q,&result)); }++extern+int hsl_sf_hzeta_deriv_e(const double s, const double q, gsl_sf_result * result) {++	/* CHECK_POINTER(result) */++	if ((s <= 1.0) || (q <= 0.0)) {+		PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL);+		}+	else {+		const double ln_hz_term0=-s*log(q);+		if (ln_hz_term0 < GSL_LOG_DBL_MIN+1.0) {+			PLFIT_ERROR("underflow", PLFIT_UNDRFLOW);+			}+		else if (GSL_LOG_DBL_MAX-1.0 < ln_hz_term0) {+			PLFIT_ERROR("overflow", PLFIT_OVERFLOW);+			}+		else { // Euler-Maclaurin summation formula+			const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q;+			const double inv_qshift=1.0/qshift;+			const double sqr_inv_qshift=inv_qshift*inv_qshift;+			const double inv_sm1=1.0/(s-1.0);+			const double pmax=pow(qshift,-s);+			const double lmax=log(qshift);+			double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN};+			double delta=NAN;+			double tscp=s;+			double scp=tscp;+			double pcp=pmax*inv_qshift;+			double lcp=lmax-1.0/s;+			double ratio=scp*pcp*lcp;+			double qs=NAN;+			size_t n=0;+			size_t j=0;+			double ans=0.0;+			double mjr=NAN;++			for(j=0,qs=q;j<HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT;++qs,++j) ans+=(terms[n++]=log(qs)*pow(qs,-s));+			ans+=(terms[n++]=0.5*lmax*pmax);+			ans+=(terms[n++]=pmax*qshift*inv_sm1*(lmax+inv_sm1));+			for(j=1;j<=HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER;++j) {+				delta=hsl_sf_hzeta_eulermaclaurin_series_coeffs[j]*ratio;+				ans+=(terms[n++]=delta);+				scp*=++tscp; lcp-=1.0/tscp;+				scp*=++tscp; lcp-=1.0/tscp;+				pcp*=sqr_inv_qshift;+				ratio=scp*pcp*lcp;+				if ((fabs(delta/ans)) < (0.5*GSL_DBL_EPSILON)) break;+				}++			ans=0.0; while (n) ans+=terms[--n];+			mjr=hsl_sf_hzeta_eulermaclaurin_series_majorantratios[j]*ratio;++			result->val=-ans;+			result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr);+			return (PLFIT_SUCCESS);+			}+		}++	return (PLFIT_SUCCESS); }++extern+double hsl_sf_hzeta_deriv(const double s, const double q) {+	HSL_SF_EVAL_RESULT(hsl_sf_hzeta_deriv_e(s,q,&result)); }++extern+int hsl_sf_hzeta_deriv2_e(const double s, const double q, gsl_sf_result * result) {++	/* CHECK_POINTER(result) */++	if ((s <= 1.0) || (q <= 0.0)) {+		PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL);+		}+	else {+		const double ln_hz_term0=-s*log(q);+		if (ln_hz_term0 < GSL_LOG_DBL_MIN+1.0) {+			PLFIT_ERROR("underflow", PLFIT_UNDRFLOW);+			}+		else if (GSL_LOG_DBL_MAX-1.0 < ln_hz_term0) {+			PLFIT_ERROR("overflow", PLFIT_OVERFLOW);+			}+		else { // Euler-Maclaurin summation formula+			const double qshift=HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+q;+			const double inv_qshift=1.0/qshift;+			const double sqr_inv_qshift=inv_qshift*inv_qshift;+			const double inv_sm1=1.0/(s-1.0);+			const double pmax=pow(qshift,-s);+			const double lmax=log(qshift);+			const double lmax_p_inv_sm1=lmax+inv_sm1;+			const double sqr_inv_sm1=inv_sm1*inv_sm1;+			const double sqr_lmax=lmax*lmax;+			const double sqr_lmax_p_inv_sm1=lmax_p_inv_sm1*lmax_p_inv_sm1;+			double terms[HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN};+			double delta=NAN;+			double tscp=s;+			double slcp=NAN;+			double plcp=NAN;+			double scp=tscp;+			double pcp=pmax*inv_qshift;+			double lcp=1.0/s-lmax;+			double sqr_lcp=lmax*(lmax-2.0/s);+			double ratio=scp*pcp*sqr_lcp;+			double qs=NAN;+			double lqs=NAN;+			size_t n=0;+			size_t j=0;+			double ans=0.0;+			double mjr=NAN;++			for(j=0,qs=q;j<HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT;++qs,++j) {+				lqs=log(qs);+				ans+=(terms[n++]=lqs*lqs*pow(qs,-s));+				}+			ans+=(terms[n++]=0.5*sqr_lmax*pmax);+			ans+=(terms[n++]=pmax*qshift*inv_sm1*(sqr_lmax_p_inv_sm1+sqr_inv_sm1));+			for(j=1;j<=HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER;++j) {+				delta=hsl_sf_hzeta_eulermaclaurin_series_coeffs[j]*ratio;+				ans+=(terms[n++]=delta);+				scp*=++tscp; slcp=plcp=1.0/tscp;+				scp*=++tscp; slcp+=1.0/tscp; plcp/=tscp;+				pcp*=sqr_inv_qshift;+				sqr_lcp+=2.0*(plcp+slcp*lcp);+				ratio=scp*pcp*sqr_lcp;+				if ((fabs(delta/ans)) < (0.5*GSL_DBL_EPSILON)) break;+				lcp+=slcp;+				}++			ans=0.0; while (n) ans+=terms[--n];+			mjr=hsl_sf_hzeta_eulermaclaurin_series_majorantratios[j]*ratio;++			result->val=+ans;+			result->err=2.0*((HSL_SF_HZETA_EULERMACLAURIN_SERIES_SHIFT+1.0)*GSL_DBL_EPSILON*fabs(ans)+mjr);+			return (PLFIT_SUCCESS);+			}+		}++	return (PLFIT_SUCCESS); }++extern+double hsl_sf_hzeta_deriv2(const double s, const double q) {+	HSL_SF_EVAL_RESULT(hsl_sf_hzeta_deriv2_e(s,q,&result)); }++static inline+double hsl_sf_hZeta0_zed(const double s, const double q) {+#if 1+	const long double ld_q=(long double)(q);+	const long double ld_s=(long double)(s);+	const long double ld_log1prq=log1pl(1.0L/ld_q);+	const long double ld_epsilon=expm1l(-ld_s*ld_log1prq);+	const long double ld_z=ld_s+(ld_q+0.5L*ld_s+0.5L)*ld_epsilon;+	const double z=(double)(ld_z);+#else+	double z=s+(q+0.5*s+0.5)*expm1(-s*log1p(1.0/q));+#endif+	return (z); }++// Z_{0}(s,a) = a^s \left(\frac{1}{2}+\frac{a}{s-1}\right)^{-1} \zeta(s,a) - 1+// Z_{0}(s,a) = O\left(\frac{(s-1)s}{6a^{2}}\right)+static+int hsl_sf_hZeta0(const double s, const double q, double * value, double * abserror) {+	const double criterion=ceil(10.0*s-q);+	const size_t shift=(criterion<0.0)?0:+		(criterion<HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX)?(size_t)(llrint(criterion)):+			HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX;+	const double qshift=(double)(shift)+q;+	const double inv_qshift=1.0/qshift;+	const double sqr_inv_qshift=inv_qshift*inv_qshift;+	const double sm1=s-1.0;+	double terms[HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN};+	double delta=NAN;+	double tscp=s;+	double scp=s*sm1;+	double pcp=inv_qshift/(2.0*qshift+sm1);+	double ratio=NAN;+	size_t n=0;+	size_t j=0;+	double ans=0.0;+	double mjr=NAN;++	if (shift) {+		const double hsm1=0.5*sm1;+		const double inv_q=1.0/q;+		const double qphsm1=q+hsm1;+		const double inv_qphsm1=1.0/qphsm1;+		const double qshiftphsm1=qshift+hsm1;+		double qs=q;+		double a=1.0;+		for(j=0;j<shift;) {+			ans+=(terms[n++]=a*hsl_sf_hZeta0_zed(s,qs++)*inv_qphsm1);+			a=exp(-s*log1p((++j)*inv_q));+			}+		pcp*=a*qshiftphsm1*inv_qphsm1;+		}+	ratio=scp*pcp;+	ans+=terms[n++]=ratio/6.0;+	scp*=++tscp;+	scp*=++tscp;+	pcp*=2.0*sqr_inv_qshift;+	ratio=scp*pcp;+	for(j=2;j<=HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER;++j) {+		delta=hsl_sf_hzeta_eulermaclaurin_series_coeffs[j]*ratio;+		ans+=(terms[n++]=delta);+		scp*=++tscp;+		scp*=++tscp;+		pcp*=sqr_inv_qshift;+		ratio=scp*pcp;+		if ((fabs(delta/ans)) < (0.5*GSL_DBL_EPSILON)) break;+		}++	ans=0.0; while (n) ans+=terms[--n];+	mjr=hsl_sf_hzeta_eulermaclaurin_series_majorantratios[j]*ratio;++	*value=ans;+	*abserror=2.0*((shift+1)*GSL_DBL_EPSILON*fabs(ans)+mjr);++	return (PLFIT_SUCCESS); }++static inline+double hsl_sf_hZeta1_zed(const double s, const double q) {+#if 1+	const long double ld_q=(long double)(q);+	const long double ld_s=(long double)(s);+	const long double ld_sm1=ld_s-1.0L;+	const long double ld_logq=logl(ld_q);+	const long double ld_log1prq=log1pl(1.0L/ld_q);+	const long double ld_inv_logq=1.0L/ld_logq;+	const long double ld_logratiom1=ld_log1prq*ld_inv_logq;+	const long double ld_powratiom1=expm1l(-ld_s*ld_log1prq);+	const long double ld_varepsilon=expm1l(-ld_sm1*ld_log1prq);+	const long double ld_epsilon=ld_logratiom1+ld_powratiom1+ld_logratiom1*ld_powratiom1;+	const long double ld_z=ld_s+(ld_q+0.5L*ld_s+0.5L)*ld_epsilon+ld_q/ld_sm1*ld_inv_logq*ld_varepsilon;+	const double z=(double)(ld_z);+#else+	const double sm1=s-1.0;+	const double inv_ln_q=1.0/log(q);+	const double log1prq=log1p(1.0/q);+	const double logratiom1=log1prq*inv_ln_q;+	const double powratiom1=expm1(-s*log1prq);+	const double epsilon=logratiom1+powratiom1+logratiom1*powratiom1;+	const double z=s+(q+0.5*s+0.5)*epsilon+q/sm1*inv_ln_q*expm1(-sm1*log1prq);+#endif+	return (z); }++// Z_{1}(s,a) = -\frac{a^s}{\ln(a)} \left(\frac{1}{2}+\frac{a}{s-1}\,\left[1+\frac{1}{(s-1)\,\ln(a)}\right]\right)^{-1} \zeta^{\prime}(s,a) - 1+// Z_{1}(s,a) = O\left(\frac{(s-1)s}{6a^{2}}\right)+static+int hsl_sf_hZeta1(const double s, const double q, const double ln_q, double * value, double * abserror, double * coeff1) {+	const double criterion=ceil(10.0*s-q);+	const size_t shift=(criterion<0.0)?0:+		(criterion<HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX)?(size_t)(llrint(criterion)):+			HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX;+	const double qshift=(double)(shift)+q;+	const double ln_qshift=log(qshift);+	const double inv_qshift=1.0/qshift;+	const double inv_ln_q=1.0/ln_q;+	const double inv_ln_qshift=1.0/ln_qshift;+	const double sqr_inv_qshift=inv_qshift*inv_qshift;+	const double sm1=s-1.0;+	const double hsm1=0.5*sm1;+	const double q_over_ln_q=q*inv_ln_q;+	const double qshift_over_ln_qshift=qshift*inv_ln_qshift;+	const double qphsm1=q+hsm1;+	const double qshiftphsm1=qshift+hsm1;+	double terms[HSL_SF_LNHZETA_EULERMACLAURIN_SERIES_SHIFT_MAX+HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER+1]={NAN};+	double delta=NAN;+	double tscp=s;+	double scp=s*sm1;+	double pcp=inv_qshift*sm1/(qshift_over_ln_qshift+sm1*qshiftphsm1);+	double lcp=1.0-inv_ln_qshift/s;+	double ratio=NAN;+	size_t n=0;+	size_t j=0;+	double ans=0.0;+	double mjr=NAN;++	if (shift) {+		const double inv_q=1.0/q;+		const double inv_sm1=1.0/sm1;+		const double w=1.0+inv_sm1*inv_ln_q;+		const double wshift=1.0+inv_sm1*inv_ln_qshift;+		const double qwphsm1=q*w+hsm1;+		const double inv_qwphsm1=1.0/qwphsm1;+		const double qshiftwshiftphsm1=qshift*wshift+hsm1;+		double qs=q;+		double a=1.0;+		for(j=0;j<shift;) {+			ans+=(terms[n++]=a*hsl_sf_hZeta1_zed(s,qs++)*inv_qwphsm1);+			a=log(qs)*inv_ln_q*exp(-s*log1p((++j)*inv_q));+			}+		pcp*=a*qshiftwshiftphsm1*inv_qwphsm1;+		}+	ratio=scp*pcp*lcp;+	ans+=terms[n++]=ratio/12.0;+	scp*=++tscp; lcp-=inv_ln_qshift/tscp;+	scp*=++tscp; lcp-=inv_ln_qshift/tscp;+	pcp*=sqr_inv_qshift;+	ratio=scp*pcp*lcp;+	for(j=2;j<=HSL_SF_HZETA_EULERMACLAURIN_SERIES_ORDER;++j) {+		delta=hsl_sf_hzeta_eulermaclaurin_series_coeffs[j]*ratio;+		ans+=(terms[n++]=delta);+		scp*=++tscp; lcp-=inv_ln_qshift/tscp;+		scp*=++tscp; lcp-=inv_ln_qshift/tscp;+		pcp*=sqr_inv_qshift;+		ratio=scp*pcp*lcp;+		if ((fabs(delta/ans)) < (0.5*GSL_DBL_EPSILON)) break;+		}++	ans=0.0; while (n) ans+=terms[--n];+	mjr=hsl_sf_hzeta_eulermaclaurin_series_majorantratios[j]*ratio;++	*value=ans;+	*abserror=2.0*((shift+1)*GSL_DBL_EPSILON*fabs(ans)+mjr);++	if (coeff1) *coeff1=1.0+q_over_ln_q/qphsm1/sm1;++	return (PLFIT_SUCCESS); }++extern+int hsl_sf_lnhzeta_deriv_tuple_e(const double s, const double q, gsl_sf_result * result, gsl_sf_result * result_deriv) {++	/* CHECK_POINTER(result) */++	if ((s <= 1.0) || (q <= 0.0)) {+		PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL);+		}+	else if (q == 1.0) {+		const double inv_sm1=1.0/(s-1.0);+		const double inv_qsm1=4.0*inv_sm1;+		const double hz_coeff0=exp2(s+1.0);+		const double hz_coeff1=1.0+inv_qsm1;+		double hZeta0_value=NAN;+		double hZeta0_abserror=NAN;+		hsl_sf_hZeta0(s,2.0,&hZeta0_value,&hZeta0_abserror);+		hZeta0_value+=1.0;+		if (result) {+			const double ln_hz_coeff=hz_coeff1/hz_coeff0;+			const double ln_hZeta0_value=ln_hz_coeff*hZeta0_value;+			result->val=log1p(ln_hZeta0_value);+			result->err=(2.0*GSL_DBL_EPSILON*ln_hz_coeff+hZeta0_abserror)/(1.0+ln_hZeta0_value);+			}++		if (result_deriv) {+			const double ld_hz_coeff2=1.0+inv_sm1*M_LOG2E;+			const double ld_hz_coeff1=1.0+inv_qsm1*ld_hz_coeff2;+			double hZeta1_value=NAN;+			double hZeta1_abserror=NAN;+			hsl_sf_hZeta1(s,2.0,M_LN2,&hZeta1_value,&hZeta1_abserror,NULL);+			hZeta0_value*=hz_coeff1;+			hZeta0_value+=hz_coeff0;+			hZeta1_value+=1.0;+			hZeta1_value*=-M_LN2*ld_hz_coeff1;+			result_deriv->val=hZeta1_value/hZeta0_value;+			result_deriv->err=2.0*GSL_DBL_EPSILON*fabs(result_deriv->val)+(hZeta0_abserror+hZeta1_abserror);+			}+		}+	else {+		const double ln_q=log(q);+		double hZeta0_value=NAN;+		double hZeta0_abserror=NAN;+		hsl_sf_hZeta0(s,q,&hZeta0_value,&hZeta0_abserror);+		if (result) {+			const double ln_hz_term0=-s*ln_q;+			const double ln_hz_term1=log(0.5+q/(s-1.0));+			result->val=ln_hz_term0+ln_hz_term1+log1p(hZeta0_value);+			result->err=2.0*GSL_DBL_EPSILON*(fabs(ln_hz_term0)+fabs(ln_hz_term1))+hZeta0_abserror/(1.0+hZeta0_value);+			}+		if (result_deriv) {+			double hZeta1_value=NAN;+			double hZeta1_abserror=NAN;+			double ld_hz_coeff1=NAN;+			hsl_sf_hZeta1(s,q,ln_q,&hZeta1_value,&hZeta1_abserror,&ld_hz_coeff1);+			result_deriv->val=-ln_q*ld_hz_coeff1*(1.0+hZeta1_value)/(1.0+hZeta0_value);+			result_deriv->err=2.0*GSL_DBL_EPSILON*fabs(result_deriv->val)+(hZeta0_abserror+hZeta1_abserror);+			}+		}++	return (PLFIT_SUCCESS); }++extern+double hsl_sf_lnhzeta_deriv_tuple(const double s, const double q, double * tuple0, double * tuple1) {+	HSL_SF_EVAL_TUPLE_RESULT(hsl_sf_lnhzeta_deriv_tuple_e(s,q,&result0,&result1)); }++extern+int hsl_sf_lnhzeta_e(const double s, const double q, gsl_sf_result * result) {+	return (hsl_sf_lnhzeta_deriv_tuple_e(s,q,result,NULL)); }++extern+double hsl_sf_lnhzeta(const double s, const double q) {+	HSL_SF_EVAL_RESULT(hsl_sf_lnhzeta_e(s,q,&result)); }++extern+int hsl_sf_lnhzeta_deriv_e(const double s, const double q, gsl_sf_result * result) {+	return (hsl_sf_lnhzeta_deriv_tuple_e(s,q,NULL,result)); }++extern+double hsl_sf_lnhzeta_deriv(const double s, const double q) {+	HSL_SF_EVAL_RESULT(hsl_sf_lnhzeta_deriv_e(s,q,&result)); }++//+// End of file `hsl/specfunc/hzeta.c'.
igraph/src/igraph_fixed_vectorlist.c view
@@ -50,7 +50,7 @@     }     IGRAPH_FINALLY(igraph_free, l->vecs);     IGRAPH_CHECK(igraph_vector_ptr_init(&l->v, size));-    IGRAPH_FINALLY(igraph_fixed_vectorlist_destroy, &l->v);+    IGRAPH_FINALLY(igraph_vector_ptr_destroy, &l->v);     IGRAPH_VECTOR_INIT_FINALLY(&sizes, size);      for (i = 0; i < no; i++) {
igraph/src/igraph_hashtable.c view
@@ -32,7 +32,7 @@     IGRAPH_CHECK(igraph_trie_init(&ht->keys, 1));     IGRAPH_FINALLY(igraph_trie_destroy, &ht->keys);     IGRAPH_CHECK(igraph_strvector_init(&ht->elements, 0));-    IGRAPH_FINALLY(igraph_trie_destroy, &ht->elements);+    IGRAPH_FINALLY(igraph_strvector_destroy, &ht->elements);     IGRAPH_CHECK(igraph_strvector_init(&ht->defaults, 0));      IGRAPH_FINALLY_CLEAN(2);@@ -87,7 +87,7 @@     if (tmp == 0) {         IGRAPH_ERROR("cannot add element to hash table", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, tmp);+    IGRAPH_FINALLY(igraph_free, tmp);     strncpy(tmp, elem, elemlen);     tmp[elemlen] = '\0'; 
igraph/src/igraph_hrg.cc view
@@ -82,7 +82,7 @@ }; } -int markovChainMonteCarlo(dendro *d, unsigned int period,+static int markovChainMonteCarlo(dendro *d, unsigned int period,                           igraph_hrg_t *hrg) {      igraph_real_t bestL = d->getLikelihood();@@ -121,7 +121,7 @@     return 0; } -int markovChainMonteCarlo2(dendro *d, int num_samples) {+static int markovChainMonteCarlo2(dendro *d, int num_samples) {     bool flag_taken;     double dL, ptest = 1.0 / (50.0 * (double)(d->g->numNodes()));     int sample_num = 0, t = 1, thresh = 200 * d->g->numNodes();@@ -150,7 +150,7 @@     return 0; } -int MCMCEquilibrium_Find(dendro *d, igraph_hrg_t *hrg) {+static int MCMCEquilibrium_Find(dendro *d, igraph_hrg_t *hrg) {      // We want to run the MCMC until we've found equilibrium; we     // use the heuristic of the average log-likelihood (which is@@ -187,8 +187,8 @@     return 0; } -int igraph_i_hrg_getgraph(const igraph_t *igraph,-                          dendro *d) {+static int igraph_i_hrg_getgraph(const igraph_t *igraph,+                                 dendro *d) {      int no_of_nodes = igraph_vcount(igraph);     int no_of_edges = igraph_ecount(igraph);@@ -217,9 +217,9 @@     return 0; } -int igraph_i_hrg_getsimplegraph(const igraph_t *igraph,-                                dendro *d, simpleGraph **sg,-                                int num_bins) {+static int igraph_i_hrg_getsimplegraph(const igraph_t *igraph,+                                       dendro *d, simpleGraph **sg,+                                       int num_bins) {      int no_of_nodes = igraph_vcount(igraph);     int no_of_edges = igraph_ecount(igraph);@@ -448,7 +448,7 @@ int igraph_hrg_sample(const igraph_t *input_graph,                       igraph_t *sample,                       igraph_vector_ptr_t *samples,-                      int no_samples,+                      igraph_integer_t no_samples,                       igraph_hrg_t *hrg,                       igraph_bool_t start) { @@ -693,7 +693,7 @@     return 0; } -int MCMCEquilibrium_Sample(dendro *d, int num_samples) {+static int MCMCEquilibrium_Sample(dendro *d, int num_samples) {      // Because moves in the dendrogram space are chosen (Monte     // Carlo) so that we sample dendrograms with probability@@ -725,7 +725,7 @@     return 0; } -int QsortPartition (pblock* array, int left, int right, int index) {+static int QsortPartition (pblock* array, int left, int right, int index) {     pblock p_value, temp;     p_value.L = array[index].L;     p_value.i = array[index].i;@@ -772,7 +772,7 @@     return stored; } -void QsortMain (pblock* array, int left, int right) {+static void QsortMain (pblock* array, int left, int right) {     if (right > left) {         int pivot = left;         int part  = QsortPartition(array, left, right, pivot);@@ -782,7 +782,7 @@     return; } -int rankCandidatesByProbability(simpleGraph *sg, dendro *d,+static int rankCandidatesByProbability(simpleGraph *sg, dendro *d,                                 pblock *br_list, int mk) {     int mkk = 0;     int n = sg->getNumNodes();@@ -804,7 +804,7 @@     return 0; } -int recordPredictions(pblock *br_list, igraph_vector_t *edges,+static int recordPredictions(pblock *br_list, igraph_vector_t *edges,                       igraph_vector_t *prob, int mk) {      IGRAPH_CHECK(igraph_vector_resize(edges, mk * 2));
igraph/src/igraph_hrg_types.cc view
@@ -41,6 +41,7 @@ #include "igraph_constructors.h" #include "igraph_random.h" +using namespace std; using namespace fitHRG;  // ******** Red-Black Tree Methods ***************************************
igraph/src/igraph_psumtree.c view
@@ -31,7 +31,7 @@ #include <math.h> #include <stdio.h> -double igraph_i_log2(double f) {+static double igraph_i_log2(double f) {     return log(f) / log(2.0); } 
igraph/src/igraph_strvector.c view
@@ -24,7 +24,6 @@ #include "igraph_types.h" #include "igraph_strvector.h" #include "igraph_memory.h"-#include "igraph_random.h" #include "igraph_error.h" #include "config.h" 
igraph/src/igraph_trie.c view
@@ -39,7 +39,7 @@  *         igraph_vector_ptr_init() and igraph_vector_init() might be returned.  */ -int igraph_i_trie_init_node(igraph_trie_node_t *t) {+static int igraph_i_trie_init_node(igraph_trie_node_t *t) {     IGRAPH_STRVECTOR_INIT_FINALLY(&t->strs, 0);     IGRAPH_VECTOR_PTR_INIT_FINALLY(&t->children, 0);     IGRAPH_VECTOR_INIT_FINALLY(&t->values, 0);@@ -47,7 +47,7 @@     return 0; } -void igraph_i_trie_destroy_node(igraph_trie_node_t *t, igraph_bool_t sfree);+static void igraph_i_trie_destroy_node(igraph_trie_node_t *t);  /**  * \ingroup igraphtrie@@ -59,8 +59,8 @@ int igraph_trie_init(igraph_trie_t *t, igraph_bool_t storekeys) {     t->maxvalue = -1;     t->storekeys = storekeys;-    IGRAPH_CHECK(igraph_i_trie_init_node( (igraph_trie_node_t *)t ));-    IGRAPH_FINALLY(igraph_i_trie_destroy_node, t);+    IGRAPH_CHECK(igraph_i_trie_init_node( (igraph_trie_node_t *) t ));+    IGRAPH_FINALLY(igraph_i_trie_destroy_node, (igraph_trie_node_t *) t );     if (storekeys) {         IGRAPH_CHECK(igraph_strvector_init(&t->keys, 0));     }@@ -74,13 +74,13 @@  * \brief Destroys a node of a trie (not to be called directly).  */ -void igraph_i_trie_destroy_node(igraph_trie_node_t *t, igraph_bool_t sfree) {+static void igraph_i_trie_destroy_node_helper(igraph_trie_node_t *t, igraph_bool_t sfree) {     long int i;     igraph_strvector_destroy(&t->strs);     for (i = 0; i < igraph_vector_ptr_size(&t->children); i++) {         igraph_trie_node_t *child = VECTOR(t->children)[i];         if (child != 0) {-            igraph_i_trie_destroy_node(child, 1);+            igraph_i_trie_destroy_node_helper(child, 1);         }     }     igraph_vector_ptr_destroy(&t->children);@@ -90,6 +90,10 @@     } } +static void igraph_i_trie_destroy_node(igraph_trie_node_t *t) {+    igraph_i_trie_destroy_node_helper(t, 0);+}+ /**  * \ingroup igraphtrie  * \brief Destroys a trie (frees allocated memory).@@ -99,7 +103,7 @@     if (t->storekeys) {         igraph_strvector_destroy(&t->keys);     }-    igraph_i_trie_destroy_node( (igraph_trie_node_t*) t, 0);+    igraph_i_trie_destroy_node( (igraph_trie_node_t*) t); }  @@ -108,7 +112,7 @@  * \brief Internal helping function for igraph_trie_t  */ -long int igraph_i_strdiff(const char *str, const char *key) {+static long int igraph_i_strdiff(const char *str, const char *key) {      long int diff = 0;     while (key[diff] != '\0' && str[diff] != '\0' && str[diff] == key[diff]) {@@ -210,9 +214,9 @@                 IGRAPH_ERROR("cannot add to trie", IGRAPH_ENOMEM);             }             str2[diff] = '\0';-            IGRAPH_FINALLY(free, str2);+            IGRAPH_FINALLY(igraph_free, str2);             IGRAPH_CHECK(igraph_strvector_set(&t->strs, i, str2));-            free(str2);+            igraph_Free(str2);             IGRAPH_FINALLY_CLEAN(4);              VECTOR(t->values)[i] = newvalue;@@ -246,9 +250,9 @@                 IGRAPH_ERROR("cannot add to trie", IGRAPH_ENOMEM);             }             str2[diff] = '\0';-            IGRAPH_FINALLY(free, str2);+            IGRAPH_FINALLY(igraph_free, str2);             IGRAPH_CHECK(igraph_strvector_set(&t->strs, i, str2));-            free(str2);+            igraph_Free(str2);             IGRAPH_FINALLY_CLEAN(4);              VECTOR(t->values)[i] = -1;@@ -345,7 +349,7 @@      strncpy(tmp, key, length);     tmp[length] = '\0';-    IGRAPH_FINALLY(free, tmp);+    IGRAPH_FINALLY(igraph_free, tmp);     IGRAPH_CHECK(igraph_trie_get(t, tmp, id));     igraph_Free(tmp);     IGRAPH_FINALLY_CLEAN(1);
igraph/src/infomap.cc view
@@ -318,5 +318,8 @@      delete fgraph;     IGRAPH_FINALLY_CLEAN(1);++	IGRAPH_CHECK(igraph_reindex_membership(membership, 0, 0));+     return IGRAPH_SUCCESS; }
igraph/src/infomap_FlowGraph.cc view
@@ -26,6 +26,8 @@  #define plogp( x ) ( (x) > 0.0 ? (x)*log(x) : 0.0 ) +using namespace std;+ void FlowGraph::init(int n, const igraph_vector_t *v_weights) {     alpha = 0.15;     beta  = 1.0 - alpha;
igraph/src/infomap_Greedy.cc view
@@ -26,6 +26,8 @@ #include <iterator> #define plogp( x ) ( (x) > 0.0 ? (x)*log(x) : 0.0 ) +using namespace std;+ Greedy::Greedy(FlowGraph * fgraph) {     graph = fgraph;     Nnode = graph->Nnode;
igraph/src/infomap_Node.cc view
@@ -24,6 +24,8 @@  #include "infomap_Node.h" +using namespace std;+ Node::Node() {     exit = 0.0;     size = 0.0;
igraph/src/interrupt.c view
@@ -24,10 +24,6 @@ #include "igraph_interrupt.h" #include "config.h" -#include <stdio.h>-#include <stdlib.h>-#include <assert.h>- IGRAPH_THREAD_LOCAL igraph_interruption_handler_t *igraph_i_interruption_handler = 0; 
igraph/src/iterators.c view
@@ -23,7 +23,6 @@  #include "igraph_iterators.h" #include "igraph_memory.h"-#include "igraph_random.h" #include "igraph_interface.h" #include "config.h" @@ -878,7 +877,7 @@  * \function igraph_ess_all  * \brief Edge set, all edges (immediate version)  *- * The immediate version of the all-vertices selector.+ * The immediate version of the all-edges selector.  *  * \param order Constant giving the order of the edges in the edge  *        selector. See \ref igraph_es_all() for the possible values.@@ -1430,12 +1429,12 @@     return es->type; } -int igraph_i_es_pairs_size(const igraph_t *graph,-                           const igraph_es_t *es, igraph_integer_t *result);-int igraph_i_es_path_size(const igraph_t *graph,-                          const igraph_es_t *es, igraph_integer_t *result);-int igraph_i_es_multipairs_size(const igraph_t *graph,-                                const igraph_es_t *es, igraph_integer_t *result);+static int igraph_i_es_pairs_size(const igraph_t *graph,+                                  const igraph_es_t *es, igraph_integer_t *result);+static int igraph_i_es_path_size(const igraph_t *graph,+                                 const igraph_es_t *es, igraph_integer_t *result);+static int igraph_i_es_multipairs_size(const igraph_t *graph,+                                       const igraph_es_t *es, igraph_integer_t *result);  /**  * \function igraph_es_size@@ -1514,8 +1513,8 @@     return 0; } -int igraph_i_es_pairs_size(const igraph_t *graph,-                           const igraph_es_t *es, igraph_integer_t *result) {+static int igraph_i_es_pairs_size(const igraph_t *graph,+                                  const igraph_es_t *es, igraph_integer_t *result) {     long int n = igraph_vector_size(es->data.path.ptr);     long int no_of_nodes = igraph_vcount(graph);     long int i;@@ -1542,8 +1541,8 @@     return 0; } -int igraph_i_es_path_size(const igraph_t *graph,-                          const igraph_es_t *es, igraph_integer_t *result) {+static int igraph_i_es_path_size(const igraph_t *graph,+                                 const igraph_es_t *es, igraph_integer_t *result) {     long int n = igraph_vector_size(es->data.path.ptr);     long int no_of_nodes = igraph_vcount(graph);     long int i;@@ -1569,27 +1568,27 @@     return 0; } -int igraph_i_es_multipairs_size(const igraph_t *graph,-                                const igraph_es_t *es, igraph_integer_t *result) {+static int igraph_i_es_multipairs_size(const igraph_t *graph,+                                       const igraph_es_t *es, igraph_integer_t *result) {     IGRAPH_UNUSED(graph); IGRAPH_UNUSED(es); IGRAPH_UNUSED(result);     IGRAPH_ERROR("Cannot calculate edge selector length", IGRAPH_UNIMPLEMENTED); }  /**************************************************/ -int igraph_i_eit_create_allfromto(const igraph_t *graph,-                                  igraph_eit_t *eit,-                                  igraph_neimode_t mode);-int igraph_i_eit_pairs(const igraph_t *graph,-                       igraph_es_t es, igraph_eit_t *eit);-int igraph_i_eit_multipairs(const igraph_t *graph,-                            igraph_es_t es, igraph_eit_t *eit);-int igraph_i_eit_path(const igraph_t *graph,-                      igraph_es_t es, igraph_eit_t *eit);+static int igraph_i_eit_create_allfromto(const igraph_t *graph,+                                         igraph_eit_t *eit,+                                         igraph_neimode_t mode);+static int igraph_i_eit_pairs(const igraph_t *graph,+                              igraph_es_t es, igraph_eit_t *eit);+static int igraph_i_eit_multipairs(const igraph_t *graph,+                                   igraph_es_t es, igraph_eit_t *eit);+static int igraph_i_eit_path(const igraph_t *graph,+                             igraph_es_t es, igraph_eit_t *eit); -int igraph_i_eit_create_allfromto(const igraph_t *graph,-                                  igraph_eit_t *eit,-                                  igraph_neimode_t mode) {+static int igraph_i_eit_create_allfromto(const igraph_t *graph,+                                         igraph_eit_t *eit,+                                         igraph_neimode_t mode) {     igraph_vector_t *vec;     long int no_of_nodes = igraph_vcount(graph);     long int i;@@ -1647,8 +1646,8 @@     return 0; } -int igraph_i_eit_pairs(const igraph_t *graph,-                       igraph_es_t es, igraph_eit_t *eit) {+static int igraph_i_eit_pairs(const igraph_t *graph,+                              igraph_es_t es, igraph_eit_t *eit) {     long int n = igraph_vector_size(es.data.path.ptr);     long int no_of_nodes = igraph_vcount(graph);     long int i;@@ -1686,8 +1685,8 @@     return 0; } -int igraph_i_eit_multipairs(const igraph_t *graph,-                            igraph_es_t es, igraph_eit_t *eit) {+static int igraph_i_eit_multipairs(const igraph_t *graph,+                                   igraph_es_t es, igraph_eit_t *eit) {     long int n = igraph_vector_size(es.data.path.ptr);     long int no_of_nodes = igraph_vcount(graph); @@ -1718,8 +1717,8 @@     return 0; } -int igraph_i_eit_path(const igraph_t *graph,-                      igraph_es_t es, igraph_eit_t *eit) {+static int igraph_i_eit_path(const igraph_t *graph,+                             igraph_es_t es, igraph_eit_t *eit) {     long int n = igraph_vector_size(es.data.path.ptr);     long int no_of_nodes = igraph_vcount(graph);     long int i, len;
igraph/src/kolmogorov.c view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
igraph/src/lad.c view
@@ -46,13 +46,7 @@    -- Tamas Nepusz, 11 July 2013 */ -#include <stdio.h>-#include <stdlib.h>-#include <string.h>-#include <unistd.h>-#include <time.h>-#include <limits.h>-+#include "igraph_topology.h" #include "igraph_interface.h" #include "igraph_adjlist.h" #include "igraph_vector.h"@@ -61,6 +55,12 @@ #include "igraph_matrix.h" #include "igraph_interrupt_internal.h" +#include <stdlib.h>+#include <string.h>+#include <time.h>+#include <limits.h>++ /* define boolean type as char */ #define true 1 #define false 0@@ -99,7 +99,7 @@     igraph_matrix_char_t isEdge; } Tgraph; -int igraph_i_lad_createGraph(const igraph_t *igraph, Tgraph* graph) {+static int igraph_i_lad_createGraph(const igraph_t *igraph, Tgraph* graph) {     long int i, j, n;     long int no_of_nodes = igraph_vcount(igraph);     igraph_vector_int_t *neis;@@ -112,8 +112,7 @@      IGRAPH_CHECK(igraph_adjlist_init(igraph, &graph->succ, IGRAPH_OUT));     IGRAPH_FINALLY(igraph_adjlist_destroy, &graph->succ);-    IGRAPH_CHECK(igraph_matrix_char_init(&graph->isEdge,-                                         no_of_nodes, no_of_nodes));+    IGRAPH_CHECK(igraph_matrix_char_init(&graph->isEdge, no_of_nodes, no_of_nodes));     IGRAPH_FINALLY(igraph_matrix_char_destroy, &graph->isEdge);      for (i = 0; i < no_of_nodes; i++) {@@ -129,9 +128,18 @@         }     } -    return 0;+    IGRAPH_FINALLY_CLEAN(3);++    return IGRAPH_SUCCESS; } +static void igraph_i_lad_destroyGraph(Tgraph *graph) {+    igraph_matrix_char_destroy(&graph->isEdge);+    igraph_adjlist_destroy(&graph->succ);+    igraph_vector_destroy(&graph->nbSucc);+}++ /* ---------------------------------------------------------*/ /* Coming from domains.c                                    */ /* ---------------------------------------------------------*/@@ -169,19 +177,19 @@        or -1 if v is not matched */ } Tdomain; -bool igraph_i_lad_toFilterEmpty(Tdomain* D) {+static bool igraph_i_lad_toFilterEmpty(Tdomain* D) {     /* return true if there is no more nodes in toFilter */     return (D->nextOutToFilter < 0); } -void igraph_i_lad_resetToFilter(Tdomain *D) {+static void igraph_i_lad_resetToFilter(Tdomain *D) {     /* empty to filter and unmark the vertices that are marked to be filtered */     igraph_vector_char_null(&D->markedToFilter);     D->nextOutToFilter = -1; }  -int igraph_i_lad_nextToFilter(Tdomain* D, int size) {+static int igraph_i_lad_nextToFilter(Tdomain* D, int size) {     /* precondition: emptyToFilter = false        remove a node from toFilter (FIFO)        unmark this node and return it */@@ -198,7 +206,7 @@     return u; } -void igraph_i_lad_addToFilter(int u, Tdomain* D, int size) {+static void igraph_i_lad_addToFilter(int u, Tdomain* D, int size) {     /* if u is not marked, then add it to toFilter and mark it */     if (VECTOR(D->markedToFilter)[u]) {         return;@@ -215,13 +223,13 @@     VECTOR(D->toFilter)[D->lastInToFilter] = u; } -bool igraph_i_lad_isInD(int u, int v, Tdomain* D) {+static bool igraph_i_lad_isInD(int u, int v, Tdomain* D) {     /* returns true if v belongs to D(u); false otherwise */     return (MATRIX(D->posInVal, u, v) <             VECTOR(D->firstVal)[u] + VECTOR(D->nbVal)[u]); } -int igraph_i_lad_augmentingPath(int u, Tdomain* D, int nbV, bool* result) {+static int igraph_i_lad_augmentingPath(int u, Tdomain* D, int nbV, bool* result) {     /* return true if there exists an augmenting path starting from u and        ending on a free vertex v in the bipartite directed graph G=(U,        V, E) such that U=pattern nodes, V=target nodes, and@@ -289,7 +297,7 @@     return 0; } -int igraph_i_lad_removeAllValuesButOne(int u, int v, Tdomain* D, Tgraph* Gp,+static int igraph_i_lad_removeAllValuesButOne(int u, int v, Tdomain* D, Tgraph* Gp,                                        Tgraph* Gt, bool* result) {     /* remove all values but v from D(u) and add all successors of u in        toFilter return false if an inconsistency is detected wrt to@@ -323,7 +331,7 @@ }  -int igraph_i_lad_removeValue(int u, int v, Tdomain* D, Tgraph* Gp,+static int igraph_i_lad_removeValue(int u, int v, Tdomain* D, Tgraph* Gp,                              Tgraph* Gt, bool* result) {     /* remove v from D(u) and add all successors of u in toFilter        return false if an inconsistency is detected wrt global all diff */@@ -358,7 +366,7 @@ }  -int igraph_i_lad_matchVertices(int nb, igraph_vector_int_t* toBeMatched,+static int igraph_i_lad_matchVertices(int nb, igraph_vector_int_t* toBeMatched,                                bool induced, Tdomain* D, Tgraph* Gp,                                Tgraph* Gt, int *invalid) {     /* for each u in toBeMatched[0..nb-1], match u to@@ -439,7 +447,7 @@ }  -bool igraph_i_lad_matchVertex(int u, bool induced, Tdomain* D, Tgraph* Gp,+static bool igraph_i_lad_matchVertex(int u, bool induced, Tdomain* D, Tgraph* Gp,                               Tgraph *Gt) {     int invalid;     /* match u to D->val[D->firstVal[u]] and filter domains of other non@@ -461,13 +469,13 @@ }  -int igraph_i_lad_qcompare (void const *a, void const *b) {+static int igraph_i_lad_qcompare (void const *a, void const *b) {     /* function used by the qsort function */     int pa = *((int*)a) - *((int*)b);     return pa; } -bool igraph_i_lad_compare(int size_mu, int* mu, int size_mv, int* mv) {+static bool igraph_i_lad_compare(int size_mu, int* mu, int size_mv, int* mv) {     /* return true if for every element u of mu there exists        a different element v of mv such that u <= v;        return false otherwise */@@ -484,9 +492,9 @@     return true; } -int igraph_i_lad_initDomains(bool initialDomains,-                             igraph_vector_ptr_t *domains, Tdomain* D,-                             Tgraph* Gp, Tgraph* Gt, int *empty) {+static int igraph_i_lad_initDomains(bool initialDomains,+                                    const igraph_vector_ptr_t *domains, Tdomain *D,+                                    const Tgraph *Gp, const Tgraph *Gt, int *empty) {     /* for every pattern node u, initialize D(u) with every vertex v        such that for every neighbor u' of u there exists a different        neighbor v' of v such that degree(u) <= degree(v)@@ -498,8 +506,6 @@     int *mu, *mv;     int matchingSize, u, v, i, j;     igraph_vector_t *vec;-    igraph_vector_t *Gp_uneis;-    igraph_vector_t *Gt_vneis;      val = igraph_Calloc(Gp->nbVertices * Gt->nbVertices, int);     if (val == 0) {@@ -512,16 +518,13 @@         IGRAPH_ERROR("cannot allocated 'dom' array in igraph_i_lad_initDomains", IGRAPH_ENOMEM);     } -    IGRAPH_CHECK(igraph_vector_int_init(&D->globalMatchingP, Gp->nbVertices));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->globalMatchingP);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->globalMatchingP, Gp->nbVertices);     igraph_vector_int_fill(&D->globalMatchingP, -1L); -    IGRAPH_CHECK(igraph_vector_int_init(&D->globalMatchingT, Gt->nbVertices));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->globalMatchingT);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->globalMatchingT, Gt->nbVertices);     igraph_vector_int_fill(&D->globalMatchingT, -1L); -    IGRAPH_CHECK(igraph_vector_int_init(&D->nbVal, Gp->nbVertices));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->nbVal);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->nbVal, Gp->nbVertices);      IGRAPH_CHECK(igraph_vector_int_init(&D->firstVal, Gp->nbVertices));     IGRAPH_FINALLY(igraph_vector_int_destroy, &D->firstVal);@@ -537,8 +540,7 @@     IGRAPH_CHECK(igraph_vector_char_init(&D->markedToFilter, Gp->nbVertices));     IGRAPH_FINALLY(igraph_vector_char_destroy, &D->markedToFilter); -    IGRAPH_CHECK(igraph_vector_int_init(&D->toFilter, Gp->nbVertices));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->toFilter);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->toFilter, Gp->nbVertices);      D->valSize = 0;     matchingSize = 0;@@ -603,30 +605,55 @@         }         if (VECTOR(D->nbVal)[u] == 0) {             *empty = 1;  /* empty domain */+             igraph_free(val);             igraph_free(dom);-            return 0;++            /* On this branch, 'val' and 'matching' are unused.+             * We init them anyway so that we can have a consistent destructor. */+            IGRAPH_VECTOR_INT_INIT_FINALLY(&D->val, 0);+            IGRAPH_VECTOR_INT_INIT_FINALLY(&D->matching, 0);+            IGRAPH_FINALLY_CLEAN(10);++            return IGRAPH_SUCCESS;         }     }-    IGRAPH_CHECK(igraph_vector_int_init(&D->val, D->valSize));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->val);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->val, D->valSize);     for (i = 0; i < D->valSize; i++) {         VECTOR(D->val)[i] = val[i];     } -    IGRAPH_CHECK(igraph_vector_int_init(&D->matching, matchingSize));-    IGRAPH_FINALLY(igraph_vector_int_destroy, &D->matching);+    IGRAPH_VECTOR_INT_INIT_FINALLY(&D->matching, matchingSize);     igraph_vector_int_fill(&D->matching, -1);      D->nextOutToFilter = 0;     D->lastInToFilter = (int) (Gp->nbVertices - 1);+     *empty = 0;      igraph_free(val);     igraph_free(dom);-    return 0;++    IGRAPH_FINALLY_CLEAN(10);++    return IGRAPH_SUCCESS; } +static void igraph_i_lad_destroyDomains(Tdomain *D) {+    igraph_vector_int_destroy(&D->globalMatchingP);+    igraph_vector_int_destroy(&D->globalMatchingT);+    igraph_vector_int_destroy(&D->nbVal);+    igraph_vector_int_destroy(&D->firstVal);+    igraph_matrix_int_destroy(&D->posInVal);+    igraph_matrix_int_destroy(&D->firstMatch);+    igraph_vector_char_destroy(&D->markedToFilter);+    igraph_vector_int_destroy(&D->toFilter);++    igraph_vector_int_destroy(&D->val);+    igraph_vector_int_destroy(&D->matching);+}++ /* ---------------------------------------------------------*/ /* Coming from allDiff.c                                    */ /* ---------------------------------------------------------*/@@ -637,14 +664,14 @@ #define toBeDeleted 3 #define deleted 4 -void igraph_i_lad_addToDelete(int u, int* list, int* nb, int* marked) {+static void igraph_i_lad_addToDelete(int u, int* list, int* nb, int* marked) {     if (marked[u] < toBeDeleted) {         list[(*nb)++] = u;         marked[u] = toBeDeleted;     } } -int igraph_i_lad_updateMatching(int sizeOfU, int sizeOfV,+static int igraph_i_lad_updateMatching(int sizeOfU, int sizeOfV,                                 igraph_vector_int_t *degree,                                 igraph_vector_int_t *firstAdj,                                 igraph_vector_int_t *adj,@@ -897,7 +924,7 @@     return 0; } -void igraph_i_lad_DFS(int nbU, int nbV, int u, bool* marked, int* nbSucc,+static void igraph_i_lad_DFS(int nbU, int nbV, int u, bool* marked, int* nbSucc,                       int* succ, igraph_vector_int_t * matchedWithU,                       int* order, int* nb) {     /* perform a depth first search, starting from u, in the bipartite@@ -925,7 +952,7 @@     order[*nb] = u; (*nb)--; } -int igraph_i_lad_SCC(int nbU, int nbV, int* numV, int* numU,+static int igraph_i_lad_SCC(int nbU, int nbV, int* numV, int* numU,                      int* nbSucc, int* succ,                      int* nbPred, int* pred,                      igraph_vector_int_t * matchedWithU,@@ -1000,7 +1027,7 @@ }  -int igraph_i_lad_ensureGACallDiff(bool induced, Tgraph* Gp, Tgraph* Gt,+static int igraph_i_lad_ensureGACallDiff(bool induced, Tgraph* Gp, Tgraph* Gt,                                   Tdomain* D, int *invalid) {     /* precondition: D->globalMatchingP is an all different matching of        the pattern vertices@@ -1127,7 +1154,7 @@ /* Coming from lad.c                                        */ /* ---------------------------------------------------------*/ -int igraph_i_lad_checkLAD(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt,+static int igraph_i_lad_checkLAD(int u, int v, Tdomain* D, Tgraph* Gp, Tgraph* Gt,                           bool *result) {     /* return true if G_(u, v) has a adj(u)-covering matching; false        otherwise */@@ -1278,7 +1305,7 @@ /* Coming from main.c                                      */ /* ---------------------------------------------------------*/ -int igraph_i_lad_filter(bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt,+static int igraph_i_lad_filter(bool induced, Tdomain* D, Tgraph* Gp, Tgraph* Gt,                         bool *result) {     /* filter domains of all vertices in D->toFilter wrt LAD and ensure        GAC(allDiff)@@ -1327,7 +1354,7 @@   -int igraph_i_lad_solve(int timeLimit, bool firstSol, bool induced,+static int igraph_i_lad_solve(int timeLimit, bool firstSol, bool induced,                        Tdomain* D, Tgraph* Gp, Tgraph* Gt,                        int *invalid, igraph_bool_t *iso,                        igraph_vector_t *map, igraph_vector_ptr_t *maps,@@ -1575,14 +1602,18 @@     }      IGRAPH_CHECK(igraph_i_lad_createGraph(pattern, &Gp));+    IGRAPH_FINALLY(igraph_i_lad_destroyGraph, &Gp);+     IGRAPH_CHECK(igraph_i_lad_createGraph(target, &Gt));+    IGRAPH_FINALLY(igraph_i_lad_destroyGraph, &Gt);      if (Gp.nbVertices > Gt.nbVertices) {         goto exit3;     } -    IGRAPH_CHECK(igraph_i_lad_initDomains(initialDomains, domains, &D, &Gp,-                                          &Gt, &invalidDomain));+    IGRAPH_CHECK(igraph_i_lad_initDomains(initialDomains, domains, &D, &Gp, &Gt, &invalidDomain));+    IGRAPH_FINALLY(igraph_i_lad_destroyDomains, &D);+     if (invalidDomain) {         goto exit2;     }@@ -1634,32 +1665,16 @@     IGRAPH_FINALLY_CLEAN(1);  exit:--    igraph_vector_int_destroy(&D.val);-    igraph_vector_int_destroy(&D.matching);-    IGRAPH_FINALLY_CLEAN(2);- exit2: -    igraph_vector_int_destroy(&D.globalMatchingP);-    igraph_vector_int_destroy(&D.globalMatchingT);-    igraph_vector_int_destroy(&D.nbVal);-    igraph_vector_int_destroy(&D.firstVal);-    igraph_matrix_int_destroy(&D.posInVal);-    igraph_matrix_int_destroy(&D.firstMatch);-    igraph_vector_char_destroy(&D.markedToFilter);-    igraph_vector_int_destroy(&D.toFilter);-    IGRAPH_FINALLY_CLEAN(8);+    igraph_i_lad_destroyDomains(&D);+    IGRAPH_FINALLY_CLEAN(1);  exit3: -    igraph_matrix_char_destroy(&Gt.isEdge);-    igraph_adjlist_destroy(&Gt.succ);-    igraph_vector_destroy(&Gt.nbSucc);-    igraph_matrix_char_destroy(&Gp.isEdge);-    igraph_adjlist_destroy(&Gp.succ);-    igraph_vector_destroy(&Gp.nbSucc);-    IGRAPH_FINALLY_CLEAN(6);+    igraph_i_lad_destroyGraph(&Gt);+    igraph_i_lad_destroyGraph(&Gp);+    IGRAPH_FINALLY_CLEAN(2);      return 0; }
igraph/src/lapack.c view
@@ -21,6 +21,7 @@  */ +#include "igraph_blas.h" #include "igraph_lapack.h" #include "igraph_lapack_internal.h" @@ -615,7 +616,7 @@  *  * </para><para>  * Optionally also, it computes a balancing transformation to improve- * the conditioning of the eigenvalues and eigenvectors (\p ilo, \pihi,+ * the conditioning of the eigenvalues and eigenvectors (\p ilo, \p ihi,  * \p scale, and \p abnrm), reciprocal condition numbers for the  * eigenvalues (\p rconde), and reciprocal condition numbers for the  * right eigenvectors (\p rcondv).@@ -625,8 +626,8 @@  *                   A * v(j) = lambda(j) * v(j)  * where lambda(j) is its eigenvalue.  * The left eigenvector u(j) of A satisfies- *               u(j)**H * A = lambda(j) * u(j)**H- * where u(j)**H denotes the conjugate transpose of u(j).+ *               u(j)^H * A = lambda(j) * u(j)^H+ * where u(j)^H denotes the conjugate transpose of u(j).  *  * </para><para>  * The computed eigenvectors are normalized to have Euclidean norm@@ -635,7 +636,7 @@  * </para><para>  * Balancing a matrix means permuting the rows and columns to make it  * more nearly upper triangular, and applying a diagonal similarity- * transformation D * A * D**(-1), where D is a diagonal matrix, to+ * transformation D * A * D^(-1), where D is a diagonal matrix, to  * make its rows and columns closer in norm and the condition numbers  * of its eigenvalues and eigenvectors smaller.  The computed  * reciprocal condition numbers correspond to the balanced matrix.@@ -654,7 +655,7 @@  *          triangular. Do not diagonally scale.  *     \cli IGRAPH_LAPACK_DGEEVX_BALANCE_SCALE  *          diagonally scale the matrix, i.e. replace A by- *          D*A*D**(-1), where D is a diagonal matrix, chosen to make+ *          D*A*D^(-1), where D is a diagonal matrix, chosen to make  *          the rows and columns of A more equal in norm. Do not  *          permute.  *     \cli IGRAPH_LAPACK_DGEEVX_BALANCE_BOTH@@ -683,7 +684,7 @@  *   J=1,...,ilo-1 or I=ihi+1,...,N.  * \param scale Pointer to an initialized vector or a NULL pointer. If  *   not a NULL pointer, then details of the permutations and scaling- *   factors applied when balancing \param A, are stored here.+ *   factors applied when balancing \p A, are stored here.  *   If P(j) is the index of the row and column  *   interchanged with row and column j, and D(j) is the scaling  *   factor applied to row and column j, then@@ -938,17 +939,10 @@  int igraph_lapack_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2,                        igraph_real_t *res) {--    int n = igraph_vector_size(v1);-    int one = 1;--    if (igraph_vector_size(v2) != n) {-        IGRAPH_ERROR("Dot product of vectors with different dimensions",-                     IGRAPH_EINVAL);-    }--    *res = igraphddot_(&n, VECTOR(*v1), &one, VECTOR(*v2), &one);--    return 0;+    IGRAPH_WARNING(+        "igraph_lapack_ddot() is a misnomer; use igraph_blas_ddot() instead. "+        "igraph_lapack_ddot() will be removed in igraph 0.9.0."+    );+    return igraph_blas_ddot(v1, v2, res); } 
igraph/src/layout.c view
@@ -44,7 +44,6 @@ #include "config.h" #include <math.h> #include "igraph_math.h"-#include <stdio.h> /* FIXME */   /**@@ -380,9 +379,7 @@     return 0; } -void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y);--void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y) {+static void igraph_i_norm2d(igraph_real_t *x, igraph_real_t *y) {     igraph_real_t len = sqrt((*x) * (*x) + (*y) * (*y));     if (len != 0) {         *x /= len;@@ -696,13 +693,7 @@  } -int igraph_i_layout_reingold_tilford_unreachable(-    const igraph_t *graph,-    igraph_neimode_t mode,-    long int real_root,-    long int no_of_nodes,-    igraph_vector_t *pnewedges);-int igraph_i_layout_reingold_tilford_unreachable(+static int igraph_i_layout_reingold_tilford_unreachable(     const igraph_t *graph,     igraph_neimode_t mode,     long int real_root,@@ -782,24 +773,27 @@               of the subtree rooted at this node */     long int right_contour; /* Next right node of the contour               of the subtree rooted at this node */-    igraph_real_t offset_follow_lc;  /* X offset when following the left contour */-    igraph_real_t offset_follow_rc;  /* X offset when following the right contour */+    igraph_real_t offset_to_left_contour;  /* X offset when following the left contour */+    igraph_real_t offset_to_right_contour;  /* X offset when following the right contour */+    long int left_extreme;  /* Leftmost node on the deepest layer of the subtree rooted at this node */+    long int right_extreme; /* Rightmost node on the deepest layer of the subtree rooted at this node */+    igraph_real_t offset_to_left_extreme;  /* X offset when jumping to the left extreme node */+    igraph_real_t offset_to_right_extreme;  /* X offset when jumping to the right extreme node */ }; -int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata,-        long int node, long int vcount);-int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata,-        igraph_matrix_t *res, long int node,-        long int vcount, igraph_real_t xpos);+static int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata,+                                                      long int node, long int vcount);+static int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata,+                                                        igraph_matrix_t *res, long int node,+                                                        long int vcount, igraph_real_t xpos); -int igraph_i_layout_reingold_tilford(const igraph_t *graph,-                                     igraph_matrix_t *res,-                                     igraph_neimode_t mode,-                                     long int root);-int igraph_i_layout_reingold_tilford(const igraph_t *graph,-                                     igraph_matrix_t *res,-                                     igraph_neimode_t mode,-                                     long int root) {+/* uncomment the next line for debugging the Reingold-Tilford layout */+/* #define LAYOUT_RT_DEBUG 1 */++static int igraph_i_layout_reingold_tilford(const igraph_t *graph,+                                            igraph_matrix_t *res,+                                            igraph_neimode_t mode,+                                            long int root) {     long int no_of_nodes = igraph_vcount(graph);     long int i, n, j;     igraph_dqueue_t q = IGRAPH_DQUEUE_NULL;@@ -825,8 +819,12 @@         vdata[i].offset = 0.0;         vdata[i].left_contour = -1;         vdata[i].right_contour = -1;-        vdata[i].offset_follow_lc = 0.0;-        vdata[i].offset_follow_rc = 0.0;+        vdata[i].offset_to_left_contour = 0.0;+        vdata[i].offset_to_right_contour = 0.0;+        vdata[i].left_extreme = i;+        vdata[i].right_extreme = i;+        vdata[i].offset_to_left_extreme = 0.0;+        vdata[i].offset_to_right_extreme = 0.0;     }     vdata[root].parent = root;     vdata[root].level = 0;@@ -868,10 +866,29 @@      IGRAPH_PROGRESS("Reingold-Tilford tree layout", 100.0, NULL); +#ifdef LAYOUT_RT_DEBUG+    for (i = 0; i < no_of_nodes; i++) {+        printf(+            "%3ld: offset = %.2f, contours = [%ld, %ld], contour offsets = [%.2f, %.2f]\n",+            i, vdata[i].offset,+            vdata[i].left_contour, vdata[i].right_contour,+            vdata[i].offset_to_left_contour, vdata[i].offset_to_right_contour+        );+        if (vdata[i].left_extreme != i || vdata[i].right_extreme != i) {+            printf(+                "     extrema = [%ld, %ld], offsets to extrema = [%.2f, %.2f]\n",+                vdata[i].left_extreme, vdata[i].right_extreme,+                vdata[i].offset_to_left_extreme, vdata[i].offset_to_right_extreme+            );+        }+    }+#endif+     return 0; } -int igraph_i_layout_reingold_tilford_calc_coords(struct igraph_i_reingold_tilford_vertex *vdata,+static int igraph_i_layout_reingold_tilford_calc_coords(+        struct igraph_i_reingold_tilford_vertex *vdata,         igraph_matrix_t *res, long int node,         long int vcount, igraph_real_t xpos) {     long int i;@@ -888,12 +905,16 @@     return 0; } -int igraph_i_layout_reingold_tilford_postorder(struct igraph_i_reingold_tilford_vertex *vdata,+static int igraph_i_layout_reingold_tilford_postorder(+        struct igraph_i_reingold_tilford_vertex *vdata,         long int node, long int vcount) {     long int i, j, childcount, leftroot, leftrootidx;+    const igraph_real_t minsep = 1;     igraph_real_t avg; -    /* printf("Starting visiting node %d\n", node); */+#ifdef LAYOUT_RT_DEBUG+    printf("Starting visiting node %ld\n", node);+#endif      /* Check whether this node is a leaf node */     childcount = 0;@@ -922,93 +943,156 @@      * will be checked against the left contour of the next subtree */     leftroot = leftrootidx = -1;     avg = 0.0;-    /*printf("Visited node %d and arranged its subtrees\n", node);*/+#ifdef LAYOUT_RT_DEBUG+    printf("Visited node %ld and arranged its subtrees\n", node);+#endif     for (i = 0, j = 0; i < vcount; i++) {         if (i == node) {             continue;         }         if (vdata[i].parent == node) {-            /*printf("  Placing child %d on level %d\n", i, vdata[i].level);*/             if (leftroot >= 0) {                 /* Now we will follow the right contour of leftroot and the                  * left contour of the subtree rooted at i */-                long lnode, rnode;-                igraph_real_t loffset, roffset, minsep, rootsep;+                long lnode, rnode, auxnode;+                igraph_real_t loffset, roffset, rootsep, newoffset;++#ifdef LAYOUT_RT_DEBUG+                printf("  Placing child %ld on level %ld, to the right of %ld\n", i, vdata[i].level, leftroot);+#endif                 lnode = leftroot; rnode = i;-                minsep = 1;                 rootsep = vdata[leftroot].offset + minsep;-                loffset = 0; roffset = minsep;-                /*printf("    Contour: [%d, %d], offsets: [%lf, %lf], rootsep: %lf\n",-                       lnode, rnode, loffset, roffset, rootsep);*/+                loffset = vdata[leftroot].offset; roffset = loffset + minsep;++                /* Keep on updating the right contour now that we have attached+                 * a new node to the subtree being built */+                vdata[node].right_contour = i;+                vdata[node].offset_to_right_contour = rootsep;++#ifdef LAYOUT_RT_DEBUG+                printf("    Contour: [%ld, %ld], offsets: [%lf, %lf], rootsep: %lf\n",+                       lnode, rnode, loffset, roffset, rootsep);+#endif                 while ((lnode >= 0) && (rnode >= 0)) {                     /* Step to the next level on the right contour of the left subtree */                     if (vdata[lnode].right_contour >= 0) {-                        loffset += vdata[lnode].offset_follow_rc;+                        loffset += vdata[lnode].offset_to_right_contour;                         lnode = vdata[lnode].right_contour;                     } else {-                        /* Left subtree ended there. The right contour of the left subtree-                         * will continue to the next step on the right subtree. */+                        /* Left subtree ended there. The left and right contour+                         * of the left subtree will continue to the next step+                         * on the right subtree. */                         if (vdata[rnode].left_contour >= 0) {-                            /*printf("      Left subtree ended, continuing left subtree's left and right contour on right subtree (node %ld)\n", vdata[rnode].left_contour);*/-                            vdata[lnode].left_contour = vdata[rnode].left_contour;-                            vdata[lnode].right_contour = vdata[rnode].left_contour;-                            vdata[lnode].offset_follow_lc = vdata[lnode].offset_follow_rc =-                                                                (roffset - loffset) + vdata[rnode].offset_follow_lc;-                            /*printf("      vdata[lnode].offset_follow_* = %.4f\n", vdata[lnode].offset_follow_lc);*/+                            auxnode = vdata[node].left_extreme;++                            /* this is the "threading" step that the original+                             * paper is talking about */+                            newoffset = (vdata[node].offset_to_right_extreme - vdata[node].offset_to_left_extreme) + minsep + vdata[rnode].offset_to_left_contour;+                            vdata[auxnode].left_contour = vdata[rnode].left_contour;+                            vdata[auxnode].right_contour = vdata[rnode].left_contour;+                            vdata[auxnode].offset_to_left_contour = vdata[auxnode].offset_to_right_contour = newoffset;++                            /* since we attached a larger subtree to the+                             * already placed left subtree, we need to update+                             * the extrema of the subtree rooted at 'node' */+                            vdata[node].left_extreme = vdata[i].left_extreme;+                            vdata[node].right_extreme = vdata[i].right_extreme;+                            vdata[node].offset_to_left_extreme = vdata[i].offset_to_left_extreme + rootsep;+                            vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme + rootsep;+#ifdef LAYOUT_RT_DEBUG+                            printf("      Left subtree ended earlier, continuing left subtree's left and right contour on right subtree (node %ld gets connected to node %ld)\n", auxnode, vdata[rnode].left_contour);+                            printf("      New contour following offset for node %ld is %lf\n", auxnode, vdata[auxnode].offset_to_left_contour);+#endif+                        } else {+                            /* Both subtrees are ending at the same time; the+                             * left extreme node of the subtree rooted at+                             * 'node' remains the same but the right extreme+                             * will change */+                            vdata[node].right_extreme = vdata[i].right_extreme;+                            vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme + rootsep;                         }                         lnode = -1;                     }                     /* Step to the next level on the left contour of the right subtree */                     if (vdata[rnode].left_contour >= 0) {-                        roffset += vdata[rnode].offset_follow_lc;+                        roffset += vdata[rnode].offset_to_left_contour;                         rnode = vdata[rnode].left_contour;                     } else {-                        /* Right subtree ended here. The left contour of the right+                        /* Right subtree ended here. The right contour of the right                          * subtree will continue to the next step on the left subtree.                          * Note that lnode has already been advanced here */                         if (lnode >= 0) {-                            /*printf("      Right subtree ended, continuing right subtree's left and right contour on left subtree (node %ld)\n", lnode);*/-                            vdata[rnode].left_contour = lnode;-                            vdata[rnode].right_contour = lnode;-                            vdata[rnode].offset_follow_lc = vdata[rnode].offset_follow_rc =-                                                                (loffset - roffset); /* loffset has also been increased earlier */-                            /*printf("      vdata[rnode].offset_follow_* = %.4f\n", vdata[rnode].offset_follow_lc);*/+                            auxnode = vdata[i].right_extreme;++                            /* this is the "threading" step that the original+                             * paper is talking about */+                            newoffset = loffset - rootsep - vdata[i].offset_to_right_extreme;+                            vdata[auxnode].left_contour = lnode;+                            vdata[auxnode].right_contour = lnode;+                            vdata[auxnode].offset_to_left_contour = vdata[auxnode].offset_to_right_contour = newoffset;++                            /* no need to update the extrema of the subtree+                             * rooted at 'node' because the right subtree was+                             * smaller */+#ifdef LAYOUT_RT_DEBUG+                            printf("      Right subtree ended earlier, continuing right subtree's left and right contour on left subtree (node %ld gets connected to node %ld)\n", auxnode, lnode);+                            printf("      New contour following offset for node %ld is %lf\n", auxnode, vdata[auxnode].offset_to_left_contour);+#endif                         }                         rnode = -1;                     }-                    /*printf("    Contour: [%d, %d], offsets: [%lf, %lf], rootsep: %lf\n",-                           lnode, rnode, loffset, roffset, rootsep);*/+#ifdef LAYOUT_RT_DEBUG+                    printf("    Contour: [%ld, %ld], offsets: [%lf, %lf], rootsep: %lf\n", +                           lnode, rnode, loffset, roffset, rootsep);+#endif                      /* Push subtrees away if necessary */                     if ((lnode >= 0) && (rnode >= 0) && (roffset - loffset < minsep)) {-                        /*printf("    Pushing right subtree away by %lf\n", minsep-roffset+loffset);*/+#ifdef LAYOUT_RT_DEBUG+                        printf("    Pushing right subtree away by %lf\n", minsep-roffset+loffset);+#endif                         rootsep += minsep - roffset + loffset;                         roffset = loffset + minsep;+                        vdata[node].offset_to_right_contour = rootsep;                     }                 } -                /*printf("  Offset of subtree with root node %d will be %lf\n", i, rootsep);*/+#ifdef LAYOUT_RT_DEBUG+                printf("  Offset of subtree with root node %ld will be %lf\n", i, rootsep);+#endif                 vdata[i].offset = rootsep;-                vdata[node].right_contour = i;-                vdata[node].offset_follow_rc = rootsep;+                vdata[node].offset_to_right_contour = rootsep;                 avg = (avg * j) / (j + 1) + rootsep / (j + 1);                 leftrootidx = j;                 leftroot = i;             } else {+                /* This is the first child of the node being considered so we+                 * can simply place the subtree on our virtual canvas */+#ifdef LAYOUT_RT_DEBUG+                printf("  Placing child %ld on level %ld as first child\n", i, vdata[i].level);+#endif                 leftrootidx = j;                 leftroot = i;                 vdata[node].left_contour = i;                 vdata[node].right_contour = i;-                vdata[node].offset_follow_lc = 0.0;-                vdata[node].offset_follow_rc = 0.0;+                vdata[node].offset_to_left_contour = 0.0;+                vdata[node].offset_to_right_contour = 0.0;+                vdata[node].left_extreme = vdata[i].left_extreme;+                vdata[node].right_extreme = vdata[i].right_extreme;+                vdata[node].offset_to_left_extreme = vdata[i].offset_to_left_extreme;+                vdata[node].offset_to_right_extreme = vdata[i].offset_to_right_extreme;                 avg = vdata[i].offset;             }             j++;         }     }-    /*printf("Shifting node to be centered above children. Shift amount: %lf\n", avg);*/-    vdata[node].offset_follow_lc -= avg;-    vdata[node].offset_follow_rc -= avg;+#ifdef LAYOUT_RT_DEBUG+    printf("Shifting node %ld to be centered above children. Shift amount: %lf\n", node, avg);+#endif+    vdata[node].offset_to_left_contour -= avg;+    vdata[node].offset_to_right_contour -= avg;+    vdata[node].offset_to_left_extreme -= avg;+    vdata[node].offset_to_right_extreme -= avg;     for (i = 0, j = 0; i < vcount; i++) {         if (i == node) {             continue;@@ -1419,10 +1503,12 @@ #define COULOMBS_CONSTANT 8987500000.0  -igraph_real_t igraph_i_distance_between(const igraph_matrix_t *c, long int a,-                                        long int b);+static igraph_real_t igraph_i_distance_between(+        const igraph_matrix_t *c,+        long int a, long int b); -int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos,+static int igraph_i_determine_electric_axal_forces(+        const igraph_matrix_t *pos,         igraph_real_t *x,         igraph_real_t *y,         igraph_real_t directed_force,@@ -1430,14 +1516,16 @@         long int other_node,         long int this_node); -int igraph_i_apply_electrical_force(const igraph_matrix_t *pos,-                                    igraph_vector_t *pending_forces_x,-                                    igraph_vector_t *pending_forces_y,-                                    long int other_node, long int this_node,-                                    igraph_real_t node_charge,-                                    igraph_real_t distance);+static int igraph_i_apply_electrical_force(+        const igraph_matrix_t *pos,+        igraph_vector_t *pending_forces_x,+        igraph_vector_t *pending_forces_y,+        long int other_node, long int this_node,+        igraph_real_t node_charge,+        igraph_real_t distance); -int igraph_i_determine_spring_axal_forces(const igraph_matrix_t *pos,+static int igraph_i_determine_spring_axal_forces(+        const igraph_matrix_t *pos,         igraph_real_t *x, igraph_real_t *y,         igraph_real_t directed_force,         igraph_real_t distance,@@ -1445,27 +1533,30 @@         long int other_node,         long int this_node); -int igraph_i_apply_spring_force(const igraph_matrix_t *pos,-                                igraph_vector_t *pending_forces_x,-                                igraph_vector_t *pending_forces_y,-                                long int other_node,-                                long int this_node, int spring_length,-                                igraph_real_t spring_constant);+static int igraph_i_apply_spring_force(+        const igraph_matrix_t *pos,+        igraph_vector_t *pending_forces_x,+        igraph_vector_t *pending_forces_y,+        long int other_node,+        long int this_node, int spring_length,+        igraph_real_t spring_constant); -int igraph_i_move_nodes(igraph_matrix_t *pos,-                        const igraph_vector_t *pending_forces_x,-                        const igraph_vector_t *pending_forces_y,-                        igraph_real_t node_mass,-                        igraph_real_t max_sa_movement);+static int igraph_i_move_nodes(+        igraph_matrix_t *pos,+        const igraph_vector_t *pending_forces_x,+        const igraph_vector_t *pending_forces_y,+        igraph_real_t node_mass,+        igraph_real_t max_sa_movement); -igraph_real_t igraph_i_distance_between(const igraph_matrix_t *c, long int a,-                                        long int b) {+static igraph_real_t igraph_i_distance_between(+        const igraph_matrix_t *c,+        long int a, long int b) {     igraph_real_t diffx = MATRIX(*c, a, 0) - MATRIX(*c, b, 0);     igraph_real_t diffy = MATRIX(*c, a, 1) - MATRIX(*c, b, 1);     return sqrt( diffx * diffx + diffy * diffy ); } -int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos,+static int igraph_i_determine_electric_axal_forces(const igraph_matrix_t *pos,         igraph_real_t *x,         igraph_real_t *y,         igraph_real_t directed_force,@@ -1518,12 +1609,13 @@     return 0; } -int igraph_i_apply_electrical_force(const igraph_matrix_t *pos,-                                    igraph_vector_t *pending_forces_x,-                                    igraph_vector_t *pending_forces_y,-                                    long int other_node, long int this_node,-                                    igraph_real_t node_charge,-                                    igraph_real_t distance) {+static int igraph_i_apply_electrical_force(+        const igraph_matrix_t *pos,+        igraph_vector_t *pending_forces_x,+        igraph_vector_t *pending_forces_y,+        long int other_node, long int this_node,+        igraph_real_t node_charge,+        igraph_real_t distance) {      igraph_real_t directed_force = COULOMBS_CONSTANT *                                    ((node_charge * node_charge) / (distance * distance));@@ -1541,7 +1633,8 @@     return 0; } -int igraph_i_determine_spring_axal_forces(const igraph_matrix_t *pos,+static int igraph_i_determine_spring_axal_forces(+        const igraph_matrix_t *pos,         igraph_real_t *x, igraph_real_t *y,         igraph_real_t directed_force,         igraph_real_t distance,@@ -1579,12 +1672,13 @@     return 0; } -int igraph_i_apply_spring_force(const igraph_matrix_t *pos,-                                igraph_vector_t *pending_forces_x,-                                igraph_vector_t *pending_forces_y,-                                long int other_node,-                                long int this_node, int spring_length,-                                igraph_real_t spring_constant) {+static int igraph_i_apply_spring_force(+        const igraph_matrix_t *pos,+        igraph_vector_t *pending_forces_x,+        igraph_vector_t *pending_forces_y,+        long int other_node,+        long int this_node, int spring_length,+        igraph_real_t spring_constant) {      // determined using Hooke's Law:     //   force = -kx@@ -1625,11 +1719,12 @@     return 0; } -int igraph_i_move_nodes(igraph_matrix_t *pos,-                        const igraph_vector_t *pending_forces_x,-                        const igraph_vector_t *pending_forces_y,-                        igraph_real_t node_mass,-                        igraph_real_t max_sa_movement) {+static int igraph_i_move_nodes(+        igraph_matrix_t *pos,+        const igraph_vector_t *pending_forces_x,+        const igraph_vector_t *pending_forces_y,+        igraph_real_t node_mass,+        igraph_real_t max_sa_movement) {      // Since each iteration is isolated, time is constant at 1.     // Therefore:@@ -1822,11 +1917,13 @@     return 0; } +/* not 'static', used in tests */ int igraph_i_layout_merge_dla(igraph_i_layout_mergegrid_t *grid,                               long int actg, igraph_real_t *x, igraph_real_t *y, igraph_real_t r,                               igraph_real_t cx, igraph_real_t cy, igraph_real_t startr,                               igraph_real_t killr); +/* TODO: not 'static' because used in tests */ int igraph_i_layout_sphere_2d(igraph_matrix_t *coords, igraph_real_t *x,                               igraph_real_t *y, igraph_real_t *r); int igraph_i_layout_sphere_3d(igraph_matrix_t *coords, igraph_real_t *x,@@ -1981,7 +2078,8 @@     return 0; } -int igraph_i_layout_sphere_2d(igraph_matrix_t *coords, igraph_real_t *x, igraph_real_t *y,+int igraph_i_layout_sphere_2d(igraph_matrix_t *coords,+                              igraph_real_t *x, igraph_real_t *y,                               igraph_real_t *r) {     long int nodes = igraph_matrix_nrow(coords);     long int i;@@ -2012,7 +2110,8 @@     return 0; } -int igraph_i_layout_sphere_3d(igraph_matrix_t *coords, igraph_real_t *x, igraph_real_t *y,+int igraph_i_layout_sphere_3d(igraph_matrix_t *coords,+                              igraph_real_t *x, igraph_real_t *y,                               igraph_real_t *z, igraph_real_t *r) {     long int nodes = igraph_matrix_nrow(coords);     long int i;@@ -2094,14 +2193,14 @@     return 0; } -int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from,-                             int n, void *extra);+static int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from,+                                    int n, void *extra); -int igraph_i_layout_mds_single(const igraph_t* graph, igraph_matrix_t *res,-                               igraph_matrix_t *dist, long int dim);+static int igraph_i_layout_mds_single(const igraph_t* graph, igraph_matrix_t *res,+                                      igraph_matrix_t *dist, long int dim); -int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from,-                             int n, void *extra) {+static int igraph_i_layout_mds_step(igraph_real_t *to, const igraph_real_t *from,+                                    int n, void *extra) {     igraph_matrix_t* matrix = (igraph_matrix_t*)extra;     IGRAPH_UNUSED(n);     igraph_blas_dgemv_array(0, 1, matrix, from, 0, to);
igraph/src/layout_dh.c view
@@ -26,9 +26,11 @@ #include "igraph_interface.h" #include "igraph_random.h" #include "igraph_math.h"+#include "igraph_interrupt_internal.h"  #include <math.h> +/* not 'static', used in tests */ igraph_bool_t igraph_i_segments_intersect(float p0_x, float p0_y,         float p1_x, float p1_y,         float p2_x, float p2_y,@@ -52,6 +54,7 @@     return s >= 0 && s <= 1 && t >= 0 && t <= 1 ? 1 : 0; } +/* not 'static', used in tests */ float igraph_i_point_segment_dist2(float v_x, float v_y,                                    float u1_x, float u1_y,                                    float u2_x, float u2_y) {@@ -240,6 +243,8 @@     for (round = 0; round < maxiter + fineiter; round++) {         igraph_integer_t p;         igraph_vector_int_shuffle(&perm);++        IGRAPH_ALLOW_INTERRUPTION();          fine_tuning = round >= maxiter;         if (fine_tuning) {
igraph/src/layout_fr.c view
@@ -28,16 +28,16 @@ #include "igraph_components.h" #include "igraph_types_internal.h" -int igraph_layout_i_fr(const igraph_t *graph,-                       igraph_matrix_t *res,-                       igraph_bool_t use_seed,-                       igraph_integer_t niter,-                       igraph_real_t start_temp,-                       const igraph_vector_t *weight,-                       const igraph_vector_t *minx,-                       const igraph_vector_t *maxx,-                       const igraph_vector_t *miny,-                       const igraph_vector_t *maxy) {+static int igraph_layout_i_fr(const igraph_t *graph,+                              igraph_matrix_t *res,+                              igraph_bool_t use_seed,+                              igraph_integer_t niter,+                              igraph_real_t start_temp,+                              const igraph_vector_t *weight,+                              const igraph_vector_t *minx,+                              const igraph_vector_t *maxx,+                              const igraph_vector_t *miny,+                              const igraph_vector_t *maxy) {      igraph_integer_t no_nodes = igraph_vcount(graph);     igraph_integer_t no_edges = igraph_ecount(graph);@@ -188,12 +188,13 @@     return 0; } -int igraph_layout_i_grid_fr(const igraph_t *graph,-                            igraph_matrix_t *res, igraph_bool_t use_seed,-                            igraph_integer_t niter, igraph_real_t start_temp,-                            const igraph_vector_t *weight, const igraph_vector_t *minx,-                            const igraph_vector_t *maxx, const igraph_vector_t *miny,-                            const igraph_vector_t *maxy) {+static int igraph_layout_i_grid_fr(+        const igraph_t *graph,+        igraph_matrix_t *res, igraph_bool_t use_seed,+        igraph_integer_t niter, igraph_real_t start_temp,+        const igraph_vector_t *weight, const igraph_vector_t *minx,+        const igraph_vector_t *maxx, const igraph_vector_t *miny,+        const igraph_vector_t *maxy) {      igraph_integer_t no_nodes = igraph_vcount(graph);     igraph_integer_t no_edges = igraph_ecount(graph);
igraph/src/layout_kk.c view
@@ -41,8 +41,10 @@  *        contain the result (x-positions in column zero and  *        y-positions in column one) and will be resized if needed.  * \param use_seed Boolean, whether to use the values supplied in the- *        \p res argument as the initial configuration. If zero then a- *        random initial configuration is used.+ *        \p res argument as the initial configuration. If zero and there+ *        are any limits on the X or Y coordinates, then a random initial+ *        configuration is used. Otherwise the vertices are placed on a+ *        circle of radius 1 as the initial configuration.  * \param maxiter The maximum number of iterations to perform. A reasonable  *        default value is at least ten (or more) times the number of  *        vertices.@@ -285,7 +287,7 @@         /* Update delta, only with/for the affected node */         VECTOR(D1)[m] = VECTOR(D2)[m] = 0.0;         for (i = 0; i < no_nodes; i++) {-            igraph_real_t old_dx, old_dy, old_mi, new_dx, new_dy, new_mi_dist, old_mi_dist;+            igraph_real_t old_dx, old_dy, new_dx, new_dy, new_mi_dist, old_mi_dist;             if (i == m) {                 continue;             }@@ -340,8 +342,10 @@  *        contain the result (x-positions in column zero and  *        y-positions in column one) and will be resized if needed.  * \param use_seed Boolean, whether to use the values supplied in the- *        \p res argument as the initial configuration. If zero then a- *        random initial configuration is used.+ *        \p res argument as the initial configuration. If zero and there+ *        are any limits on the X, Y or Z coordinates, then a random initial+ *        configuration is used. Otherwise the vertices are placed uniformly+ *        on a sphere of radius 1 as the initial configuration.  * \param maxiter The maximum number of iterations to perform. A reasonable  *        default value is at least ten (or more) times the number of  *        vertices.@@ -577,6 +581,7 @@             dz = old_z - MATRIX(*res, i, 2);             dist = sqrt(dx * dx + dy * dy + dz * dz);             den = dist * (dx * dx + dy * dy + dz * dz);+             k_mi = MATRIX(kij, m, i);             l_mi = MATRIX(lij, m, i);             Axx += k_mi * (1 - l_mi * (dy * dy + dz * dz) / den);@@ -594,9 +599,16 @@ #define DET(a,b,c,d,e,f,g,h,i) ((a*e*i+b*f*g+c*d*h)-(c*e*g+b*d*i+a*f*h))          detnum  = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Axz, Ayz, Azz);-        delta_x = DET(Ax, Ay, Az, Axy, Ayy, Ayz, Axz, Ayz, Azz) / detnum;-        delta_y = DET(Axx, Axy, Axz, Ax, Ay, Az, Axz, Ayz, Azz) / detnum;-        delta_z = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Ax, Ay, Az ) / detnum;+        if (detnum != 0) {+            delta_x = DET(Ax, Ay, Az, Axy, Ayy, Ayz, Axz, Ayz, Azz) / detnum;+            delta_y = DET(Axx, Axy, Axz, Ax, Ay, Az, Axz, Ayz, Azz) / detnum;+            delta_z = DET(Axx, Axy, Axz, Axy, Ayy, Ayz, Ax, Ay, Az ) / detnum;+        } else {+            /* No new stable position for node m; this can happen in rare+             * cases, e.g., if the graph has two nodes only. It's best to leave+             * the node where it is. */+            delta_x = delta_y = delta_z = 0;+        }          new_x = old_x + delta_x;         new_y = old_y + delta_y;
igraph/src/lsap.c view
@@ -2,12 +2,11 @@ #include "igraph_lsap.h" #include "igraph_error.h" -#include <stdio.h>+/* #include <stdio.h> */ #include <stdlib.h> #include <math.h> #include <limits.h>     /* INT_MAX */ #include <float.h>      /* DBL_MAX */-#include <assert.h> #include <time.h>  /* constants used for improving readability of code */@@ -40,30 +39,30 @@ /* public interface */  /* constructors and destructor */-AP     *ap_create_problem(double *t, int n);-AP     *ap_create_problem_from_matrix(double **t, int n);-AP     *ap_read_problem(char *file);-void    ap_free(AP *p);+static AP     *ap_create_problem(double *t, int n);+static AP     *ap_create_problem_from_matrix(double **t, int n);+static AP     *ap_read_problem(char *file);+static void    ap_free(AP *p); -int     ap_assignment(AP *p, int *res);-int     ap_costmatrix(AP *p, double **m);-int     ap_datamatrix(AP *p, double **m);-int     ap_iterations(AP *p);-int     ap_hungarian(AP *p);-double  ap_mincost(AP *p);-void    ap_print_solution(AP *p);-void    ap_show_data(AP *p);-int     ap_size(AP *p);-int     ap_time(AP *p);+static int     ap_assignment(AP *p, int *res);+static int     ap_costmatrix(AP *p, double **m);+static int     ap_datamatrix(AP *p, double **m);+static int     ap_iterations(AP *p);+static int     ap_hungarian(AP *p);+static double  ap_mincost(AP *p);+/* static void    ap_print_solution(AP *p); */+/* static void    ap_show_data(AP *p); */+static int     ap_size(AP *p);+static int     ap_time(AP *p);  /* error reporting */-void ap_error(char *message);+/* static void ap_error(char *message); */  /* private functions */-void    preprocess(AP *p);-void    preassign(AP *p);-int     cover(AP *p, int *ri, int *ci);-void    reduce(AP *p, int *ri, int *ci);+static void    preprocess(AP *p);+static void    preassign(AP *p);+static int     cover(AP *p, int *ri, int *ci);+static void    reduce(AP *p, int *ri, int *ci);  int ap_hungarian(AP *p) {     int      n;            /* size of problem */
igraph/src/matching.c view
@@ -21,17 +21,15 @@  */ -#include <assert.h>-#include <math.h>-#include "config.h" #include "igraph_adjlist.h" #include "igraph_constructors.h" #include "igraph_conversion.h" #include "igraph_dqueue.h"-#include "igraph_flow.h" #include "igraph_interface.h" #include "igraph_matching.h" #include "igraph_structural.h"+#include "config.h"+#include <math.h>  /* #define MATCHING_DEBUG */ @@ -207,10 +205,12 @@     return IGRAPH_SUCCESS; } -int igraph_i_maximum_bipartite_matching_unweighted(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_unweighted(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_integer_t* matching_size,         igraph_vector_long_t* matching);-int igraph_i_maximum_bipartite_matching_weighted(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_weighted(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_integer_t* matching_size,         igraph_real_t* matching_weight, igraph_vector_long_t* matching,         const igraph_vector_t* weights, igraph_real_t eps);@@ -306,7 +306,8 @@     } } -int igraph_i_maximum_bipartite_matching_unweighted_relabel(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_unweighted_relabel(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_vector_t* labels,         igraph_vector_long_t* matching, igraph_bool_t smaller_set); @@ -323,7 +324,8 @@  * Avancée en Calcul Scientifique).  * http://www.cerfacs.fr/algor/reports/2011/TR_PA_11_33.pdf  */-int igraph_i_maximum_bipartite_matching_unweighted(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_unweighted(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_integer_t* matching_size,         igraph_vector_long_t* matching) {     long int i, j, k, n, no_of_nodes = igraph_vcount(graph);@@ -460,7 +462,8 @@     return IGRAPH_SUCCESS; } -int igraph_i_maximum_bipartite_matching_unweighted_relabel(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_unweighted_relabel(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_vector_t* labels,         igraph_vector_long_t* match, igraph_bool_t smaller_set) {     long int i, j, n, no_of_nodes = igraph_vcount(graph), matched_to;@@ -529,7 +532,8 @@  * an edge falls below \c eps, it will be considered tight. If all your  * weights are integers, you can safely set \c eps to zero.  */-int igraph_i_maximum_bipartite_matching_weighted(const igraph_t* graph,+static int igraph_i_maximum_bipartite_matching_weighted(+        const igraph_t* graph,         const igraph_vector_bool_t* types, igraph_integer_t* matching_size,         igraph_real_t* matching_weight, igraph_vector_long_t* matching,         const igraph_vector_t* weights, igraph_real_t eps) {
igraph/src/math.c view
@@ -33,9 +33,7 @@ #endif  int igraph_finite(double x) {-#ifdef isfinite-    return isfinite(x);-#elif HAVE_ISFINITE == 1+#if HAVE_DECL_ISFINITE     return isfinite(x); #elif HAVE_FINITE == 1     return finite(x);@@ -79,11 +77,13 @@     int i;      if (n < 1 || n > 1000) {-        IGRAPH_NAN;+        IGRAPH_WARNING("chebyshev_eval: argument out of domain");+        return IGRAPH_NAN;     }      if (x < -1.1 || x > 1.1) {-        IGRAPH_NAN;+        IGRAPH_WARNING("chebyshev_eval: argument out of domain");+        return IGRAPH_NAN;     }      twox = x * 2;@@ -256,11 +256,11 @@ }  int igraph_is_posinf(double x) {-    return isinf(x) == 1;+    return isinf(x) && x > 0; }  int igraph_is_neginf(double x) {-    return isinf(x) == -1;+    return isinf(x) && x < 0; }  /**
igraph/src/maximal_cliques.c view
@@ -35,13 +35,14 @@ #define CONCAT2(a,b) CONCAT2x(a,b) #define FUNCTION(name,sfx) CONCAT2(name,sfx) -int igraph_i_maximal_cliques_reorder_adjlists(-    const igraph_vector_int_t *PX,-    int PS, int PE, int XS, int XE,-    const igraph_vector_int_t *pos,-    igraph_adjlist_t *adjlist);+static int igraph_i_maximal_cliques_reorder_adjlists(+        const igraph_vector_int_t *PX,+        int PS, int PE, int XS, int XE,+        const igraph_vector_int_t *pos,+        igraph_adjlist_t *adjlist); -int igraph_i_maximal_cliques_select_pivot(const igraph_vector_int_t *PX,+static int igraph_i_maximal_cliques_select_pivot(+        const igraph_vector_int_t *PX,         int PS, int PE, int XS, int XE,         const igraph_vector_int_t *pos,         const igraph_adjlist_t *adjlist,@@ -49,23 +50,26 @@         igraph_vector_int_t *nextv,         int oldPS, int oldXE); -int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX,-                                  int PS, int PE, int XS, int XE,-                                  igraph_vector_int_t *pos,-                                  igraph_adjlist_t *adjlist, int mynextv,-                                  igraph_vector_int_t *R,-                                  int *newPS, int *newXE);+static int igraph_i_maximal_cliques_down(+        igraph_vector_int_t *PX,+        int PS, int PE, int XS, int XE,+        igraph_vector_int_t *pos,+        igraph_adjlist_t *adjlist, int mynextv,+        igraph_vector_int_t *R,+        int *newPS, int *newXE); -int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE,-                                int *XS, int XE, igraph_vector_int_t *pos,-                                igraph_adjlist_t *adjlist, int v,-                                igraph_vector_int_t *H);+static int igraph_i_maximal_cliques_PX(+        igraph_vector_int_t *PX, int PS, int *PE,+        int *XS, int XE, igraph_vector_int_t *pos,+        igraph_adjlist_t *adjlist, int v,+        igraph_vector_int_t *H); -int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE,-                                int XS, int XE, igraph_vector_int_t *pos,-                                igraph_adjlist_t *adjlist,-                                igraph_vector_int_t *R,-                                igraph_vector_int_t *H);+static int igraph_i_maximal_cliques_up(+        igraph_vector_int_t *PX, int PS, int PE,+        int XS, int XE, igraph_vector_int_t *pos,+        igraph_adjlist_t *adjlist,+        igraph_vector_int_t *R,+        igraph_vector_int_t *H);  #define PRINT_PX do {                              \         int j;                                 \@@ -109,11 +113,11 @@         printf("\n");                              \     } while (0) -int igraph_i_maximal_cliques_reorder_adjlists(-    const igraph_vector_int_t *PX,-    int PS, int PE, int XS, int XE,-    const igraph_vector_int_t *pos,-    igraph_adjlist_t *adjlist) {+static int igraph_i_maximal_cliques_reorder_adjlists(+        const igraph_vector_int_t *PX,+        int PS, int PE, int XS, int XE,+        const igraph_vector_int_t *pos,+        igraph_adjlist_t *adjlist) {     int j;     int sPS = PS + 1, sPE = PE + 1; @@ -140,7 +144,8 @@     return 0; } -int igraph_i_maximal_cliques_select_pivot(const igraph_vector_int_t *PX,+static int igraph_i_maximal_cliques_select_pivot(+        const igraph_vector_int_t *PX,         int PS, int PE, int XS, int XE,         const igraph_vector_int_t *pos,         const igraph_adjlist_t *adjlist,@@ -216,12 +221,12 @@         VECTOR(*pos)[v2] = (p1)+1;          \     } while (0) -int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX,-                                  int PS, int PE, int XS, int XE,-                                  igraph_vector_int_t *pos,-                                  igraph_adjlist_t *adjlist, int mynextv,-                                  igraph_vector_int_t *R,-                                  int *newPS, int *newXE) {+static int igraph_i_maximal_cliques_down(igraph_vector_int_t *PX,+                                         int PS, int PE, int XS, int XE,+                                         igraph_vector_int_t *pos,+                                         igraph_adjlist_t *adjlist, int mynextv,+                                         igraph_vector_int_t *R,+                                         int *newPS, int *newXE) {      igraph_vector_int_t *vneis = igraph_adjlist_get(adjlist, mynextv);     int j, vneislen = igraph_vector_int_size(vneis);@@ -247,10 +252,10 @@  #undef SWAP -int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE,-                                int *XS, int XE, igraph_vector_int_t *pos,-                                igraph_adjlist_t *adjlist, int v,-                                igraph_vector_int_t *H) {+static int igraph_i_maximal_cliques_PX(igraph_vector_int_t *PX, int PS, int *PE,+                                       int *XS, int XE, igraph_vector_int_t *pos,+                                       igraph_adjlist_t *adjlist, int v,+                                       igraph_vector_int_t *H) {      int vpos = VECTOR(*pos)[v] - 1;     int tmp = VECTOR(*PX)[*PE];@@ -264,11 +269,11 @@     return 0; } -int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE,-                                int XS, int XE, igraph_vector_int_t *pos,-                                igraph_adjlist_t *adjlist,-                                igraph_vector_int_t *R,-                                igraph_vector_int_t *H) {+static int igraph_i_maximal_cliques_up(igraph_vector_int_t *PX, int PS, int PE,+                                       int XS, int XE, igraph_vector_int_t *pos,+                                       igraph_adjlist_t *adjlist,+                                       igraph_vector_int_t *R,+                                       igraph_vector_int_t *H) {     int vv;     igraph_vector_int_pop_back(R); @@ -287,7 +292,7 @@  /**  * \function igraph_maximal_cliques- * \brief Find all maximal cliques of a graph+ * \brief Finds all maximal cliques in a graph.  *  * </para><para>  * A maximal clique is a clique which can't be extended any more by@@ -311,7 +316,7 @@  *  * \param graph The input graph.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_vector_t+ *   here, i.e. \p res will contain pointers to \ref igraph_vector_t  *   objects which contain the indices of vertices involved in a clique.  *   The pointer vector will be resized if needed but note that the  *   objects in the pointer vector will not be freed. Note that vertices@@ -415,11 +420,11 @@  /**  * \function igraph_maximal_cliques_callback- * \brief Finds maximal cliques in a graph and calls a function for each one+ * \brief Finds maximal cliques in a graph and calls a function for each one.  *  * This function enumerates all maximal cliques within the given size range  * and calls \p cliquehandler_fn for each of them. The cliques are passed to the- * callback function as an <type>igraph_vector_t *</type>.  Destroying and+ * callback function as a pointer to an \ref igraph_vector_t.  Destroying and  * freeing this vector is left up to the user.  Use \ref igraph_vector_destroy()  * to destroy it first, then free it using \ref igraph_free().  *@@ -457,7 +462,7 @@  /**  * \function igraph_maximal_cliques_hist- * \brief Count the number of maximal cliques of each size in a graph.+ * \brief Counts the number of maximal cliques of each size in a graph.  *  * This function counts how many maximal cliques of each size are present in  * the graph. Size-1 maximal cliques are simply isolated vertices.@@ -472,7 +477,7 @@  * \param hist Pointer to an initialized vector. The result will be stored  * here. The first element will store the number of size-1 maximal cliques,  * the second element the number of size-2 maximal cliques, etc.- * For cliques smaller than \c min_size, zero counts will be returned.+ * For cliques smaller than \p min_size, zero counts will be returned.  * \param min_size Integer giving the minimum size of the cliques to be  *   returned. If negative or zero, no lower bound will be used.  * \param max_size Integer giving the maximum size of the cliques to be
igraph/src/motifs.c view
@@ -27,31 +27,17 @@ #include "igraph_adjlist.h" #include "igraph_interrupt_internal.h" #include "igraph_interface.h"+#include "igraph_isoclasses.h" #include "igraph_nongraph.h"-#include "igraph_structural.h" #include "igraph_stack.h" #include "config.h" -#include <string.h>--extern unsigned int igraph_i_isoclass_3[];-extern unsigned int igraph_i_isoclass_4[];-extern unsigned int igraph_i_isoclass_3u[];-extern unsigned int igraph_i_isoclass_4u[];-extern unsigned int igraph_i_isoclass2_3[];-extern unsigned int igraph_i_isoclass2_4[];-extern unsigned int igraph_i_isoclass2_3u[];-extern unsigned int igraph_i_isoclass2_4u[];-extern unsigned int igraph_i_isoclass_3_idx[];-extern unsigned int igraph_i_isoclass_4_idx[];-extern unsigned int igraph_i_isoclass_3u_idx[];-extern unsigned int igraph_i_isoclass_4u_idx[];- /**  * Callback function for igraph_motifs_randesu that counts the motifs by  * isomorphism class in a histogram.  */-igraph_bool_t igraph_i_motifs_randesu_update_hist(const igraph_t *graph,+static igraph_bool_t igraph_i_motifs_randesu_update_hist(+        const igraph_t *graph,         igraph_vector_t *vids, int isoclass, void* extra) {     igraph_vector_t *hist = (igraph_vector_t*)extra;     IGRAPH_UNUSED(graph); IGRAPH_UNUSED(vids);@@ -65,14 +51,14 @@  *  * </para><para>  * Motifs are small connected subgraphs of a given structure in a- * graph. It is argued that the motif profile (ie. the number of+ * graph. It is argued that the motif profile (i.e. the number of  * different motifs in the graph) is characteristic for different  * types of networks and network function is related to the motifs in  * the graph.  *  * </para><para>  * This function is able to find the different motifs of size three- * and four (ie. the number of different subgraphs with three and four+ * and four (i.e. the number of different subgraphs with three and four  * vertices) in the network.  *  * </para><para>@@ -108,7 +94,7 @@  *        in a graph.  * \return Error code.  * \sa \ref igraph_motifs_randesu_estimate() for estimating the number- * of motifs in a graph, this can help to set the \c cut_prob+ * of motifs in a graph, this can help to set the \p cut_prob  * parameter; \ref igraph_motifs_randesu_no() to calculate the total  * number of motifs of a given size in a graph;  * \ref igraph_motifs_randesu_callback() for calling a callback function@@ -169,14 +155,14 @@  *  * </para><para>  * Similarly to \ref igraph_motifs_randesu(), this function is able to find the- * different motifs of size three and four (ie. the number of different+ * different motifs of size three and four (i.e. the number of different  * subgraphs with three and four vertices) in the network. However, instead of  * counting them, the function will call a callback function for each motif  * found to allow further tests or post-processing.  *  * </para><para>- * The \c cut_prob argument also allows sampling the motifs, just like for- * \ref igraph_motifs_randesu(). Set the \c cut_prob argument to a zero vector+ * The \p cut_prob argument also allows sampling the motifs, just like for+ * \ref igraph_motifs_randesu(). Set the \p cut_prob argument to a zero vector  * for finding all motifs.  *  * \param graph The graph to find the motifs in.@@ -214,7 +200,7 @@     long int *added;     char *subg; -    unsigned int *arr_idx, *arr_code;+    const unsigned int *arr_idx, *arr_code;     int code = 0;     unsigned char mul, idx; @@ -447,7 +433,7 @@  * </para><para>  * The total number of motifs is estimated by taking a sample of  * vertices and counts all motifs in which these vertices are- * included. (There is also a \c cut_prob parameter which gives the+ * included. (There is also a \p cut_prob parameter which gives the  * probabilities to cut a branch of the search tree.)  *  * </para><para>@@ -658,12 +644,9 @@  * \brief Count the total number of motifs in a graph  *  * </para><para>- * This function counts the total number of motifs in a graph without- * assigning isomorphism classes to them.- *- * </para><para>- * Directed motifs will be counted in directed graphs and undirected- * motifs in undirected graphs.+ * This function counts the total number of motifs in a graph,+ * i.e. the number of of (weakly) connected triplets or quadruplets,+ * without assigning isomorphism classes to them.  *  * \param graph The graph object to study.  * \param no Pointer to an integer type, the result will be stored
+ igraph/src/mt.c view
@@ -0,0 +1,95 @@+/* mt.c+ *+ * Mersenne Twister random number generator, based on the implementation of+ * Michael Brundage (which has been placed in the public domain).+ *+ * Author: Tamas Nepusz (original by Michael Brundage)+ *+ * See the following URL for the original implementation:+ * http://www.qbrundage.com/michaelb/pubs/essays/random_number_generation.html+ *+ * This file has been placed in the public domain.+ */++#include <stdlib.h>++#include "igraph_random.h"++#include "mt.h"++static uint16_t get_random_uint16() {+    return RNG_INT31() & 0xFFFF;+}++void mt_init(mt_rng_t* rng) {+    mt_init_from_rng(rng, 0);+}++void mt_init_from_rng(mt_rng_t* rng, mt_rng_t* seeder) {+    int i;++    if (seeder == 0) {+        for (i = 0; i < MT_LEN; i++) {+            /* RAND_MAX is guaranteed to be at least 32767, so we can use two+             * calls to rand() to produce a random 32-bit number */+            rng->mt_buffer[i] = (get_random_uint16() << 16) + get_random_uint16();+        }+    } else {+        for (i = 0; i < MT_LEN; i++) {+            rng->mt_buffer[i] = mt_random(seeder);+        }+    }++    rng->mt_index = 0;+}++#define MT_IA           397+#define MT_IB           (MT_LEN - MT_IA)+#define UPPER_MASK      0x80000000+#define LOWER_MASK      0x7FFFFFFF+#define MATRIX_A        0x9908B0DF+#define TWIST(b,i,j)    ((b)[i] & UPPER_MASK) | ((b)[j] & LOWER_MASK)+#define MAGIC(s)        (((s)&1)*MATRIX_A)++uint32_t mt_random(mt_rng_t* rng) {+    uint32_t * b = rng->mt_buffer;+    int idx = rng->mt_index;+    uint32_t s;+    int i;+	+    if (idx == MT_LEN * sizeof(uint32_t)) {+        idx = 0;+        i = 0;+        for (; i < MT_IB; i++) {+            s = TWIST(b, i, i+1);+            b[i] = b[i + MT_IA] ^ (s >> 1) ^ MAGIC(s);+        }+        for (; i < MT_LEN-1; i++) {+            s = TWIST(b, i, i+1);+            b[i] = b[i - MT_IB] ^ (s >> 1) ^ MAGIC(s);+        }+        +        s = TWIST(b, MT_LEN-1, 0);+        b[MT_LEN-1] = b[MT_IA-1] ^ (s >> 1) ^ MAGIC(s);+    }++    rng->mt_index = idx + sizeof(uint32_t);+    return *(uint32_t *)((unsigned char *)b + idx);+    /*+    Matsumoto and Nishimura additionally confound the bits returned to the caller+    but this doesn't increase the randomness, and slows down the generator by+    as much as 25%.  So I omit these operations here.+    +    r ^= (r >> 11);+    r ^= (r << 7) & 0x9D2C5680;+    r ^= (r << 15) & 0xEFC60000;+    r ^= (r >> 18);+    */+}+++double mt_uniform_01(mt_rng_t* rng) {+    return ((double)mt_random(rng)) / MT_RAND_MAX;+}++
igraph/src/operators.c view
@@ -31,8 +31,8 @@ #include "igraph_attributes.h" #include "igraph_conversion.h" #include "igraph_qsort.h"-#include <limits.h> #include "config.h"+#include <limits.h>  /**  * \function igraph_disjoint_union@@ -47,7 +47,7 @@  * and |E1|+|E2| edges.  *  * </para><para>- * Both graphs need to have the same directedness, ie. either both+ * Both graphs need to have the same directedness, i.e. either both  * directed or both undirected.  *  * </para><para>@@ -119,7 +119,7 @@  * of vertices and edges in the graphs.  *  * </para><para>- * Both graphs need to have the same directedness, ie. either both+ * Both graphs need to have the same directedness, i.e. either both  * directed or both undirected.  *  * </para><para>@@ -183,8 +183,7 @@     return 0; } -int igraph_i_order_edgelist_cmp(void *edges, const void *e1,-                                const void *e2) {+static int igraph_i_order_edgelist_cmp(void *edges, const void *e1, const void *e2) {     igraph_vector_t *edgelist = edges;     long int edge1 = (*(const long int*) e1) * 2;     long int edge2 = (*(const long int*) e2) * 2;@@ -210,9 +209,9 @@ #define IGRAPH_MODE_UNION        1 #define IGRAPH_MODE_INTERSECTION 2 -int igraph_i_merge(igraph_t *res, int mode,-                   const igraph_t *left, const igraph_t *right,-                   igraph_vector_t *edge_map1, igraph_vector_t *edge_map2) {+static int igraph_i_merge(igraph_t *res, int mode,+                          const igraph_t *left, const igraph_t *right,+                          igraph_vector_t *edge_map1, igraph_vector_t *edge_map2) {      long int no_of_nodes_left = igraph_vcount(left);     long int no_of_nodes_right = igraph_vcount(right);@@ -431,7 +430,7 @@                           edge_map1, edge_map2); } -void igraph_i_union_many_free(igraph_vector_ptr_t *v) {+static void igraph_i_union_many_free(igraph_vector_ptr_t *v) {     long int i, n = igraph_vector_ptr_size(v);     for (i = 0; i < n; i++) {         if (VECTOR(*v)[i] != 0) {@@ -442,7 +441,7 @@     igraph_vector_ptr_destroy(v); } -void igraph_i_union_many_free2(igraph_vector_ptr_t *v) {+static void igraph_i_union_many_free2(igraph_vector_ptr_t *v) {     long int i, n = igraph_vector_ptr_size(v);     for (i = 0; i < n; i++) {         if (VECTOR(*v)[i] != 0) {@@ -453,7 +452,7 @@     igraph_vector_ptr_destroy(v); } -void igraph_i_union_many_free3(igraph_vector_ptr_t *v) {+static void igraph_i_union_many_free3(igraph_vector_ptr_t *v) {     long int i, n = igraph_vector_ptr_size(v);     for (i = 0; i < n; i++) {         if (VECTOR(*v)[i] != 0) {@@ -469,8 +468,8 @@  *  * </para><para>  * This function calculates the intersection of the graphs stored in- * the \c graphs argument. Only those edges will be included in the- * result graph which are part of every graph in \c graphs.+ * the \p graphs argument. Only those edges will be included in the+ * result graph which are part of every graph in \p graphs.  *  * </para><para>  * The number of vertices in the result graph will be the maximum@@ -492,7 +491,7 @@  * igraph_difference() for other operators.  *  * Time complexity: O(|V|+|E|), |V| is the number of vertices,- * |E| is the number of edges in the smallest graph (ie. the graph having+ * |E| is the number of edges in the smallest graph (i.e. the graph having  * the less vertices).  */ @@ -924,9 +923,9 @@  *  * </para><para>  * The number of vertices in the result is the number of vertices in- * the original graph, ie. the left, first operand. In the results- * graph only edges will be included from \c orig which are not- * present in \c sub.+ * the original graph, i.e. the left, first operand. In the results+ * graph only edges will be included from \p orig which are not+ * present in \p sub.  *  * \param res Pointer to an uninitialized graph object, the result  * will be stored here.@@ -999,6 +998,10 @@                 IGRAPH_CHECK(igraph_vector_push_back(&edges, i));                 IGRAPH_CHECK(igraph_vector_push_back(&edges, v1));                 n1--;+                /* handle loop edges properly in undirected graphs */+                if (!directed && i == v1) {+                    n1--;+                }             } else if (v2 > v1) {                 n2--;             } else {@@ -1015,6 +1018,11 @@                 IGRAPH_CHECK(igraph_vector_push_back(&edge_ids, e1));                 IGRAPH_CHECK(igraph_vector_push_back(&edges, i));                 IGRAPH_CHECK(igraph_vector_push_back(&edges, v1));++                /* handle loop edges properly in undirected graphs */+                if (!directed && v1 == i) {+                    n1--;+                }             }             n1--;         }@@ -1032,6 +1040,11 @@                 IGRAPH_CHECK(igraph_vector_push_back(&edge_ids, e1));                 IGRAPH_CHECK(igraph_vector_push_back(&edges, i));                 IGRAPH_CHECK(igraph_vector_push_back(&edges, v1));++                /* handle loop edges properly in undirected graphs */+                if (!directed && v1 == i) {+                    n1--;+                }             }             n1--;         }
igraph/src/optimal_modularity.c view
@@ -23,7 +23,6 @@ */  #include "igraph_interface.h"-#include "igraph_structural.h" #include "igraph_community.h" #include "igraph_error.h" #include "igraph_glpk_support.h"
igraph/src/options.c view
@@ -4,14 +4,14 @@  *  * This program is free software; you can redistribute it and/or modify  * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at+ * the Free Software Foundation; either version 2 of the License, or (at  * your option) any later version.- * + *  * This program is distributed in the hope that it will be useful, but  * WITHOUT ANY WARRANTY; without even the implied warranty of  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  * General Public License for more details.- * + *  * You should have received a copy of the GNU General Public License  * along with this program; if not, write to the Free Software  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.@@ -21,18 +21,24 @@ #include "plfit.h"  const plfit_continuous_options_t plfit_continuous_default_options = {-  /* .finite_size_correction = */ 0,-  /* .xmin_method = */ PLFIT_GSS_OR_LINEAR+    /* .finite_size_correction = */ 0,+    /* .xmin_method = */ PLFIT_DEFAULT_CONTINUOUS_METHOD,+    /* .p_value_method = */ PLFIT_DEFAULT_P_VALUE_METHOD,+    /* .p_value_precision = */ 0.01,+    /* .rng = */ 0 };  const plfit_discrete_options_t plfit_discrete_default_options = {-  /* .finite_size_correction = */ 0,-  /* .alpha_method = */ PLFIT_LBFGS,-  /* .alpha = */ {-    /* .min = */ 1.01,-    /* .max = */ 5,-    /* .step = */ 0.01-  }+    /* .finite_size_correction = */ 0,+    /* .alpha_method = */ PLFIT_DEFAULT_DISCRETE_METHOD,+    /* .alpha = */ {+        /* .min = */ 1.01,+        /* .max = */ 5,+        /* .step = */ 0.01+    },+    /* .p_value_method = */ PLFIT_DEFAULT_P_VALUE_METHOD,+    /* .p_value_precision = */ 0.01,+    /* .rng = */ 0 };  int plfit_continuous_options_init(plfit_continuous_options_t* options) {@@ -44,4 +50,3 @@ 	*options = plfit_discrete_default_options; 	return PLFIT_SUCCESS; }-
igraph/src/orbit.cc view
@@ -1,5 +1,5 @@-#include <stdlib.h>-#include <assert.h>+#include <cstdlib>+#include <cassert> #include "defs.hh" #include "orbit.hh" 
igraph/src/other.c view
@@ -22,16 +22,13 @@ */  #include "igraph_nongraph.h"+#include "igraph_random.h" #include "igraph_types.h"-#include "igraph_memory.h" #include "igraph_interrupt_internal.h"-#include "igraph_types_internal.h" #include "config.h" #include "plfit/error.h" #include "plfit/plfit.h" #include <math.h>-#include <stdarg.h>-#include <string.h>  /**  * \ingroup nongraph@@ -356,9 +353,13 @@         }     } +    RNG_BEGIN();+     plfit_stored_error_handler = plfit_set_error_handler(igraph_i_plfit_error_handler_store);     if (discrete) {         plfit_discrete_options_init(&disc_options);+        /* approximation method should be switched to PLFIT_P_VALUE_EXACT in igraph 0.9 */+        disc_options.p_value_method = PLFIT_P_VALUE_APPROXIMATE;         disc_options.finite_size_correction = (plfit_bool_t) finite_size_correction;          if (xmin >= 0) {@@ -369,6 +370,10 @@         }     } else {         plfit_continuous_options_init(&cont_options);+        /* approximation method should be switched to PLFIT_P_VALUE_EXACT in igraph 0.9 */+        cont_options.p_value_method = PLFIT_P_VALUE_APPROXIMATE;+        /* xmin method should be switched to PLFIT_STRATIFIED_SAMPLING in igraph 0.9 */+        cont_options.xmin_method = PLFIT_GSS_OR_LINEAR;         cont_options.finite_size_correction = (plfit_bool_t) finite_size_correction;          if (xmin >= 0) {@@ -379,6 +384,8 @@         }     }     plfit_set_error_handler(plfit_stored_error_handler);++    RNG_END();      switch (retval) {     case PLFIT_FAILURE:
igraph/src/partition.cc view
@@ -1,4 +1,4 @@-#include <assert.h>+#include <cassert> #include <vector> #include <list> #include "graph.hh"@@ -344,7 +344,7 @@ }   -+#if 0 size_t Partition::print(FILE* const fp, const bool add_newline) const {@@ -388,7 +388,7 @@   if(add_newline) r += fprintf(fp, "\n");   return r; }-+#endif   void
igraph/src/paths.c view
@@ -21,6 +21,7 @@  */ +#include "igraph_paths.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h" #include "igraph_vector_ptr.h"
+ igraph/src/platform.c view
@@ -0,0 +1,36 @@+/* platform.c+ *+ * Copyright (C) 2014 Tamas Nepusz+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or (at+ * your option) any later version.+ *+ * This program is distributed in the hope that it will be useful, but+ * WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU+ * General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License+ * along with this program; if not, write to the Free Software+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.+ */++#include "platform.h"++#ifdef _MSC_VER++inline double _plfit_fmin(double a, double b) {+	return (a < b) ? a : b;+}++inline double _plfit_round(double x) {+	return floor(x+0.5);+}++#endif++/* Dummy function to prevent a warning when compiling with Clang - the file+ * would contain no symbols */+void _plfit_i_unused() {}
igraph/src/plfit.c view
@@ -1,778 +1,1309 @@-/* plfit.c- *- * Copyright (C) 2010-2011 Tamas Nepusz- *- * This program is free software; you can redistribute it and/or modify- * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at- * your option) any later version.- * - * This program is distributed in the hope that it will be useful, but- * WITHOUT ANY WARRANTY; without even the implied warranty of- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU- * General Public License for more details.- * - * You should have received a copy of the GNU General Public License- * along with this program; if not, write to the Free Software- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.- */--#include <stdio.h>-#include <float.h>-#include <math.h>-#include <stdlib.h>-#include <string.h>-#include "error.h"-#include "gss.h"-#include "lbfgs.h"-#include "platform.h"-#include "plfit.h"-#include "kolmogorov.h"-#include "zeta.h"--/* #define PLFIT_DEBUG */--#define DATA_POINTS_CHECK \-    if (n <= 0) { \-        PLFIT_ERROR("no data points", PLFIT_EINVAL); \-    }--#define XMIN_CHECK_ZERO \-    if (xmin <= 0) { \-        PLFIT_ERROR("xmin must be greater than zero", PLFIT_EINVAL); \-    }-#define XMIN_CHECK_ONE \-    if (xmin < 1) { \-        PLFIT_ERROR("xmin must be at least 1", PLFIT_EINVAL); \-    }--static int double_comparator(const void *a, const void *b) {-    const double *da = (const double*)a;-    const double *db = (const double*)b;-    return (*da > *db) - (*da < *db);-}--/**- * Given a sorted array of doubles, return another array that contains pointers- * into the array for the start of each block of identical elements.- *- * \param  begin          pointer to the beginning of the array- * \param  end            pointer to the first element after the end of the array- * \param  result_length  if not \c NULL, the number of unique elements in the- *                        given array is returned here- */-static double** unique_element_pointers(double* begin, double* end, size_t* result_length) {-    double* ptr = begin;-    double** result;-    double prev_x;-    size_t num_elts = 15;-    size_t used_elts = 0;--    /* Special case: empty array */-    if (begin == end) {-        result = calloc(1, sizeof(double*));-        if (result != 0) {-            result[0] = 0;-        }-        return result;-    }--    /* Allocate initial result array, including the guard element */-    result = calloc(num_elts+1, sizeof(double*));-    if (result == 0)-        return 0;--    prev_x = *begin;-    result[used_elts++] = begin;--    /* Process the input array */-    for (ptr = begin+1; ptr < end; ptr++) {-        if (*ptr == prev_x)-            continue;--        /* New block found */-        if (used_elts >= num_elts) {-            /* Array full; allocate a new chunk */-            num_elts = num_elts*2 + 1;-            result = realloc(result, sizeof(double*) * (num_elts+1));-            if (result == 0)-                return 0;-        }--        /* Store the new element */-        result[used_elts++] = ptr;-        prev_x = *ptr;-    }--    /* Calculate the result length */-    if (result_length != 0) {-        *result_length = used_elts;-    }--    /* Add the guard entry to the end of the result */-    result[used_elts++] = 0;--    return result;-}--static void plfit_i_perform_finite_size_correction(plfit_result_t* result, size_t n) {-    result->alpha = result->alpha * (n-1) / n + 1.0 / n;-}--/********** Continuous power law distribution fitting **********/--void plfit_i_logsum_less_than_continuous(double* begin, double* end,-        double xmin, double* result, size_t* m) {-    double logsum = 0.0;-    size_t count = 0;--    for (; begin != end; begin++) {-        if (*begin >= xmin) {-            count++;-            logsum += log(*begin / xmin);-        }-    }--    *m = count;-    *result = logsum;-}--double plfit_i_logsum_continuous(double* begin, double* end, double xmin) {-    double logsum = 0.0;-    for (; begin != end; begin++)-        logsum += log(*begin / xmin);-    return logsum;-}--int plfit_i_estimate_alpha_continuous(double* xs, size_t n,-        double xmin, double* alpha) {-    double result;-    size_t m;--    XMIN_CHECK_ZERO;--    plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &result, &m);--    if (m == 0) {-        PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL);-    }--    *alpha = 1 + m / result;--    return PLFIT_SUCCESS;-}--int plfit_i_estimate_alpha_continuous_sorted(double* xs, size_t n,-        double xmin, double* alpha) {-	double* end = xs+n;--    XMIN_CHECK_ZERO;--    for (; xs != end && *xs < xmin; xs++);-    if (xs == end) {-        PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL);-    }--    *alpha = 1 + (end-xs) / plfit_i_logsum_continuous(xs, end, xmin);--    return PLFIT_SUCCESS;-}--static int plfit_i_ks_test_continuous(double* xs, double* xs_end,-        const double alpha, const double xmin, double* D) {-    /* Assumption: xs is sorted and cut off at xmin so the first element is-     * always larger than or equal to xmin. */-    double result = 0, n;-    int m = 0;--    n = xs_end - xs;--    while (xs < xs_end) {-        double d = fabs(1-pow(xmin / *xs, alpha-1) - m / n);--        if (d > result)-            result = d;--        xs++; m++;-    }--    *D = result;--    return PLFIT_SUCCESS;-}--int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha,-        double xmin, double* L) {-    double logsum, c;-    size_t m;--    if (alpha <= 1) {-        PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL);-    }-    XMIN_CHECK_ZERO;--    c = (alpha - 1) / xmin;-    plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &logsum, &m);-    *L = -alpha * logsum + log(c) * m;--    return PLFIT_SUCCESS;-}--int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin,-        const plfit_continuous_options_t* options, plfit_result_t *result) {-    double *xs_copy;--	if (!options)-		options = &plfit_continuous_default_options;--    /* Make a copy of xs and sort it */-    xs_copy = (double*)malloc(sizeof(double) * n);-    memcpy(xs_copy, xs, sizeof(double) * n);-    qsort(xs_copy, n, sizeof(double), double_comparator);--    PLFIT_CHECK(plfit_estimate_alpha_continuous_sorted(xs_copy, n, xmin,-				options, result));--    free(xs_copy);--    return PLFIT_SUCCESS;-}--int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin,-        const plfit_continuous_options_t* options, plfit_result_t *result) {-    double* end;--	if (!options)-		options = &plfit_continuous_default_options;--	end = xs + n;-    while (xs < end && *xs < xmin)-        xs++;-    n = (size_t) (end - xs);--    PLFIT_CHECK(plfit_i_estimate_alpha_continuous_sorted(xs, n,-				xmin, &result->alpha));-    PLFIT_CHECK(plfit_i_ks_test_continuous(xs, end, result->alpha,-				xmin, &result->D));--    if (options->finite_size_correction)-        plfit_i_perform_finite_size_correction(result, n);-    result->xmin = xmin;-    result->p = plfit_ks_test_one_sample_p(result->D, n);-    plfit_log_likelihood_continuous(xs, n, result->alpha, result->xmin, &result->L);--    return PLFIT_SUCCESS;-}--typedef struct {-	double *begin;        /**< Pointer to the beginning of the array holding the data */-	double *end;          /**< Pointer to after the end of the array holding the data */-	double **uniques;     /**< Pointers to unique elements of the input array */-	plfit_result_t last;  /**< Result of the last evaluation */-} plfit_continuous_xmin_opt_data_t;--double plfit_i_continuous_xmin_opt_evaluate(void* instance, double x) {-	plfit_continuous_xmin_opt_data_t* data = (plfit_continuous_xmin_opt_data_t*)instance;-	double* begin = data->uniques[(int)x];--	data->last.xmin = *begin;--#ifdef PLFIT_DEBUG-	printf("Trying with xmin = %.4f\n", *begin);-#endif--	plfit_i_estimate_alpha_continuous_sorted(begin, (size_t) (data->end-begin), *begin,-			&data->last.alpha);-	plfit_i_ks_test_continuous(begin, data->end, data->last.alpha, *begin,-			&data->last.D);--	return data->last.D;-}--int plfit_i_continuous_xmin_opt_progress(void* instance, double x, double fx,-		double min, double fmin, double left, double right, int k) {-#ifdef PLFIT_DEBUG-    printf("Iteration #%d: [%.4f; %.4f), x=%.4f, fx=%.4f, min=%.4f, fmin=%.4f\n",-            k, left, right, x, fx, min, fmin);-#endif--	/* Continue only if `left' and `right' point to different integers */-	return (int)left == (int)right;-}--int plfit_continuous(double* xs, size_t n, const plfit_continuous_options_t* options,-        plfit_result_t* result) {-	gss_parameter_t gss_param;-	plfit_continuous_xmin_opt_data_t opt_data;-	plfit_result_t best_result;-	int success;-	size_t i, best_n, num_uniques;-    double x, *px;--    DATA_POINTS_CHECK;--	if (!options)-		options = &plfit_continuous_default_options;--    /* Make a copy of xs and sort it */-    opt_data.begin = (double*)malloc(sizeof(double) * n);-    memcpy(opt_data.begin, xs, sizeof(double) * n);-    qsort(opt_data.begin, n, sizeof(double), double_comparator);-    opt_data.end = opt_data.begin + n;--    /* Create an array containing pointers to the unique elements of the input. From-     * each block of unique elements, we add the pointer to the first one. */-    opt_data.uniques = unique_element_pointers(opt_data.begin, opt_data.end,-			&num_uniques);-    if (opt_data.uniques == 0)-        return PLFIT_ENOMEM;--    /* We will now determine the best xmin that yields the lowest D-score.-	 * First we try a golden section search if needed. If that fails, we try-	 * a linear search.-     */-	if (options->xmin_method == PLFIT_GSS_OR_LINEAR && num_uniques > 5) {-		gss_parameter_init(&gss_param);-		success = (gss(0, num_uniques-5, &x, 0,-				plfit_i_continuous_xmin_opt_evaluate,-				plfit_i_continuous_xmin_opt_progress, &opt_data, &gss_param) == 0);-		best_result = opt_data.last;-		/* plfit_i_continuous_xmin_opt_evaluate will set opt_data.last to-		 * indicate the location of the optimum and the value of D */-	} else {-		success = 0;-	}--	if (success) {-		/* calculate best_n because we'll need it later. Luckily x indicates-		 * the index in opt_data.uniques that we have to look up in order to-		 * find the first element in the array that is included */-		px = opt_data.uniques[(int)x];-		best_n = (size_t) (opt_data.end-px+1);-	} else {-		/* GSS failed or skipped; try linear search */--		/* Prepare some variables */-		best_n = 0;-		best_result.D = DBL_MAX;-		best_result.xmin = 0;-		best_result.alpha = 0;-		-		for (i = 0; i < num_uniques-1; i++) {-			plfit_i_continuous_xmin_opt_evaluate(&opt_data, i);-			if (opt_data.last.D < best_result.D) {-				best_result = opt_data.last;-				best_n = (size_t) (opt_data.end - -						   opt_data.uniques[i] + 1);-			}-		}-	}--    /* Get rid of the uniques array, we don't need it any more */-    free(opt_data.uniques);--    /* Sort out the result */-    *result = best_result;-    if (options->finite_size_correction)-        plfit_i_perform_finite_size_correction(result, best_n);-    result->p = plfit_ks_test_one_sample_p(result->D, best_n);-    plfit_log_likelihood_continuous(opt_data.begin + n - best_n, best_n,-			result->alpha, result->xmin, &result->L);--    /* Get rid of the copied data as well */-    free(opt_data.begin);--    return PLFIT_SUCCESS;-}--/********** Discrete power law distribution fitting **********/--typedef struct {-    size_t m;-    double logsum;-    double xmin;-} plfit_i_estimate_alpha_discrete_data_t;--double plfit_i_logsum_discrete(double* begin, double* end, double xmin) {-    double logsum = 0.0;-    for (; begin != end; begin++)-        logsum += log(*begin);-    return logsum;-}--void plfit_i_logsum_less_than_discrete(double* begin, double* end, double xmin,-        double* logsum, size_t* m) {-    double result = 0.0;-    size_t count = 0;--    for (; begin != end; begin++) {-        if (*begin < xmin)-            continue;--        result += log(*begin);-        count++;-    }--    *logsum = result;-    *m = count;-}--lbfgsfloatval_t plfit_i_estimate_alpha_discrete_lbfgs_evaluate(-        void* instance, const lbfgsfloatval_t* x,-        lbfgsfloatval_t* g, const int n,-        const lbfgsfloatval_t step) {-    plfit_i_estimate_alpha_discrete_data_t* data;-    lbfgsfloatval_t result;-    double dx = step;-    double huge = 1e10;     /* pseudo-infinity; apparently DBL_MAX does not work */--    data = (plfit_i_estimate_alpha_discrete_data_t*)instance;--#ifdef PLFIT_DEBUG-    printf("- Evaluating at %.4f (step = %.4f, xmin = %.4f)\n", *x, step, data->xmin);-#endif--	if (isnan(*x)) {-		g[0] = huge;-		return huge;-	}--    /* Find the delta X value to estimate the gradient */-    if (dx > 0.001 || dx == 0)-        dx = 0.001;-    else if (dx < -0.001)-        dx = -0.001;--	/* Is x[0] in its valid range? */-	if (x[0] <= 1.0) {-		/* The Hurwitz zeta function is infinite in this case */-        g[0] = (dx > 0) ? -huge : huge;-		return huge;-	}-	if (x[0] + dx <= 1.0)-		g[0] = huge;-	else-		g[0] = data->logsum + data->m *-			(log(gsl_sf_hzeta(x[0] + dx, data->xmin)) - log(gsl_sf_hzeta(x[0], data->xmin))) / dx;--    result = x[0] * data->logsum + data->m * log(gsl_sf_hzeta(x[0], data->xmin));--#ifdef PLFIT_DEBUG-    printf("  - Gradient: %.4f\n", g[0]);-    printf("  - Result: %.4f\n", result);-#endif--    return result;-}--int plfit_i_estimate_alpha_discrete_lbfgs_progress(void* instance,-        const lbfgsfloatval_t* x, const lbfgsfloatval_t* g,-        const lbfgsfloatval_t fx, const lbfgsfloatval_t xnorm,-        const lbfgsfloatval_t gnorm, const lbfgsfloatval_t step,-        int n, int k, int ls) {-    return 0;-}--int plfit_i_estimate_alpha_discrete_linear_scan(double* xs, size_t n, double xmin,-        double* alpha, const plfit_discrete_options_t* options,-		plfit_bool_t sorted) {-    double curr_alpha, best_alpha, L, L_max;-    double logsum;-    size_t m;--    XMIN_CHECK_ONE;-	if (options->alpha.min <= 1.0) {-		PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);-	}-	if (options->alpha.max < options->alpha.min) {-		PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);-	}-	if (options->alpha.step <= 0) {-		PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);-	}--    if (sorted) {-        logsum = plfit_i_logsum_discrete(xs, xs+n, xmin);-        m = n;-    } else {-        plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &logsum, &m);-    }--    best_alpha = options->alpha.min; L_max = -DBL_MAX;-    for (curr_alpha = options->alpha.min; curr_alpha <= options->alpha.max;-			curr_alpha += options->alpha.step) {-        L = -curr_alpha * logsum - m * log(gsl_sf_hzeta(curr_alpha, xmin));-        if (L > L_max) {-            L_max = L;-            best_alpha = curr_alpha;-        }-    }--    *alpha = best_alpha;--    return PLFIT_SUCCESS;-}--int plfit_i_estimate_alpha_discrete_lbfgs(double* xs, size_t n, double xmin,-		double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) {-    lbfgs_parameter_t param;-    lbfgsfloatval_t* variables;-    plfit_i_estimate_alpha_discrete_data_t data;-    int ret;--    XMIN_CHECK_ONE;--    /* Initialize algorithm parameters */-    lbfgs_parameter_init(&param);-    param.max_iterations = 0;   /* proceed until infinity */--    /* Set up context for optimization */-    data.xmin = xmin;-    if (sorted) {-        data.logsum = plfit_i_logsum_discrete(xs, xs+n, xmin);-        data.m = n;-    } else {-        plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &data.logsum, &data.m);-    }--    /* Allocate space for the single alpha variable */-    variables = lbfgs_malloc(1);-    variables[0] = 3.0;       /* initial guess */--    /* Optimization */-    ret = lbfgs(1, variables, /* ptr_fx = */ 0,-            plfit_i_estimate_alpha_discrete_lbfgs_evaluate,-            plfit_i_estimate_alpha_discrete_lbfgs_progress,-            &data, &param);--    if (ret < 0 &&-        ret != LBFGSERR_ROUNDING_ERROR &&-        ret != LBFGSERR_MAXIMUMLINESEARCH &&-        ret != LBFGSERR_CANCELED) {-        char buf[4096];-        snprintf(buf, 4096, "L-BFGS optimization signaled an error (error code = %d)", ret);-        lbfgs_free(variables);-        PLFIT_ERROR(buf, PLFIT_FAILURE);-    }-    *alpha = variables[0];-    -    /* Deallocate the variable array */-    lbfgs_free(variables);--    return PLFIT_SUCCESS;-}--int plfit_i_estimate_alpha_discrete_fast(double* xs, size_t n, double xmin,-        double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) {-	plfit_continuous_options_t cont_options;--	if (!options)-		options = &plfit_discrete_default_options;--	plfit_continuous_options_init(&cont_options);-	cont_options.finite_size_correction = options->finite_size_correction;--    XMIN_CHECK_ONE;--	if (sorted) {-		return plfit_i_estimate_alpha_continuous_sorted(xs, n, xmin-0.5, alpha);-	} else {-		return plfit_i_estimate_alpha_continuous(xs, n, xmin-0.5, alpha);-	}-}--int plfit_i_estimate_alpha_discrete(double* xs, size_t n, double xmin,-		double* alpha, const plfit_discrete_options_t* options,-		plfit_bool_t sorted) {-	switch (options->alpha_method) {-		case PLFIT_LBFGS:-			PLFIT_CHECK(plfit_i_estimate_alpha_discrete_lbfgs(xs, n, xmin, alpha,-						options, sorted));-			break;--		case PLFIT_LINEAR_SCAN:-			PLFIT_CHECK(plfit_i_estimate_alpha_discrete_linear_scan(xs, n, xmin,-						alpha, options, sorted));-			break;--		case PLFIT_PRETEND_CONTINUOUS:-			PLFIT_CHECK(plfit_i_estimate_alpha_discrete_fast(xs, n, xmin,-						alpha, options, sorted));-			break;--		default:-			PLFIT_ERROR("unknown optimization method specified", PLFIT_EINVAL);-	}--	return PLFIT_SUCCESS;-}--static int plfit_i_ks_test_discrete(double* xs, double* xs_end, const double alpha,-        const double xmin, double* D) {-    /* Assumption: xs is sorted and cut off at xmin so the first element is-     * always larger than or equal to xmin. */-    double result = 0, n, hzeta, x;-    int m = 0;--    n = xs_end - xs;-    hzeta = gsl_sf_hzeta(alpha, xmin);--    while (xs < xs_end) {-        double d;--        x = *xs;-        d = fabs(1-(gsl_sf_hzeta(alpha, x) / hzeta) - m / n);--        if (d > result)-            result = d;--        do {-            xs++; m++;-        } while (xs < xs_end && *xs == x);-    }--    *D = result;--    return PLFIT_SUCCESS;-}--int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* L) {-    double result;-    size_t m;--    if (alpha <= 1) {-        PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL);-    }-    XMIN_CHECK_ONE;--    plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &result, &m);-    result = - alpha * result - m * log(gsl_sf_hzeta(alpha, xmin));--    *L = result;--    return PLFIT_SUCCESS;-}--int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin,-        const plfit_discrete_options_t* options, plfit_result_t *result) {-    double *xs_copy, *end;--	if (!options)-		options = &plfit_discrete_default_options;--	/* Check the validity of the input parameters */-    DATA_POINTS_CHECK;-	if (options->alpha_method == PLFIT_LINEAR_SCAN) {-		if (options->alpha.min <= 1.0) {-			PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);-		}-		if (options->alpha.max < options->alpha.min) {-			PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);-		}-		if (options->alpha.step <= 0) {-			PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);-		}-	}--    /* Make a copy of xs and sort it */-    xs_copy = (double*)malloc(sizeof(double) * n);-    memcpy(xs_copy, xs, sizeof(double) * n);-    qsort(xs_copy, n, sizeof(double), double_comparator);--    xs = xs_copy; end = xs_copy + n;-    while (xs < end && *xs < xmin)-        xs++;-    n = (size_t) (end - xs);--    PLFIT_CHECK(plfit_i_estimate_alpha_discrete(xs, n, xmin, &result->alpha,-				options, /* sorted = */ 1));-    PLFIT_CHECK(plfit_i_ks_test_discrete(xs, end, result->alpha, xmin, &result->D));--    result->xmin = xmin;-    if (options->finite_size_correction)-        plfit_i_perform_finite_size_correction(result, n);-    result->p = plfit_ks_test_one_sample_p(result->D, n);-    plfit_log_likelihood_discrete(xs, n, result->alpha, result->xmin, &result->L);--    free(xs_copy);--    return PLFIT_SUCCESS;-}--int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options,-        plfit_result_t* result) {-    double curr_D, curr_alpha;-    plfit_result_t best_result;-    double *xs_copy, *px, *end, *end_xmin, prev_x;-	size_t best_n;-    size_t m;--	if (!options)-		options = &plfit_discrete_default_options;--	/* Check the validity of the input parameters */-    DATA_POINTS_CHECK;-	if (options->alpha_method == PLFIT_LINEAR_SCAN) {-		if (options->alpha.min <= 1.0) {-			PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);-		}-		if (options->alpha.max < options->alpha.min) {-			PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);-		}-		if (options->alpha.step <= 0) {-			PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);-		}-	}--    /* Make a copy of xs and sort it */-    xs_copy = (double*)malloc(sizeof(double) * n);-    memcpy(xs_copy, xs, sizeof(double) * n);-    qsort(xs_copy, n, sizeof(double), double_comparator);--    best_result.D = DBL_MAX;-    best_result.xmin = 1;-    best_result.alpha = 1;-	best_n = 0;--    /* Make sure there are at least three distinct values if possible */-    px = xs_copy; end = px + n; end_xmin = end - 1; m = 0;-    prev_x = *end_xmin;-    while (*end_xmin == prev_x && end_xmin > px)-        end_xmin--;-    prev_x = *end_xmin;-    while (*end_xmin == prev_x && end_xmin > px)-        end_xmin--;--    prev_x = 0;-    while (px < end_xmin) {-        while (px < end_xmin && *px == prev_x) {-            px++; m++;-        }--	plfit_i_estimate_alpha_discrete(px, n - m, *px,-					&curr_alpha, options, /* sorted = */ 1);-        plfit_i_ks_test_discrete(px, end, curr_alpha, *px, &curr_D);--        if (curr_D < best_result.D) {-            best_result.alpha = curr_alpha;-            best_result.xmin = *px;-            best_result.D = curr_D;-	    best_n = n - m;-        }--        prev_x = *px;-        px++; m++;-    }--    *result = best_result;-    if (options->finite_size_correction)-        plfit_i_perform_finite_size_correction(result, best_n);-    result->p = plfit_ks_test_one_sample_p(result->D, best_n);-    plfit_log_likelihood_discrete(xs_copy+(n-best_n), best_n,-			result->alpha, result->xmin, &result->L);--    free(xs_copy);--    return PLFIT_SUCCESS;-}-+/* vim:set ts=4 sw=4 sts=4 et: */+/* plfit.c+ *+ * Copyright (C) 2010-2011 Tamas Nepusz+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or (at+ * your option) any later version.+ *+ * This program is distributed in the hope that it will be useful, but+ * WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU+ * General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License+ * along with this program; if not, write to the Free Software+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.+ */++#include <stdio.h>+#include <float.h>+#include <math.h>+#include <stdlib.h>+#include <string.h>+#include "error.h"+#include "gss.h"+#include "lbfgs.h"+#include "platform.h"+#include "plfit.h"+#include "kolmogorov.h"+#include "sampling.h"+#include "hzeta.h"++/* #define PLFIT_DEBUG */++#define DATA_POINTS_CHECK \+    if (n <= 0) { \+        PLFIT_ERROR("no data points", PLFIT_EINVAL); \+    }++#define XMIN_CHECK_ZERO \+    if (xmin <= 0) { \+        PLFIT_ERROR("xmin must be greater than zero", PLFIT_EINVAL); \+    }+#define XMIN_CHECK_ONE \+    if (xmin < 1) { \+        PLFIT_ERROR("xmin must be at least 1", PLFIT_EINVAL); \+    }++static int plfit_i_resample_continuous(double* xs_head, size_t num_smaller,+        size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng,+        double* result);+static int plfit_i_resample_discrete(double* xs_head, size_t num_smaller,+        size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng,+        double* result);++static int double_comparator(const void *a, const void *b) {+    const double *da = (const double*)a;+    const double *db = (const double*)b;+    return (*da > *db) - (*da < *db);+}++static int plfit_i_copy_and_sort(double* xs, size_t n, double** result) {+    *result = (double*)malloc(sizeof(double) * n);+    if (*result == 0) {+        PLFIT_ERROR("cannot create sorted copy of input data", PLFIT_ENOMEM);+    }++    memcpy(*result, xs, sizeof(double) * n);+    qsort(*result, n, sizeof(double), double_comparator);++    return PLFIT_SUCCESS;+}++/**+ * Given an unsorted array of doubles, counts how many elements there are that+ * are smaller than a given value.+ *+ * \param  begin          pointer to the beginning of the array+ * \param  end            pointer to the first element after the end of the array+ * \param  xmin           the threshold value+ *+ * \return the nubmer of elements in the array that are smaller than the given+ *         value.+ */+static size_t count_smaller(double* begin, double* end, double xmin) {+    double* p;+    size_t counter = 0;++    for (p = begin; p < end; p++) {+        if (*p < xmin) {+            counter++;+        }+    }++    return counter;+}++/**+ * Given an unsorted array of doubles, return another array that contains the+ * elements that are smaller than a given value+ *+ * \param  begin          pointer to the beginning of the array+ * \param  end            pointer to the first element after the end of the array+ * \param  xmin           the threshold value+ * \param  result_length  if not \c NULL, the number of unique elements in the+ *                        given array is returned here+ *+ * \return pointer to the head of the new array or 0 if there is not enough+ * memory+ */+static double* extract_smaller(double* begin, double* end, double xmin,+        size_t* result_length) {+    size_t counter = count_smaller(begin, end, xmin);+    double *p, *result;++    result = calloc(counter, sizeof(double));+    if (result == 0)+        return 0;++    for (p = result; begin < end; begin++) {+        if (*begin < xmin) {+            *p = *begin;+            p++;+        }+    }++    if (result_length) {+        *result_length = counter;+    }++    return result;+}++/**+ * Given a sorted array of doubles, return another array that contains pointers+ * into the array for the start of each block of identical elements.+ *+ * \param  begin          pointer to the beginning of the array+ * \param  end            pointer to the first element after the end of the array+ * \param  result_length  if not \c NULL, the number of unique elements in the+ *                        given array is returned here+ *+ * \return pointer to the head of the new array or 0 if there is not enough+ * memory+ */+static double** unique_element_pointers(double* begin, double* end, size_t* result_length) {+    double* ptr = begin;+    double** result;+    double prev_x;+    size_t num_elts = 15;+    size_t used_elts = 0;++    /* Special case: empty array */+    if (begin == end) {+        result = calloc(1, sizeof(double*));+        if (result != 0) {+            result[0] = 0;+        }+        return result;+    }++    /* Allocate initial result array, including the guard element */+    result = calloc(num_elts+1, sizeof(double*));+    if (result == 0)+        return 0;++    prev_x = *begin;+    result[used_elts++] = begin;++    /* Process the input array */+    for (ptr = begin+1; ptr < end; ptr++) {+        if (*ptr == prev_x)+            continue;++        /* New block found */+        if (used_elts >= num_elts) {+            /* Array full; allocate a new chunk */+            num_elts = num_elts*2 + 1;+            result = realloc(result, sizeof(double*) * (num_elts+1));+            if (result == 0)+                return 0;+        }++        /* Store the new element */+        result[used_elts++] = ptr;+        prev_x = *ptr;+    }++    /* Calculate the result length */+    if (result_length != 0) {+        *result_length = used_elts;+    }++    /* Add the guard entry to the end of the result */+    result[used_elts++] = 0;++    return result;+}++static void plfit_i_perform_finite_size_correction(plfit_result_t* result, size_t n) {+    result->alpha = result->alpha * (n-1) / n + 1.0 / n;+}++/********** Continuous power law distribution fitting **********/++static void plfit_i_logsum_less_than_continuous(double* begin, double* end,+        double xmin, double* result, size_t* m) {+    double logsum = 0.0;+    size_t count = 0;++    for (; begin != end; begin++) {+        if (*begin >= xmin) {+            count++;+            logsum += log(*begin / xmin);+        }+    }++    *m = count;+    *result = logsum;+}++static double plfit_i_logsum_continuous(double* begin, double* end, double xmin) {+    double logsum = 0.0;+    for (; begin != end; begin++)+        logsum += log(*begin / xmin);+    return logsum;+}++static int plfit_i_estimate_alpha_continuous(double* xs, size_t n,+        double xmin, double* alpha) {+    double result;+    size_t m;++    XMIN_CHECK_ZERO;++    plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &result, &m);++    if (m == 0) {+        PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL);+    }++    *alpha = 1 + m / result;++    return PLFIT_SUCCESS;+}++static int plfit_i_estimate_alpha_continuous_sorted(double* xs, size_t n,+        double xmin, double* alpha) {+    double* end = xs+n;++    XMIN_CHECK_ZERO;++    for (; xs != end && *xs < xmin; xs++);+    if (xs == end) {+        PLFIT_ERROR("no data point was larger than xmin", PLFIT_EINVAL);+    }++    *alpha = 1 + (end-xs) / plfit_i_logsum_continuous(xs, end, xmin);++    return PLFIT_SUCCESS;+}++static int plfit_i_ks_test_continuous(double* xs, double* xs_end,+        const double alpha, const double xmin, double* D) {+    /* Assumption: xs is sorted and cut off at xmin so the first element is+     * always larger than or equal to xmin. */+    double result = 0, n;+    int m = 0;++    n = xs_end - xs;++    while (xs < xs_end) {+        double d = fabs(1-pow(xmin / *xs, alpha-1) - m / n);++        if (d > result)+            result = d;++        xs++; m++;+    }++    *D = result;++    return PLFIT_SUCCESS;+}++static int plfit_i_calculate_p_value_continuous(double* xs, size_t n,+        const plfit_continuous_options_t *options, plfit_bool_t xmin_fixed,+        plfit_result_t *result) {+    long int num_trials;+    long int successes = 0;+    double *xs_head;+    size_t num_smaller;+    plfit_continuous_options_t options_no_p_value = *options;+    int retval = PLFIT_SUCCESS;++    if (options->p_value_method == PLFIT_P_VALUE_SKIP) {+        result->p = NAN;+        return PLFIT_SUCCESS;+    }++    if (options->p_value_method == PLFIT_P_VALUE_APPROXIMATE) {+        num_smaller = count_smaller(xs, xs + n, result->xmin);+        result->p = plfit_ks_test_one_sample_p(result->D, n - num_smaller);+        return PLFIT_SUCCESS;+    }++    options_no_p_value.p_value_method = PLFIT_P_VALUE_SKIP;+    num_trials = (long int)(0.25 / options->p_value_precision / options->p_value_precision);+    if (num_trials <= 0) {+        PLFIT_ERROR("invalid p-value precision", PLFIT_EINVAL);+    }++    /* Extract the head of xs that contains elements smaller than xmin */+    xs_head = extract_smaller(xs, xs+n, result->xmin, &num_smaller);+    if (xs_head == 0)+        PLFIT_ERROR("cannot calculate exact p-value", PLFIT_ENOMEM);++#ifdef _OPENMP+#pragma omp parallel+#endif+    {+        /* Parallel section starts here. If we are compiling using OpenMP, each+         * thread will use its own RNG that is seeded from the master RNG. If+         * we are compiling without OpenMP, there is only one thread and it uses+         * the master RNG. This section must be critical to ensure that only one+         * thread is using the master RNG at the same time. */+#ifdef _OPENMP+        mt_rng_t private_rng;+#endif+        mt_rng_t *p_rng;+        double *ys;+        long int i;+        plfit_result_t result_synthetic;++#ifdef _OPENMP+#pragma omp critical+        {+            p_rng = &private_rng;+            mt_init_from_rng(p_rng, options->rng);+        }+#else+        p_rng = options->rng;+#endif++        /* Allocate memory to sample into */+        ys = calloc(n, sizeof(double));+        if (ys == 0) {+            retval = PLFIT_ENOMEM;+        } else {+            /* The main for loop starts here. */+#ifdef _OPENMP+#pragma omp for reduction(+:successes)+#endif+            for (i = 0; i < num_trials; i++) {+                plfit_i_resample_continuous(xs_head, num_smaller, n, result->alpha,+                        result->xmin, n, p_rng, ys);+                if (xmin_fixed) {+                    plfit_estimate_alpha_continuous(ys, n, result->xmin,+                                &options_no_p_value, &result_synthetic);+                } else {+                    plfit_continuous(ys, n, &options_no_p_value, &result_synthetic);+                }+                if (result_synthetic.D > result->D)+                    successes++;+            }+            free(ys);+        }++        /* End of parallelized part */+    }++    free(xs_head);++    if (retval == PLFIT_SUCCESS) {+        result->p = successes / ((double)num_trials);+    } else {+        PLFIT_ERROR("cannot calculate exact p-value", retval);+    }++    return retval;+}++int plfit_log_likelihood_continuous(double* xs, size_t n, double alpha,+        double xmin, double* L) {+    double logsum, c;+    size_t m;++    if (alpha <= 1) {+        PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL);+    }+    XMIN_CHECK_ZERO;++    c = (alpha - 1) / xmin;+    plfit_i_logsum_less_than_continuous(xs, xs+n, xmin, &logsum, &m);+    *L = -alpha * logsum + log(c) * m;++    return PLFIT_SUCCESS;+}++int plfit_estimate_alpha_continuous_sorted(double* xs, size_t n, double xmin,+        const plfit_continuous_options_t* options, plfit_result_t *result) {+    double *begin, *end;++    if (!options)+        options = &plfit_continuous_default_options;++    begin = xs;+    end = xs + n;+    while (begin < end && *begin < xmin)+        begin++;++    PLFIT_CHECK(plfit_i_estimate_alpha_continuous_sorted(begin, end-begin,+                xmin, &result->alpha));+    PLFIT_CHECK(plfit_i_ks_test_continuous(begin, end, result->alpha,+                xmin, &result->D));++    if (options->finite_size_correction)+        plfit_i_perform_finite_size_correction(result, end-begin);+    result->xmin = xmin;++    PLFIT_CHECK(plfit_log_likelihood_continuous(begin, end-begin, result->alpha,+                result->xmin, &result->L));+    PLFIT_CHECK(plfit_i_calculate_p_value_continuous(xs, n, options, 1, result));++    return PLFIT_SUCCESS;+}++int plfit_estimate_alpha_continuous(double* xs, size_t n, double xmin,+        const plfit_continuous_options_t* options, plfit_result_t *result) {+    double *xs_copy;++    if (!options)+        options = &plfit_continuous_default_options;++    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy));+    PLFIT_CHECK(plfit_estimate_alpha_continuous_sorted(xs_copy, n, xmin,+                options, result));+    free(xs_copy);++    return PLFIT_SUCCESS;+}++typedef struct {+    double *begin;        /**< Pointer to the beginning of the array holding the data */+    double *end;          /**< Pointer to after the end of the array holding the data */+    double **probes;      /**< Pointers to the elements of the array that will be probed */+    size_t num_probes;    /**< Number of probes */+    plfit_result_t last;  /**< Result of the last evaluation */+} plfit_continuous_xmin_opt_data_t;++static double plfit_i_continuous_xmin_opt_evaluate(void* instance, double x) {+    plfit_continuous_xmin_opt_data_t* data = (plfit_continuous_xmin_opt_data_t*)instance;+    double* begin = data->probes[(long int)x];++    data->last.xmin = *begin;++#ifdef PLFIT_DEBUG+    printf("Trying with probes[%ld] = %.4f\n", (long int)x, *begin);+#endif++    plfit_i_estimate_alpha_continuous_sorted(begin, data->end-begin, *begin,+            &data->last.alpha);+    plfit_i_ks_test_continuous(begin, data->end, data->last.alpha, *begin,+            &data->last.D);++    return data->last.D;+}++static int plfit_i_continuous_xmin_opt_progress(void* instance, double x, double fx,+        double min, double fmin, double left, double right, int k) {+#ifdef PLFIT_DEBUG+    printf("Iteration #%d: [%.4f; %.4f), x=%.4f, fx=%.4f, min=%.4f, fmin=%.4f\n",+            k, left, right, x, fx, min, fmin);+#endif++    /* Continue only if `left' and `right' point to different integers */+    return (int)left == (int)right;+}++static int plfit_i_continuous_xmin_opt_linear_scan(+        plfit_continuous_xmin_opt_data_t* opt_data, plfit_result_t* best_result,+        size_t* best_n) {+    size_t i;+    plfit_result_t global_best_result;+    size_t global_best_n;++    /* Prepare some variables */+    global_best_n = 0;+    global_best_result.D = DBL_MAX;+    global_best_result.xmin = 0;+    global_best_result.alpha = 0;++    /* Due to the OpenMP parallelization, we do things as follows. Each+     * OpenMP thread will search for the best D-score on its own and store+     * the result in a private local_best_result variable. The end of the+     * parallel block contains a critical section that threads will enter+     * one by one and compare their private local_best_result with a+     * global_best that is shared among the threads.+     */+#ifdef _OPENMP+#pragma omp parallel shared(global_best_result, global_best_n) private(i) firstprivate(opt_data)+#endif+    {+        /* These variables are private since they are declared within the+         * parallel block */+        plfit_result_t local_best_result;+        plfit_continuous_xmin_opt_data_t local_opt_data = *opt_data;+        size_t local_best_n;++        /* Initialize the local_best_result and local_best_n variables */+        local_best_n = 0;+        local_best_result.D = DBL_MAX;+        local_best_result.xmin = 0;+        local_best_result.alpha = 0;++        /* The range of the for loop below is divided among the threads.+         * nowait means that there will be no implicit barrier at the end+         * of the loop so threads that get there earlier can enter the+         * critical section without waiting for the others */+#ifdef _OPENMP+#pragma omp for nowait schedule(dynamic,10)+#endif+        for (i = 0; i < local_opt_data.num_probes-1; i++) {+            plfit_i_continuous_xmin_opt_evaluate(&local_opt_data, i);+            if (local_opt_data.last.D < local_best_result.D) {+#ifdef PLFIT_DEBUG+                printf("Found new local best at %g with D=%g\n",+                        local_opt_data.last.xmin, local_opt_data.last.D);+#endif+                local_best_result = local_opt_data.last;+                local_best_n = local_opt_data.end - local_opt_data.probes[i] + 1;+            }+        }++        /* Critical section that finds the global best result from the+         * local ones collected by each thread */+#ifdef _OPENMP+#pragma omp critical+#endif+        if (local_best_result.D < global_best_result.D) {+            global_best_result = local_best_result;+            global_best_n = local_best_n;+#ifdef PLFIT_DEBUG+            printf("Found new global best at %g with D=%g\n", global_best_result.xmin,+                    global_best_result.D);+#endif+        }+    }++    *best_result = global_best_result;+    *best_n = global_best_n;++#ifdef PLFIT_DEBUG+    printf("Returning global best: %g\n", best_result->xmin);+#endif++    return PLFIT_SUCCESS;+}++int plfit_continuous(double* xs, size_t n, const plfit_continuous_options_t* options,+        plfit_result_t* result) {+    gss_parameter_t gss_param;+    plfit_continuous_xmin_opt_data_t opt_data;+    plfit_result_t best_result = {+        /* alpha = */ NAN,+        /* xmin = */ NAN,+        /* L = */ NAN,+        /* D = */ NAN,+        /* p = */ NAN+    };++    int success;+    size_t i, best_n, num_uniques;+    double x, *px, **uniques;++    DATA_POINTS_CHECK;++    /* Sane defaults */+    best_n = n;+    if (!options)+        options = &plfit_continuous_default_options;++    /* Make a copy of xs and sort it */+    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &opt_data.begin));+    opt_data.end = opt_data.begin + n;++    /* Create an array containing pointers to the unique elements of the input. From+     * each block of unique elements, we add the pointer to the first one. */+    uniques = unique_element_pointers(opt_data.begin, opt_data.end, &num_uniques);+    if (uniques == 0)+        PLFIT_ERROR("cannot fit continuous power-law", PLFIT_ENOMEM);++    /* We will now determine the best xmin that yields the lowest D-score. The+     * 'success' variable will denote whether the search procedure we tried was+     * successful. If it is false after having exhausted all options, we fall+     * back to a linear search. */+    success = 0;+    switch (options->xmin_method) {+        case PLFIT_GSS_OR_LINEAR:+            /* Try golden section search first. */+            if (num_uniques > 5) {+                opt_data.probes = uniques;+                opt_data.num_probes = num_uniques;+                gss_parameter_init(&gss_param);+                success = (gss(0, opt_data.num_probes-5, &x, 0,+                        plfit_i_continuous_xmin_opt_evaluate,+                        plfit_i_continuous_xmin_opt_progress, &opt_data, &gss_param) == 0);+                if (success) {+                    px = opt_data.probes[(int)x];+                    best_n = opt_data.end-px+1;+                    best_result = opt_data.last;+                }+            }+            break;++        case PLFIT_STRATIFIED_SAMPLING:+            if (num_uniques >= 50) {+                /* Try stratified sampling to narrow down the interval where the minimum+                 * is likely to reside. We check 10% of the unique items, distributed+                 * evenly, find the one with the lowest D-score, and then check the+                 * area around it more thoroughly. */+                const size_t subdivision_length = 10;+                size_t num_strata = num_uniques / subdivision_length;+                double **strata = calloc(num_strata, sizeof(double*));++                for (i = 0; i < num_strata; i++) {+                    strata[i] = uniques[i * subdivision_length];+                }++                opt_data.probes = strata;+                opt_data.num_probes = num_strata;+                plfit_i_continuous_xmin_opt_linear_scan(&opt_data, &best_result, &best_n);++                opt_data.num_probes = 0;+                for (i = 0; i < num_strata; i++) {+                    if (*strata[i] == best_result.xmin) {+                        /* Okay, scan more thoroughly from strata[i-1] to strata[i+1],+                         * which is from uniques[(i-1)*subdivision_length] to+                         * uniques[(i+1)*subdivision_length */+                        opt_data.probes = uniques + (i > 0 ? (i-1)*subdivision_length : 0);+                        opt_data.num_probes = 0;+                        if (i != 0)+                            opt_data.num_probes += subdivision_length;+                        if (i != num_strata-1)+                            opt_data.num_probes += subdivision_length;+                        break;+                    }+                }++                free(strata);+                if (opt_data.num_probes > 0) {+                    /* Do a strict linear scan in the subrange determined above */+                    plfit_i_continuous_xmin_opt_linear_scan(&opt_data,+                            &best_result, &best_n);+                    success = 1;+                } else {+                    /* This should not happen, but we handle it anyway */+                    success = 0;+                }+            }+            break;++        default:+            /* Just use the linear search */+            break;+    }++    if (!success) {+        /* More advanced search methods failed or were skipped; try linear search */+        opt_data.probes = uniques;+        opt_data.num_probes = num_uniques;+        plfit_i_continuous_xmin_opt_linear_scan(&opt_data, &best_result, &best_n);+        success = 1;+    }++    /* Get rid of the uniques array, we don't need it any more */+    free(uniques);++    /* Sort out the result */+    *result = best_result;+    if (options->finite_size_correction)+        plfit_i_perform_finite_size_correction(result, best_n);++    PLFIT_CHECK(plfit_log_likelihood_continuous(opt_data.begin + n - best_n, best_n,+            result->alpha, result->xmin, &result->L));+    PLFIT_CHECK(plfit_i_calculate_p_value_continuous(opt_data.begin, n, options, 0, result));++    /* Get rid of the copied data as well */+    free(opt_data.begin);++    return PLFIT_SUCCESS;+}++/********** Discrete power law distribution fitting **********/++typedef struct {+    size_t m;+    double logsum;+    double xmin;+} plfit_i_estimate_alpha_discrete_data_t;++static double plfit_i_logsum_discrete(double* begin, double* end, double xmin) {+    double logsum = 0.0;+    for (; begin != end; begin++)+        logsum += log(*begin);+    return logsum;+}++static void plfit_i_logsum_less_than_discrete(double* begin, double* end, double xmin,+        double* logsum, size_t* m) {+    double result = 0.0;+    size_t count = 0;++    for (; begin != end; begin++) {+        if (*begin < xmin)+            continue;++        result += log(*begin);+        count++;+    }++    *logsum = result;+    *m = count;+}++static lbfgsfloatval_t plfit_i_estimate_alpha_discrete_lbfgs_evaluate(+        void* instance, const lbfgsfloatval_t* x,+        lbfgsfloatval_t* g, const int n,+        const lbfgsfloatval_t step) {+    plfit_i_estimate_alpha_discrete_data_t* data;+    lbfgsfloatval_t result;+    double dx = step;+    double huge = 1e10;     /* pseudo-infinity; apparently DBL_MAX does not work */+    double lnhzeta_x=NAN;+    double lnhzeta_deriv_x=NAN;++    data = (plfit_i_estimate_alpha_discrete_data_t*)instance;++#ifdef PLFIT_DEBUG+    printf("- Evaluating at %.4f (step = %.4f, xmin = %.4f)\n", *x, step, data->xmin);+#endif++    if (isnan(*x)) {+        g[0] = huge;+        return huge;+    }++    /* Find the delta X value to estimate the gradient */+    if (dx > 0.001 || dx == 0)+        dx = 0.001;+    else if (dx < -0.001)+        dx = -0.001;++    /* Is x[0] in its valid range? */+    if (x[0] <= 1.0) {+        /* The Hurwitz zeta function is infinite in this case */+        g[0] = (dx > 0) ? -huge : huge;+        return huge;+    }+    if (x[0] + dx <= 1.0) {+        g[0] = huge;+        result = x[0] * data->logsum + data->m * hsl_sf_lnhzeta(x[0], data->xmin);+    } else {+        hsl_sf_lnhzeta_deriv_tuple(x[0], data->xmin, &lnhzeta_x, &lnhzeta_deriv_x);+        g[0] = data->logsum + data->m * lnhzeta_deriv_x;+        result = x[0] * data->logsum + data->m * lnhzeta_x;+    }++#ifdef PLFIT_DEBUG+    printf("  - Gradient: %.4f\n", g[0]);+    printf("  - Result: %.4f\n", result);+#endif++    return result;+}++static int plfit_i_estimate_alpha_discrete_lbfgs_progress(void* instance,+        const lbfgsfloatval_t* x, const lbfgsfloatval_t* g,+        const lbfgsfloatval_t fx, const lbfgsfloatval_t xnorm,+        const lbfgsfloatval_t gnorm, const lbfgsfloatval_t step,+        int n, int k, int ls) {+    return 0;+}++static int plfit_i_estimate_alpha_discrete_linear_scan(double* xs, size_t n,+        double xmin, double* alpha, const plfit_discrete_options_t* options,+        plfit_bool_t sorted) {+    double curr_alpha, best_alpha, L, L_max;+    double logsum;+    size_t m;++    XMIN_CHECK_ONE;+    if (options->alpha.min <= 1.0) {+        PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);+    }+    if (options->alpha.max < options->alpha.min) {+        PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);+    }+    if (options->alpha.step <= 0) {+        PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);+    }++    if (sorted) {+        logsum = plfit_i_logsum_discrete(xs, xs+n, xmin);+        m = n;+    } else {+        plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &logsum, &m);+    }++    best_alpha = options->alpha.min; L_max = -DBL_MAX;+    for (curr_alpha = options->alpha.min; curr_alpha <= options->alpha.max;+            curr_alpha += options->alpha.step) {+        L = -curr_alpha * logsum - m * hsl_sf_lnhzeta(curr_alpha, xmin);+        if (L > L_max) {+            L_max = L;+            best_alpha = curr_alpha;+        }+    }++    *alpha = best_alpha;++    return PLFIT_SUCCESS;+}++static int plfit_i_estimate_alpha_discrete_lbfgs(double* xs, size_t n, double xmin,+        double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) {+    lbfgs_parameter_t param;+    lbfgsfloatval_t* variables;+    plfit_i_estimate_alpha_discrete_data_t data;+    int ret;++    XMIN_CHECK_ONE;++    /* Initialize algorithm parameters */+    lbfgs_parameter_init(&param);+    param.max_iterations = 0;   /* proceed until infinity */++    /* Set up context for optimization */+    data.xmin = xmin;+    if (sorted) {+        data.logsum = plfit_i_logsum_discrete(xs, xs+n, xmin);+        data.m = n;+    } else {+        plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &data.logsum, &data.m);+    }++    /* Allocate space for the single alpha variable */+    variables = lbfgs_malloc(1);+    variables[0] = 3.0;       /* initial guess */++    /* Optimization */+    ret = lbfgs(1, variables, /* ptr_fx = */ 0,+            plfit_i_estimate_alpha_discrete_lbfgs_evaluate,+            plfit_i_estimate_alpha_discrete_lbfgs_progress,+            &data, &param);++    if (ret < 0 &&+        ret != LBFGSERR_ROUNDING_ERROR &&+        ret != LBFGSERR_MAXIMUMLINESEARCH &&+        ret != LBFGSERR_MINIMUMSTEP &&+        ret != LBFGSERR_CANCELED) {+        char buf[4096];+        snprintf(buf, 4096, "L-BFGS optimization signaled an error (error code = %d)", ret);+        lbfgs_free(variables);+        PLFIT_ERROR(buf, PLFIT_FAILURE);+    }+    *alpha = variables[0];++    /* Deallocate the variable array */+    lbfgs_free(variables);++    return PLFIT_SUCCESS;+}++static int plfit_i_estimate_alpha_discrete_fast(double* xs, size_t n, double xmin,+        double* alpha, const plfit_discrete_options_t* options, plfit_bool_t sorted) {+    plfit_continuous_options_t cont_options;++    if (!options)+        options = &plfit_discrete_default_options;++    plfit_continuous_options_init(&cont_options);+    cont_options.finite_size_correction = options->finite_size_correction;++    XMIN_CHECK_ONE;++    if (sorted) {+        return plfit_i_estimate_alpha_continuous_sorted(xs, n, xmin-0.5, alpha);+    } else {+        return plfit_i_estimate_alpha_continuous(xs, n, xmin-0.5, alpha);+    }+}++static int plfit_i_estimate_alpha_discrete(double* xs, size_t n, double xmin,+        double* alpha, const plfit_discrete_options_t* options,+        plfit_bool_t sorted) {+    switch (options->alpha_method) {+        case PLFIT_LBFGS:+            PLFIT_CHECK(plfit_i_estimate_alpha_discrete_lbfgs(xs, n, xmin, alpha,+                        options, sorted));+            break;++        case PLFIT_LINEAR_SCAN:+            PLFIT_CHECK(plfit_i_estimate_alpha_discrete_linear_scan(xs, n, xmin,+                        alpha, options, sorted));+            break;++        case PLFIT_PRETEND_CONTINUOUS:+            PLFIT_CHECK(plfit_i_estimate_alpha_discrete_fast(xs, n, xmin,+                        alpha, options, sorted));+            break;++        default:+            PLFIT_ERROR("unknown optimization method specified", PLFIT_EINVAL);+    }++    return PLFIT_SUCCESS;+}++static int plfit_i_ks_test_discrete(double* xs, double* xs_end, const double alpha,+        const double xmin, double* D) {+    /* Assumption: xs is sorted and cut off at xmin so the first element is+     * always larger than or equal to xmin. */+    double result = 0, n, lnhzeta, x;+    int m = 0;++    n = xs_end - xs;+    lnhzeta = hsl_sf_lnhzeta(alpha, xmin);++    while (xs < xs_end) {+        double d;++        x = *xs;++        /* Re the next line: this used to be the following:+         *+         * fabs( 1 - hzeta(alpha, x) / hzeta(alpha, xmin) - m / n)+         *+         * However, using the Hurwitz zeta directly sometimes yields+         * underflows (see Github pull request #17 and related issues).+         * hzeta(alpha, x) / hzeta(alpha, xmin) can be replaced with+         * exp(lnhzeta(alpha, x) - lnhzeta(alpha, xmin)), but then+         * we have 1 - exp(something), which is better to calculate+         * with a dedicated expm1() function.+         */+        d = fabs( expm1( hsl_sf_lnhzeta(alpha, x) - lnhzeta ) + m / n);++        if (d > result)+            result = d;++        do {+            xs++; m++;+        } while (xs < xs_end && *xs == x);+    }++    *D = result;++    return PLFIT_SUCCESS;+}++static int plfit_i_calculate_p_value_discrete(double* xs, size_t n,+        const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed,+        plfit_result_t *result) {+    long int num_trials;+    long int successes = 0;+    double *xs_head;+    size_t num_smaller;+    plfit_discrete_options_t options_no_p_value = *options;+    int retval = PLFIT_SUCCESS;++    if (options->p_value_method == PLFIT_P_VALUE_SKIP) {+        /* skipping p-value calculation */+        result->p = NAN;+        return PLFIT_SUCCESS;+    }++    if (options->p_value_method == PLFIT_P_VALUE_APPROXIMATE) {+        /* p-value approximation; most likely an upper bound */+        num_smaller = count_smaller(xs, xs + n, result->xmin);+        result->p = plfit_ks_test_one_sample_p(result->D, n - num_smaller);+        return PLFIT_SUCCESS;+    }++    options_no_p_value.p_value_method = PLFIT_P_VALUE_SKIP;+    num_trials = (long int)(0.25 / options->p_value_precision / options->p_value_precision);+    if (num_trials <= 0) {+        PLFIT_ERROR("invalid p-value precision", PLFIT_EINVAL);+    }++    /* Extract the head of xs that contains elements smaller than xmin */+    xs_head = extract_smaller(xs, xs+n, result->xmin, &num_smaller);+    if (xs_head == 0)+        PLFIT_ERROR("cannot calculate exact p-value", PLFIT_ENOMEM);++#ifdef _OPENMP+#pragma omp parallel+#endif+    {+        /* Parallel section starts here. If we are compiling using OpenMP, each+         * thread will use its own RNG that is seeded from the master RNG. If+         * we are compiling without OpenMP, there is only one thread and it uses+         * the master RNG. This section must be critical to ensure that only one+         * thread is using the master RNG at the same time. */+#ifdef _OPENMP+        mt_rng_t private_rng;+#endif+        mt_rng_t *p_rng;+        double *ys;+        long int i;+        plfit_result_t result_synthetic;++#ifdef _OPENMP+#pragma omp critical+        {+            p_rng = &private_rng;+            mt_init_from_rng(p_rng, options->rng);+        }+#else+        p_rng = options->rng;+#endif++        /* Allocate memory to sample into */+        ys = calloc(n, sizeof(double));+        if (ys == 0) {+            retval = PLFIT_ENOMEM;+        } else {+            /* The main for loop starts here. */+#ifdef _OPENMP+#pragma omp for reduction(+:successes)+#endif+            for (i = 0; i < num_trials; i++) {+                plfit_i_resample_discrete(xs_head, num_smaller, n, result->alpha,+                        result->xmin, n, p_rng, ys);+                if (xmin_fixed) {+                    plfit_estimate_alpha_discrete(ys, n, result->xmin,+                                &options_no_p_value, &result_synthetic);+                } else {+                    plfit_discrete(ys, n, &options_no_p_value, &result_synthetic);+                }+                if (result_synthetic.D > result->D)+                    successes++;+            }++            free(ys);+        }++        /* End of parallelized part */+    }++    free(xs_head);++    if (retval == PLFIT_SUCCESS) {+        result->p = successes / ((double)num_trials);+    } else {+        PLFIT_ERROR("cannot calculate exact p-value", retval);+    }++    return retval;+}++int plfit_log_likelihood_discrete(double* xs, size_t n, double alpha, double xmin, double* L) {+    double result;+    size_t m;++    if (alpha <= 1) {+        PLFIT_ERROR("alpha must be greater than one", PLFIT_EINVAL);+    }+    XMIN_CHECK_ONE;++    plfit_i_logsum_less_than_discrete(xs, xs+n, xmin, &result, &m);+    result = - alpha * result - m * hsl_sf_lnhzeta(alpha, xmin);++    *L = result;++    return PLFIT_SUCCESS;+}++int plfit_estimate_alpha_discrete(double* xs, size_t n, double xmin,+        const plfit_discrete_options_t* options, plfit_result_t *result) {+    double *xs_copy, *begin, *end;++    if (!options)+        options = &plfit_discrete_default_options;++    /* Check the validity of the input parameters */+    DATA_POINTS_CHECK;+    if (options->alpha_method == PLFIT_LINEAR_SCAN) {+        if (options->alpha.min <= 1.0) {+            PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);+        }+        if (options->alpha.max < options->alpha.min) {+            PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);+        }+        if (options->alpha.step <= 0) {+            PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);+        }+    }++    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy));++    begin = xs_copy; end = xs_copy + n;+    while (begin < end && *begin < xmin)+        begin++;++    PLFIT_CHECK(plfit_i_estimate_alpha_discrete(begin, end-begin, xmin, &result->alpha,+                options, /* sorted = */ 1));+    PLFIT_CHECK(plfit_i_ks_test_discrete(begin, end, result->alpha, xmin, &result->D));++    result->xmin = xmin;+    if (options->finite_size_correction)+        plfit_i_perform_finite_size_correction(result, end-begin);++    PLFIT_CHECK(plfit_log_likelihood_discrete(begin, end-begin, result->alpha,+                result->xmin, &result->L));+    PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs, n, options, 1, result));++    free(xs_copy);++    return PLFIT_SUCCESS;+}++int plfit_discrete(double* xs, size_t n, const plfit_discrete_options_t* options,+        plfit_result_t* result) {+    double curr_D, curr_alpha;+    plfit_result_t best_result;+    double *xs_copy, *px, *end, *end_xmin, prev_x;+    size_t best_n;+    int m;++    if (!options)+        options = &plfit_discrete_default_options;++    /* Check the validity of the input parameters */+    DATA_POINTS_CHECK;+    if (options->alpha_method == PLFIT_LINEAR_SCAN) {+        if (options->alpha.min <= 1.0) {+            PLFIT_ERROR("alpha.min must be greater than 1.0", PLFIT_EINVAL);+        }+        if (options->alpha.max < options->alpha.min) {+            PLFIT_ERROR("alpha.max must be greater than alpha.min", PLFIT_EINVAL);+        }+        if (options->alpha.step <= 0) {+            PLFIT_ERROR("alpha.step must be positive", PLFIT_EINVAL);+        }+    }++    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy));++    best_result.D = DBL_MAX;+    best_result.xmin = 1;+    best_result.alpha = 1;+    best_n = 0;++    /* Make sure there are at least three distinct values if possible */+    px = xs_copy; end = px + n; end_xmin = end - 1; m = 0;+    prev_x = *end_xmin;+    while (*end_xmin == prev_x && end_xmin > px)+        end_xmin--;+    prev_x = *end_xmin;+    while (*end_xmin == prev_x && end_xmin > px)+        end_xmin--;++    prev_x = 0;+    while (px < end_xmin) {+        while (px < end_xmin && *px == prev_x) {+            px++; m++;+        }++        plfit_i_estimate_alpha_discrete(px, n-m, *px, &curr_alpha, options,+                /* sorted = */ 1);+        plfit_i_ks_test_discrete(px, end, curr_alpha, *px, &curr_D);++        if (curr_D < best_result.D) {+            best_result.alpha = curr_alpha;+            best_result.xmin = *px;+            best_result.D = curr_D;+            best_n = n-m;+        }++        prev_x = *px;+        px++; m++;+    }++    *result = best_result;+    if (options->finite_size_correction)+        plfit_i_perform_finite_size_correction(result, best_n);++    PLFIT_CHECK(plfit_log_likelihood_discrete(xs_copy+(n-best_n), best_n,+                result->alpha, result->xmin, &result->L));+    PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs_copy, n, options, 0, result));++    free(xs_copy);++    return PLFIT_SUCCESS;+}++/***** resampling routines to generate synthetic replicates ****/++static int plfit_i_resample_continuous(double* xs_head, size_t num_smaller,+        size_t n, double alpha, double xmin, size_t num_samples, mt_rng_t* rng,+        double* result)+{+    size_t num_orig_samples, i;++    /* Calculate how many samples have to be drawn from xs_head */+    num_orig_samples = (size_t) plfit_rbinom(num_samples, num_smaller / (double)n, rng);++    /* Draw the samples from xs_head */+    for (i = 0; i < num_orig_samples; i++, result++) {+        *result = xs_head[(size_t)plfit_runif(0, num_smaller, rng)];+    }++    /* Draw the remaining samples from the fitted distribution */+    PLFIT_CHECK(plfit_rpareto_array(xmin, alpha-1, num_samples-num_orig_samples, rng,+            result));++    return PLFIT_SUCCESS;+}++int plfit_resample_continuous(double* xs, size_t n, double alpha, double xmin,+        size_t num_samples, mt_rng_t* rng, double* result) {+    double *xs_head;+    size_t num_smaller = 0;+    int retval;++    /* Extract the head of xs that contains elements smaller than xmin */+    xs_head = extract_smaller(xs, xs+n, xmin, &num_smaller);+    if (xs_head == 0)+        PLFIT_ERROR("cannot resample continuous dataset", PLFIT_ENOMEM);++    retval = plfit_i_resample_continuous(xs_head, num_smaller, n, alpha, xmin,+                num_samples, rng, result);++    /* Free xs_head; we don't need it any more */+    free(xs_head);++    return retval;+}++static int plfit_i_resample_discrete(double* xs_head, size_t num_smaller, size_t n,+        double alpha, double xmin, size_t num_samples, mt_rng_t* rng,+        double* result)+{+    size_t num_orig_samples, i;++    /* Calculate how many samples have to be drawn from xs_head */+    num_orig_samples = (size_t) plfit_rbinom(num_samples, num_smaller / (double)n, rng);++    /* Draw the samples from xs_head */+    for (i = 0; i < num_orig_samples; i++, result++) {+        *result = xs_head[(size_t)plfit_runif(0, num_smaller, rng)];+    }++    /* Draw the remaining samples from the fitted distribution */+    PLFIT_CHECK(plfit_rzeta_array((long int)xmin, alpha,+                num_samples-num_orig_samples, rng, result));++    return PLFIT_SUCCESS;+}++int plfit_resample_discrete(double* xs, size_t n, double alpha, double xmin,+        size_t num_samples, mt_rng_t* rng, double* result) {+    double *xs_head;+    size_t num_smaller = 0;+    int retval;++    /* Extract the head of xs that contains elements smaller than xmin */+    xs_head = extract_smaller(xs, xs+n, xmin, &num_smaller);+    if (xs_head == 0)+        PLFIT_ERROR("cannot resample discrete dataset", PLFIT_ENOMEM);++    retval = plfit_i_resample_discrete(xs_head, num_smaller, n, alpha, xmin,+                num_samples, rng, result);++    /* Free xs_head; we don't need it any more */+    free(xs_head);++    return retval;+}++/******** calculating the p-value of a fitted model only *******/++int plfit_calculate_p_value_continuous(double* xs, size_t n,+        const plfit_continuous_options_t* options, plfit_bool_t xmin_fixed,+        plfit_result_t *result) {+    double* xs_copy;++    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy));+    PLFIT_CHECK(plfit_i_calculate_p_value_continuous(xs_copy, n, options,+                xmin_fixed, result));+    free(xs_copy);++    return PLFIT_SUCCESS;+}++int plfit_calculate_p_value_discrete(double* xs, size_t n,+        const plfit_discrete_options_t* options, plfit_bool_t xmin_fixed,+        plfit_result_t *result) {+    double* xs_copy;++    PLFIT_CHECK(plfit_i_copy_and_sort(xs, n, &xs_copy));+    PLFIT_CHECK(plfit_i_calculate_p_value_discrete(xs_copy, n, options,+                xmin_fixed, result));+    free(xs_copy);++    return PLFIT_SUCCESS;+}
igraph/src/pottsmodel_2.cpp view
@@ -42,18 +42,17 @@  *                                                                         *  ***************************************************************************/ -#include <cstdlib>-#include <cstdio>-#include <cstring>-#include <cmath> #include "pottsmodel_2.h" #include "NetRoutines.h" -using namespace std;- #include "igraph_random.h" #include "igraph_interrupt_internal.h" #include "config.h"++#include <cstring>+#include <cmath>++using namespace std;  //################################################################################################# PottsModel::PottsModel(network *n, unsigned int qvalue, int m) : acceptance(0) {
igraph/src/prpack_solver.cpp view
@@ -237,7 +237,7 @@     } else {         // TODO: throw exception     }-    ret->method = m.c_str();+    ret->method = m;     ret->read_time = read_time;     ret->preprocess_time = preprocess_time;     ret->compute_time = compute_time;
igraph/src/prpack_utils.cpp view
@@ -16,7 +16,7 @@ #include "igraph_error.h" #endif -#if defined(_WIN32) || defined(_WIN64)+#if defined(_WIN32) #ifndef WIN32_LEAN_AND_MEAN #define WIN32_LEAN_AND_MEAN #include <windows.h>
igraph/src/qsort.c view
@@ -31,6 +31,8 @@  * SUCH DAMAGE.  */ +#include "igraph_qsort.h"+ #ifdef _MSC_VER     /* MSVC does not have inline when compiling C source files */     #define inline __inline@@ -76,9 +78,7 @@                                    es % sizeof(long) ? 2 : es == sizeof(long)? 0 : 1;  static inline void-swapfunc(a, b, n, swaptype)-char *a, *b;-int n, swaptype;+swapfunc(char *a, char *b, int n, int swaptype) {     if (swaptype <= 1)         swapcode(long, a, b, n)
igraph/src/random.c view
@@ -22,22 +22,20 @@ */  #include "igraph_random.h"+#include "igraph_nongraph.h" #include "igraph_error.h"-#include "config.h"--#include <math.h>-#include <limits.h>-#include <string.h> #include "igraph_math.h" #include "igraph_types.h" #include "igraph_vector.h" #include "igraph_memory.h"-#include "igraph_matrix.h"+#include "config.h"+#include <math.h>+#include <string.h>  /**  * \section about_rngs  *- * <section>+ * <section id="about-random-numbers-in-igraph">  * <title>About random numbers in igraph, use cases</title>  *  * <para>@@ -54,9 +52,9 @@ /**  * \section rng_use_cases  *- * <section><title>Use cases</title>+ * <section id="random-use-cases"><title>Use cases</title>  *- * <section><title>Normal (default) use</title>+ * <section id="random-normal-use"><title>Normal (default) use</title>  * <para>  * If the user does not use any of the RNG functions explicitly, but calls  * some of the randomized igraph functions, then a default RNG is set@@ -73,7 +71,7 @@  * </para>  * </section>  *- * <section><title>Reproducible simulations</title>+ * <section id="random-reproducible-simulations"><title>Reproducible simulations</title>  * <para>  * If reproducible results are needed, then the user should set the  * seed of the default random number generator explicitly, using the@@ -84,7 +82,7 @@  * </para>  * </section>  *- * <section><title>Changing the default generator</title>+ * <section id="random-changing-default-generator"><title>Changing the default generator</title>  * <para>  * By default igraph uses the \ref igraph_rng_default() random number  * generator. This can be changed any time by calling \ref@@ -94,7 +92,7 @@  * </para>  * </section>  *- * <section><title>Using multiple generators</title>+ * <section id="random-using-multiple-generators"><title>Using multiple generators</title>  * <para>  * igraph also provides functions to set up multiple random number  * generators, using the \ref igraph_rng_init() function, and then@@ -110,7 +108,7 @@  * </para>  * </section>  *- * <section><title>Example</title>+ * <section id="random-example"><title>Example</title>  * <para>  * \example examples/simple/random_seed.c  * </para>@@ -126,8 +124,7 @@     long int x[31]; } igraph_i_rng_glibc2_state_t; -unsigned long int igraph_i_rng_glibc2_get(int *i, int *j, int n,-        long int *x) {+static unsigned long int igraph_i_rng_glibc2_get(int *i, int *j, int n, long int *x) {     unsigned long int k;      x[*i] += x[*j];@@ -158,8 +155,8 @@  /* this function is independent of the bit size */ -void igraph_i_rng_glibc2_init(long int *x, int n,-                              unsigned long int s) {+static void igraph_i_rng_glibc2_init(long int *x, int n,+                                     unsigned long int s) {     int i;      if (s == 0) {@@ -514,7 +511,7 @@  *  * \param rng The random number generator to use as default from now  *    on. Calling \ref igraph_rng_destroy() on it, while it is still- *    being used as the default will result craches and/or+ *    being used as the default will result crashes and/or  *    unpredictable results.  *  * Time complexity: O(1).@@ -977,8 +974,9 @@  * result vector.  */ -int igraph_i_random_sample_alga(igraph_vector_t *res, igraph_integer_t l, igraph_integer_t h,-                                igraph_integer_t length) {+static int igraph_i_random_sample_alga(igraph_vector_t *res,+                                       igraph_integer_t l, igraph_integer_t h,+                                       igraph_integer_t length) {     igraph_real_t N = h - l + 1;     igraph_real_t n = length; @@ -1538,7 +1536,7 @@     return (x < y) ? x : y; } -#if HAVE_WORKING_ISFINITE || HAVE_ISFINITE+#if HAVE_WORKING_ISFINITE || HAVE_DECL_ISFINITE     /* isfinite is defined in <math.h> according to C99 */     #define R_FINITE(x)    isfinite(x) #elif HAVE_WORKING_FINITE || HAVE_FINITE@@ -1556,7 +1554,7 @@ #endif  int R_finite(double x) {-#if HAVE_WORKING_ISFINITE || HAVE_ISFINITE+#if HAVE_WORKING_ISFINITE || HAVE_DECL_ISFINITE     return isfinite(x); #elif HAVE_WORKING_FINITE || HAVE_FINITE     return finite(x);
igraph/src/random_walk.c view
@@ -43,7 +43,7 @@  * \param start The start vertex for the walk.  * \param steps The number of steps to take. If the random walk gets  *   stuck, then the \p stuck argument specifies what happens.- * \param mode How to walk along the edges in direted graphs.+ * \param mode How to walk along the edges in directed graphs.  *   \c IGRAPH_OUT means following edge directions, \c IGRAPH_IN means  *   going opposite the edge directions, \c IGRAPH_ALL means ignoring  *   edge directions. This argument is ignored for undirected graphs.@@ -142,7 +142,7 @@  * \param start The start vertex for the walk.  * \param steps The number of steps to take. If the random walk gets  *   stuck, then the \p stuck argument specifies what happens.- * \param mode How to walk along the edges in direted graphs.+ * \param mode How to walk along the edges in directed graphs.  *   \c IGRAPH_OUT means following edge directions, \c IGRAPH_IN means  *   going opposite the edge directions, \c IGRAPH_ALL means ignoring  *   edge directions. This argument is ignored for undirected graphs.
+ igraph/src/rbinom.c view
@@ -0,0 +1,209 @@+/*+ *  Mathlib : A C Library of Special Functions+ *  Copyright (C) 1998 Ross Ihaka+ *  Copyright (C) 2000-2002 The R Core Team+ *  Copyright (C) 2007 The R Foundation+ *+ *  This program is free software; you can redistribute it and/or modify+ *  it under the terms of the GNU General Public License as published by+ *  the Free Software Foundation; either version 2 of the License, or+ *  (at your option) any later version.+ *+ *  This program is distributed in the hope that it will be useful,+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+ *  GNU General Public License for more details.+ *+ *  You should have received a copy of the GNU General Public License+ *  along with this program; if not, a copy is available at+ *  http://www.r-project.org/Licenses/+ *+ *  SYNOPSIS+ *+ *	#include <Rmath.h>+ *	double rbinom(double nin, double pp)+ *+ *  DESCRIPTION+ *+ *	Random variates from the binomial distribution.+ *+ *  REFERENCE+ *+ *	Kachitvichyanukul, V. and Schmeiser, B. W. (1988).+ *	Binomial random variate generation.+ *	Communications of the ACM 31, 216-222.+ *	(Algorithm BTPEC).+ */++/*+ * Modifications for this file were performed by Tamas Nepusz to make it fit+ * better with plfit. The license of the original file applies to the+ * modifications as well.+ */++#include <limits.h>+#include <math.h>+#include <stdlib.h>+#include "sampling.h"+#include "platform.h"++#define repeat for(;;)++double plfit_rbinom(double nin, double pp, mt_rng_t* rng)+{+    /* FIXME: These should become THREAD_specific globals : */++    static double c, fm, npq, p1, p2, p3, p4, qn;+    static double xl, xll, xlr, xm, xr;++    static double psave = -1.0;+    static int nsave = -1;+    static int m;++    double f, f1, f2, u, v, w, w2, x, x1, x2, z, z2;+    double p, q, np, g, r, al, alv, amaxp, ffm, ynorm;+    int i, ix, k, n;++    if (!isfinite(nin)) return NAN;+    r = floor(nin + 0.5);+    if (r != nin) return NAN;+    if (!isfinite(pp) ||+	/* n=0, p=0, p=1 are not errors <TSL>*/+	r < 0 || pp < 0. || pp > 1.) return NAN;++    if (r == 0 || pp == 0.) return 0;+    if (pp == 1.) return r;++    n = (int) r;++    p = fmin(pp, 1. - pp);+    q = 1. - p;+    np = n * p;+    r = p / q;+    g = r * (n + 1);++    /* Setup, perform only when parameters change [using static (globals): */++    /* FIXING: Want this thread safe+       -- use as little (thread globals) as possible+    */+    if (pp != psave || n != nsave) {+	psave = pp;+	nsave = n;+	if (np < 30.0) {+	    /* inverse cdf logic for mean less than 30 */+	    qn = pow(q, (double) n);+	    goto L_np_small;+	} else {+	    ffm = np + p;+	    m = (int) ffm;+	    fm = m;+	    npq = np * q;+	    p1 = (int)(2.195 * sqrt(npq) - 4.6 * q) + 0.5;+	    xm = fm + 0.5;+	    xl = xm - p1;+	    xr = xm + p1;+	    c = 0.134 + 20.5 / (15.3 + fm);+	    al = (ffm - xl) / (ffm - xl * p);+	    xll = al * (1.0 + 0.5 * al);+	    al = (xr - ffm) / (xr * q);+	    xlr = al * (1.0 + 0.5 * al);+	    p2 = p1 * (1.0 + c + c);+	    p3 = p2 + c / xll;+	    p4 = p3 + c / xlr;+	}+    } else if (n == nsave) {+	if (np < 30.0)+	    goto L_np_small;+    }++    /*-------------------------- np = n*p >= 30 : ------------------- */+    repeat {+      u = plfit_runif_01(rng) * p4;+      v = plfit_runif_01(rng);+      /* triangular region */+      if (u <= p1) {+	  ix = (int)(xm - p1 * v + u);+	  goto finis;+      }+      /* parallelogram region */+      if (u <= p2) {+	  x = xl + (u - p1) / c;+	  v = v * c + 1.0 - fabs(xm - x) / p1;+	  if (v > 1.0 || v <= 0.)+	      continue;+	  ix = (int) x;+      } else {+	  if (u > p3) {	/* right tail */+	      ix = (int)(xr - log(v) / xlr);+	      if (ix > n)+		  continue;+	      v = v * (u - p3) * xlr;+	  } else {/* left tail */+	      ix = (int)(xl + log(v) / xll);+	      if (ix < 0)+		  continue;+	      v = v * (u - p2) * xll;+	  }+      }+      /* determine appropriate way to perform accept/reject test */+      k = abs(ix - m);+      if (k <= 20 || k >= npq / 2 - 1) {+	  /* explicit evaluation */+	  f = 1.0;+	  if (m < ix) {+	      for (i = m + 1; i <= ix; i++)+		  f *= (g / i - r);+	  } else if (m != ix) {+	      for (i = ix + 1; i <= m; i++)+		  f /= (g / i - r);+	  }+	  if (v <= f)+	      goto finis;+      } else {+	  /* squeezing using upper and lower bounds on log(f(x)) */+	  amaxp = (k / npq) * ((k * (k / 3. + 0.625) + 0.1666666666666) / npq + 0.5);+	  ynorm = -k * k / (2.0 * npq);+	  alv = log(v);+	  if (alv < ynorm - amaxp)+	      goto finis;+	  if (alv <= ynorm + amaxp) {+	      /* stirling's formula to machine accuracy */+	      /* for the final acceptance/rejection test */+	      x1 = ix + 1;+	      f1 = fm + 1.0;+	      z = n + 1 - fm;+	      w = n - ix + 1.0;+	      z2 = z * z;+	      x2 = x1 * x1;+	      f2 = f1 * f1;+	      w2 = w * w;+	      if (alv <= xm * log(f1 / x1) + (n - m + 0.5) * log(z / w) + (ix - m) * log(w * p / (x1 * q)) + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / f2) / f2) / f2) / f2) / f1 / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / z2) / z2) / z2) / z2) / z / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / x2) / x2) / x2) / x2) / x1 / 166320.0 + (13860.0 - (462.0 - (132.0 - (99.0 - 140.0 / w2) / w2) / w2) / w2) / w / 166320.)+		  goto finis;+	  }+      }+  }++ L_np_small:+    /*---------------------- np = n*p < 30 : ------------------------- */++  repeat {+     ix = 0;+     f = qn;+     u = plfit_runif_01(rng);+     repeat {+	 if (u < f)+	     goto finis;+	 if (ix > 110)+	     break;+	 u -= f;+	 ix++;+	 f *= (g / ix - r);+     }+  }+ finis:+    if (psave > 0.5)+	 ix = n - ix;+  return (double)ix;+}+
igraph/src/reorder.c view
+ igraph/src/sampling.c view
@@ -0,0 +1,304 @@+/* sampling.c+ *+ * Copyright (C) 2012 Tamas Nepusz+ *+ * This program is free software; you can redistribute it and/or modify+ * it under the terms of the GNU General Public License as published by+ * the Free Software Foundation; either version 2 of the License, or (at+ * your option) any later version.+ *+ * This program is distributed in the hope that it will be useful, but+ * WITHOUT ANY WARRANTY; without even the implied warranty of+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU+ * General Public License for more details.+ *+ * You should have received a copy of the GNU General Public License+ * along with this program; if not, write to the Free Software+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.+ */++#include <math.h>++#include "igraph_random.h"++#include "error.h"+#include "sampling.h"+#include "platform.h"++inline double plfit_runif(double lo, double hi, mt_rng_t* rng) {+    if (rng == 0) {+        return RNG_UNIF(lo, hi);+    }+    return lo + mt_uniform_01(rng) * (hi-lo);+}++inline double plfit_runif_01(mt_rng_t* rng) {+    if (rng == 0) {+        return RNG_UNIF01();+    }+    return mt_uniform_01(rng);+}++inline double plfit_rpareto(double xmin, double alpha, mt_rng_t* rng) {+    if (alpha <= 0 || xmin <= 0)+        return NAN;++    /* 1-u is used in the base here because we want to avoid the case of+     * sampling zero */+    return pow(1-plfit_runif_01(rng), -1.0 / alpha) * xmin;+}++int plfit_rpareto_array(double xmin, double alpha, size_t n, mt_rng_t* rng,+        double* result) {+    double gamma;++    if (alpha <= 0 || xmin <= 0)+        return PLFIT_EINVAL;++    if (result == 0 || n == 0)+        return PLFIT_SUCCESS;++    gamma = -1.0 / alpha;+    while (n > 0) {+        /* 1-u is used in the base here because we want to avoid the case of+         * sampling zero */+        *result = pow(1-plfit_runif_01(rng), gamma) * xmin;+        result++; n--;+    }++    return PLFIT_SUCCESS;+}++inline double plfit_rzeta(long int xmin, double alpha, mt_rng_t* rng) {+    double u, v, t;+    long int x;+    double alpha_minus_1 = alpha-1;+    double minus_1_over_alpha_minus_1 = -1.0 / (alpha-1);+    double b;+    double one_over_b_minus_1;++    if (alpha <= 0 || xmin < 1)+        return NAN;++    xmin = (long int) round(xmin);++    /* Rejection sampling for the win. We use Y=floor(U^{-1/alpha} * xmin) as the+     * envelope distribution, similarly to Chapter X.6 of Luc Devroye's book+     * (where xmin is assumed to be 1): http://luc.devroye.org/chapter_ten.pdf+     *+     * Some notes that should help me recover what I was doing:+     *+     * p_i = 1/zeta(alpha, xmin) * i^-alpha+     * q_i = (xmin/i)^{alpha-1} - (xmin/(i+1))^{alpha-1}+     *     = (i/xmin)^{1-alpha} - ((i+1)/xmin)^{1-alpha}+     *     = [i^{1-alpha} - (i+1)^{1-alpha}] / xmin^{1-alpha}+     *+     * p_i / q_i attains its maximum at xmin=i, so the rejection constant is:+     *+     * c = p_xmin / q_xmin+     *+     * We have to accept the sample if V <= (p_i / q_i) * (q_xmin / p_xmin) =+     * (i/xmin)^-alpha * [xmin^{1-alpha} - (xmin+1)^{1-alpha}] / [i^{1-alpha} - (i+1)^{1-alpha}] =+     * [xmin - xmin^alpha / (xmin+1)^{alpha-1}] / [i - i^alpha / (i+1)^{alpha-1}] =+     * xmin/i * [1-(xmin/(xmin+1))^{alpha-1}]/[1-(i/(i+1))^{alpha-1}]+     *+     * In other words (and substituting i with X, which is the same),+     *+     * V * (X/xmin) <= [1 - (1+1/xmin)^{1-alpha}] / [1 - (1+1/i)^{1-alpha}]+     *+     * Let b := (1+1/xmin)^{alpha-1} and let T := (1+1/i)^{alpha-1}. Then:+     *+     * V * (X/xmin) <= [(b-1)/b] / [(T-1)/T]+     * V * (X/xmin) * (T-1) / (b-1) <= T / b+     *+     * which is the same as in Devroye's book, except for the X/xmin term, and+     * the definition of b.+     */+    b = pow(1 + 1.0/xmin, alpha_minus_1);+    one_over_b_minus_1 = 1.0/(b-1);+    do {+        do {+            u = plfit_runif_01(rng);+            v = plfit_runif_01(rng);+            /* 1-u is used in the base here because we want to avoid the case of+             * having zero in x */+            x = (long int) floor(pow(1-u, minus_1_over_alpha_minus_1) * xmin);+        } while (x < xmin);+        t = pow((x+1.0)/x, alpha_minus_1);+    } while (v*x*(t-1)*one_over_b_minus_1*b > t*xmin);++    return x;+}++int plfit_rzeta_array(long int xmin, double alpha, size_t n, mt_rng_t* rng,+        double* result) {+    double u, v, t;+    long int x;+    double alpha_minus_1 = alpha-1;+    double minus_1_over_alpha_minus_1 = -1.0 / (alpha-1);+    double b, one_over_b_minus_1;++    if (alpha <= 0 || xmin < 1)+        return PLFIT_EINVAL;++    if (result == 0 || n == 0)+        return PLFIT_SUCCESS;++    /* See the comments in plfit_rzeta for an explanation of the algorithm+     * below. */+    xmin = (long int) round(xmin);+    b = pow(1 + 1.0/xmin, alpha_minus_1);+    one_over_b_minus_1 = 1.0/(b-1);++    while (n > 0) {+        do {+            do {+                u = plfit_runif_01(rng);+                v = plfit_runif_01(rng);+                /* 1-u is used in the base here because we want to avoid the case of+                 * having zero in x */+                x = (long int) floor(pow(1-u, minus_1_over_alpha_minus_1) * xmin);+            } while (x < xmin);     /* handles overflow as well */+            t = pow((x+1.0)/x, alpha_minus_1);+        } while (v*x*(t-1)*one_over_b_minus_1*b > t*xmin);+        *result = x;+        if (x < 0) return PLFIT_EINVAL;+        result++; n--;+    }++    return PLFIT_SUCCESS;+}++int plfit_walker_alias_sampler_init(plfit_walker_alias_sampler_t* sampler,+        double* ps, size_t n) {+    double *p, *p2, *ps_end;+    double sum;+    long int *short_sticks, *long_sticks;+    long int num_short_sticks, num_long_sticks;+    size_t i;++    sampler->num_bins = n;++    ps_end = ps + n;++    /* Initialize indexes and probs */+    sampler->indexes = (long int*)calloc(n, sizeof(long int));+    if (sampler->indexes == 0) {+        return PLFIT_ENOMEM;+    }+    sampler->probs   = (double*)calloc(n, sizeof(double));+    if (sampler->probs == 0) {+        free(sampler->indexes);+        return PLFIT_ENOMEM;+    }++    /* Normalize the probability vector; count how many short and long sticks+     * are there initially */+    for (sum = 0.0, p = ps; p != ps_end; p++) {+        sum += *p;+    }+    sum = n / sum;++    num_short_sticks = num_long_sticks = 0;+    for (p = ps, p2 = sampler->probs; p != ps_end; p++, p2++) {+        *p2 = *p * sum;+        if (*p2 < 1) {+            num_short_sticks++;+        } else if (*p2 > 1) {+            num_long_sticks++;+        }+    }++    /* Allocate space for short & long stick indexes */+    long_sticks = (long int*)calloc(num_long_sticks, sizeof(long int));+    if (long_sticks == 0) {+        free(sampler->probs);+        free(sampler->indexes);+        return PLFIT_ENOMEM;+    }+    short_sticks = (long int*)calloc(num_long_sticks, sizeof(long int));+    if (short_sticks == 0) {+        free(sampler->probs);+        free(sampler->indexes);+        free(long_sticks);+        return PLFIT_ENOMEM;+    }++    /* Initialize short_sticks and long_sticks */+    num_short_sticks = num_long_sticks = 0;+    for (i = 0, p = sampler->probs; i < n; i++, p++) {+        if (*p < 1) {+            short_sticks[num_short_sticks++] = i;+        } else if (*p > 1) {+            long_sticks[num_long_sticks++] = i;+        }+    }++    /* Prepare the index table */+    while (num_short_sticks && num_long_sticks) {+        long int short_index, long_index;+        short_index = short_sticks[--num_short_sticks];+        long_index = long_sticks[num_long_sticks-1];+        sampler->indexes[short_index] = long_index;+        sampler->probs[long_index] =     /* numerical stability */+            (sampler->probs[long_index] + sampler->probs[short_index]) - 1;+        if (sampler->probs[long_index] < 1) {+            short_sticks[num_short_sticks++] = long_index;+            num_long_sticks--;+        }+    }++    /* Fix numerical stability issues */+    while (num_long_sticks) {+        i = long_sticks[--num_long_sticks];+        sampler->probs[i] = 1;+    }+    while (num_short_sticks) {+        i = short_sticks[--num_short_sticks];+        sampler->probs[i] = 1;+    }++    return PLFIT_SUCCESS;+}+++void plfit_walker_alias_sampler_destroy(plfit_walker_alias_sampler_t* sampler) {+    if (sampler->indexes) {+        free(sampler->indexes);+        sampler->indexes = 0;+    }+    if (sampler->probs) {+        free(sampler->probs);+        sampler->probs = 0;+    }+}+++int plfit_walker_alias_sampler_sample(const plfit_walker_alias_sampler_t* sampler,+        long int *xs, size_t n, mt_rng_t* rng) {+    double u;+    long int j;+    long int *x;++    x = xs;++    if (rng == 0) {+        /* Using built-in RNG */+        while (n > 0) {+            u = RNG_UNIF01();+            j = RNG_INTEGER(0, sampler->num_bins - 1);+            *x = (u < sampler->probs[j]) ? j : sampler->indexes[j];+            n--; x++;+        }+    } else {+        /* Using Mersenne Twister */+        while (n > 0) {+            u = mt_uniform_01(rng);+            j = mt_random(rng) % sampler->num_bins;+            *x = (u < sampler->probs[j]) ? j : sampler->indexes[j];+            n--; x++;+        }+    }++    return PLFIT_SUCCESS;+}
igraph/src/sbm.c view
@@ -89,7 +89,7 @@      igraph_matrix_minmax(pref_matrix, &minp, &maxp);     if (minp < 0 || maxp > 1) {-        IGRAPH_ERROR("Connection probabilities must in [0,1]", IGRAPH_EINVAL);+        IGRAPH_ERROR("Connection probabilities must be in [0,1]", IGRAPH_EINVAL);     }      if (n < 0) {@@ -106,7 +106,7 @@     }      if (igraph_vector_int_min(block_sizes) < 0) {-        IGRAPH_ERROR("Block size must be non-negative", IGRAPH_EINVAL);+        IGRAPH_ERROR("Block sizes must be non-negative", IGRAPH_EINVAL);     }      if (igraph_vector_int_sum(block_sizes) != n) {
igraph/src/scan.c view
@@ -75,7 +75,7 @@ }  /* From triangles.c */-+/* TODO add to private header */ int igraph_i_trans4_al_simplify(igraph_adjlist_t *al,                                 const igraph_vector_int_t *rank); @@ -83,8 +83,8 @@    "backwards" according to the rank vector. It works on    edge lists */ -int igraph_i_trans4_il_simplify(const igraph_t *graph, igraph_inclist_t *il,-                                const igraph_vector_int_t *rank) {+static int igraph_i_trans4_il_simplify(const igraph_t *graph, igraph_inclist_t *il,+                                       const igraph_vector_int_t *rank) {      long int i;     long int n = il->length;@@ -119,10 +119,10 @@  /* This one handles both weighted and unweighted cases */ -int igraph_i_local_scan_1_directed(const igraph_t *graph,-                                   igraph_vector_t *res,-                                   const igraph_vector_t *weights,-                                   igraph_neimode_t mode) {+static int igraph_i_local_scan_1_directed(const igraph_t *graph,+                                          igraph_vector_t *res,+                                          const igraph_vector_t *weights,+                                          igraph_neimode_t mode) {      int no_of_nodes = igraph_vcount(graph);     igraph_inclist_t incs;@@ -180,9 +180,9 @@     return 0; } -int igraph_i_local_scan_1_directed_all(const igraph_t *graph,-                                       igraph_vector_t *res,-                                       const igraph_vector_t *weights) {+static int igraph_i_local_scan_1_directed_all(const igraph_t *graph,+                                              igraph_vector_t *res,+                                              const igraph_vector_t *weights) {      int no_of_nodes = igraph_vcount(graph);     igraph_inclist_t incs;@@ -250,9 +250,9 @@     return 0; } -int igraph_i_local_scan_1_sumweights(const igraph_t *graph,-                                     igraph_vector_t *res,-                                     const igraph_vector_t *weights) {+static int igraph_i_local_scan_1_sumweights(const igraph_t *graph,+                                            igraph_vector_t *res,+                                            const igraph_vector_t *weights) {      long int no_of_nodes = igraph_vcount(graph);     long int node, i, j, nn;@@ -384,10 +384,10 @@     return 0; } -int igraph_i_local_scan_0_them_w(const igraph_t *us, const igraph_t *them,-                                 igraph_vector_t *res,-                                 const igraph_vector_t *weights_them,-                                 igraph_neimode_t mode) {+static int igraph_i_local_scan_0_them_w(const igraph_t *us, const igraph_t *them,+                                        igraph_vector_t *res,+                                        const igraph_vector_t *weights_them,+                                        igraph_neimode_t mode) {      igraph_t is;     igraph_vector_t map2;
igraph/src/scg.c view
@@ -79,6 +79,7 @@ #include "igraph_eigen.h" #include "igraph_interface.h" #include "igraph_structural.h"+#include "igraph_community.h" #include "igraph_constructors.h" #include "igraph_conversion.h" #include "igraph_memory.h"@@ -121,7 +122,7 @@  * role, as for instance is the case of dynamical processes on networks.  * </para>  *- * <section><title>SCG in brief</title>+ * <section id="scg-in-brief"><title>SCG in brief</title>  * <para>  * The main idea of SCG is to operate on a matrix a shrinkage operation  * specifically designed to preserve some of the matrix eigenpairs while@@ -209,7 +210,7 @@  * </para>  * </section>  *- * <section><title>Functions for performing SCG</title>+ * <section id="functions-for-performing-scg"><title>Functions for performing SCG</title>  * <para>  * The main functions are \ref igraph_scg_adjacency(), \ref  * igraph_scg_laplacian() and \ref igraph_scg_stochastic().@@ -240,7 +241,7 @@  * </para>  * </section>  *- * <section><title>References</title>+ * <section id="scg-references"><title>References</title>  * <para>  * [1] D. Morton de Lachapelle, D. Gfeller, and P. De Los Rios,  * Shrinking Matrices while Preserving their Eigenpairs with Application@@ -468,16 +469,18 @@     igraph_matrix_int_destroy(&gr_mat);     IGRAPH_FINALLY_CLEAN(1); +    IGRAPH_CHECK(igraph_reindex_membership(groups, 0, 0));+     return 0; } -int igraph_i_scg_semiprojectors_sym(const igraph_vector_t *groups,-                                    igraph_matrix_t *L,-                                    igraph_matrix_t *R,-                                    igraph_sparsemat_t *Lsparse,-                                    igraph_sparsemat_t *Rsparse,-                                    int no_of_groups,-                                    int no_of_nodes) {+static int igraph_i_scg_semiprojectors_sym(const igraph_vector_t *groups,+                                           igraph_matrix_t *L,+                                           igraph_matrix_t *R,+                                           igraph_sparsemat_t *Lsparse,+                                           igraph_sparsemat_t *Rsparse,+                                           int no_of_groups,+                                           int no_of_nodes) {      igraph_vector_t tab;     int i;@@ -536,14 +539,14 @@     return 0; } -int igraph_i_scg_semiprojectors_lap(const igraph_vector_t *groups,-                                    igraph_matrix_t *L,-                                    igraph_matrix_t *R,-                                    igraph_sparsemat_t *Lsparse,-                                    igraph_sparsemat_t *Rsparse,-                                    int no_of_groups,-                                    int no_of_nodes,-                                    igraph_scg_norm_t norm) {+static int igraph_i_scg_semiprojectors_lap(const igraph_vector_t *groups,+                                           igraph_matrix_t *L,+                                           igraph_matrix_t *R,+                                           igraph_sparsemat_t *Lsparse,+                                           igraph_sparsemat_t *Rsparse,+                                           int no_of_groups,+                                           int no_of_nodes,+                                           igraph_scg_norm_t norm) {      igraph_vector_t tab;     int i;@@ -633,15 +636,15 @@     return 0; } -int igraph_i_scg_semiprojectors_sto(const igraph_vector_t *groups,-                                    igraph_matrix_t *L,-                                    igraph_matrix_t *R,-                                    igraph_sparsemat_t *Lsparse,-                                    igraph_sparsemat_t *Rsparse,-                                    int no_of_groups,-                                    int no_of_nodes,-                                    const igraph_vector_t *p,-                                    igraph_scg_norm_t norm) {+static int igraph_i_scg_semiprojectors_sto(const igraph_vector_t *groups,+                                           igraph_matrix_t *L,+                                           igraph_matrix_t *R,+                                           igraph_sparsemat_t *Lsparse,+                                           igraph_sparsemat_t *Rsparse,+                                           int no_of_groups,+                                           int no_of_nodes,+                                           const igraph_vector_t *p,+                                           igraph_scg_norm_t norm) {      igraph_vector_t pgr, pnormed;     int i;@@ -974,9 +977,9 @@     return 0; } -int igraph_i_matrix_laplacian(const igraph_matrix_t *matrix,-                              igraph_matrix_t *mymatrix,-                              igraph_scg_norm_t norm) {+static int igraph_i_matrix_laplacian(const igraph_matrix_t *matrix,+                                     igraph_matrix_t *mymatrix,+                                     igraph_scg_norm_t norm) {      igraph_vector_t degree;     int i, j, n = (int) igraph_matrix_nrow(matrix);@@ -1006,9 +1009,9 @@     return 0; } -int igraph_i_sparsemat_laplacian(const igraph_sparsemat_t *sparse,-                                 igraph_sparsemat_t *mysparse,-                                 igraph_scg_norm_t norm) {+static int igraph_i_sparsemat_laplacian(const igraph_sparsemat_t *sparse,+                                        igraph_sparsemat_t *mysparse,+                                        igraph_scg_norm_t norm) {      igraph_vector_t degree;     int i, n = (int) igraph_sparsemat_nrow(sparse);@@ -1058,9 +1061,9 @@     return 0; } -int igraph_i_matrix_stochastic(const igraph_matrix_t *matrix,-                               igraph_matrix_t *mymatrix,-                               igraph_scg_norm_t norm) {+static int igraph_i_matrix_stochastic(const igraph_matrix_t *matrix,+                                      igraph_matrix_t *mymatrix,+                                      igraph_scg_norm_t norm) {      int i, j, n = (int) igraph_matrix_nrow(matrix);     IGRAPH_CHECK(igraph_matrix_copy(mymatrix, matrix));@@ -1096,12 +1099,13 @@     return 0; } +/* TODO prototype; function is defined in conversion.c */ int igraph_i_normalize_sparsemat(igraph_sparsemat_t *sparsemat,                                  igraph_bool_t column_wise); -int igraph_i_sparsemat_stochastic(const igraph_sparsemat_t *sparse,-                                  igraph_sparsemat_t *mysparse,-                                  igraph_scg_norm_t norm) {+static int igraph_i_sparsemat_stochastic(const igraph_sparsemat_t *sparse,+                                         igraph_sparsemat_t *mysparse,+                                         igraph_scg_norm_t norm) {      IGRAPH_CHECK(igraph_sparsemat_copy(mysparse, sparse));     IGRAPH_FINALLY(igraph_sparsemat_destroy, mysparse);@@ -1112,15 +1116,15 @@     return 0; } -int igraph_i_scg_get_result(igraph_scg_matrix_t type,-                            const igraph_matrix_t *matrix,-                            const igraph_sparsemat_t *sparsemat,-                            const igraph_sparsemat_t *Lsparse,-                            const igraph_sparsemat_t *Rsparse_t,-                            igraph_t *scg_graph,-                            igraph_matrix_t *scg_matrix,-                            igraph_sparsemat_t *scg_sparsemat,-                            igraph_bool_t directed) {+static int igraph_i_scg_get_result(igraph_scg_matrix_t type,+                                   const igraph_matrix_t *matrix,+                                   const igraph_sparsemat_t *sparsemat,+                                   const igraph_sparsemat_t *Lsparse,+                                   const igraph_sparsemat_t *Rsparse_t,+                                   igraph_t *scg_graph,+                                   igraph_matrix_t *scg_matrix,+                                   igraph_sparsemat_t *scg_sparsemat,+                                   igraph_bool_t directed) {      /* We need to calculate either scg_matrix (if input is dense), or        scg_sparsemat (if input is sparse). For the latter we might need@@ -1269,20 +1273,20 @@     return 0; } -int igraph_i_scg_common_checks(const igraph_t *graph,-                               const igraph_matrix_t *matrix,-                               const igraph_sparsemat_t *sparsemat,-                               const igraph_vector_t *ev,-                               igraph_integer_t nt,-                               const igraph_vector_t *nt_vec,-                               const igraph_matrix_t *vectors,-                               const igraph_matrix_complex_t *vectors_cmplx,-                               const igraph_vector_t *groups,-                               const igraph_t *scg_graph,-                               const igraph_matrix_t *scg_matrix,-                               const igraph_sparsemat_t *scg_sparsemat,-                               const igraph_vector_t *p,-                               igraph_real_t *evmin, igraph_real_t *evmax) {+static int igraph_i_scg_common_checks(const igraph_t *graph,+                                      const igraph_matrix_t *matrix,+                                      const igraph_sparsemat_t *sparsemat,+                                      const igraph_vector_t *ev,+                                      igraph_integer_t nt,+                                      const igraph_vector_t *nt_vec,+                                      const igraph_matrix_t *vectors,+                                      const igraph_matrix_complex_t *vectors_cmplx,+                                      const igraph_vector_t *groups,+                                      const igraph_t *scg_graph,+                                      const igraph_matrix_t *scg_matrix,+                                      const igraph_sparsemat_t *scg_sparsemat,+                                      const igraph_vector_t *p,+                                      igraph_real_t *evmin, igraph_real_t *evmax) {      int no_of_nodes = -1;     igraph_real_t min, max;
igraph/src/scg_approximate_methods.c view
@@ -64,10 +64,9 @@  *    centers as used in intervals_plus_kmeans.  */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_types.h"-#include "scg_headers.h"-#include "igraph_memory.h" #include "igraph_vector.h"  int igraph_i_intervals_plus_kmeans(const igraph_vector_t *v, int *gr,
igraph/src/scg_exact_scg.c view
@@ -29,8 +29,8 @@  *    See also Section 5.4.1 (last paragraph) of the above reference.  */ -#include "igraph_memory.h" #include "scg_headers.h"+#include "igraph_memory.h" #include <math.h>  int igraph_i_exact_coarse_graining(const igraph_real_t *v,
igraph/src/scg_kmeans.c view
@@ -31,8 +31,6 @@  *    See also Section 5.3.3 of the above reference.  */ -#include "igraph_memory.h"- #include "scg_headers.h"  int igraph_i_kmeans_Lloyd(const igraph_vector_t *x, int n, int p,
igraph/src/scg_optimal_method.c view
@@ -35,13 +35,12 @@  *    starting from 0.  */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_memory.h" #include "igraph_matrix.h" #include "igraph_vector.h" -#include "scg_headers.h"- int igraph_i_optimal_partition(const igraph_real_t *v, int *gr, int n,                                int nt, int matrix, const igraph_real_t *p,                                igraph_real_t *value) {@@ -114,7 +113,7 @@      IGRAPH_MATRIX_INIT_FINALLY(&F, nt, n);     IGRAPH_CHECK(igraph_matrix_int_init(&Q, nt, n));-    IGRAPH_FINALLY(igraph_matrix_destroy, &Q);+    IGRAPH_FINALLY(igraph_matrix_int_destroy, &Q);      for (i = 0; i < n; i++) {         MATRIX(Q, 0, i)++;@@ -238,4 +237,3 @@      return 0; }-
igraph/src/scg_utils.c view
@@ -27,10 +27,9 @@  *    functions used throughout the SCGlib.  */ +#include "scg_headers.h" #include "igraph_error.h" #include "igraph_memory.h"--#include "scg_headers.h"  /*to be used with qsort and struct ind_val arrays */ int igraph_i_compare_ind_val(const void *a, const void *b) {
igraph/src/separators.c view
@@ -28,21 +28,18 @@ #include "igraph_vector.h" #include "igraph_interface.h" #include "igraph_flow.h"-#include "igraph_flow_internal.h" #include "igraph_components.h" #include "igraph_structural.h"-#include "igraph_constructors.h"-#include "igraph_stack.h" #include "igraph_interrupt_internal.h" -int igraph_i_is_separator(const igraph_t *graph,-                          igraph_vit_t *vit,-                          long int except,-                          igraph_bool_t *res,-                          igraph_vector_bool_t *removed,-                          igraph_dqueue_t *Q,-                          igraph_vector_t *neis,-                          long int no_of_nodes) {+static int igraph_i_is_separator(const igraph_t *graph,+                                 igraph_vit_t *vit,+                                 long int except,+                                 igraph_bool_t *res,+                                 igraph_vector_bool_t *removed,+                                 igraph_dqueue_t *Q,+                                 igraph_vector_t *neis,+                                 long int no_of_nodes) {      long int start = 0; @@ -266,11 +263,11 @@         }                                                  \     } while (0) -int igraph_i_clusters_leaveout(const igraph_adjlist_t *adjlist,-                               igraph_vector_t *components,-                               igraph_vector_t *leaveout,-                               unsigned long int *mark,-                               igraph_dqueue_t *Q) {+static int igraph_i_clusters_leaveout(const igraph_adjlist_t *adjlist,+                                      igraph_vector_t *components,+                                      igraph_vector_t *leaveout,+                                      unsigned long int *mark,+                                      igraph_dqueue_t *Q) {      /* Another trick: we use the same 'leaveout' vector to mark the      * vertices that were already found in the BFS@@ -314,8 +311,8 @@     return 0; } -igraph_bool_t igraph_i_separators_newsep(const igraph_vector_ptr_t *comps,-        const igraph_vector_t *newc) {+static igraph_bool_t igraph_i_separators_newsep(const igraph_vector_ptr_t *comps,+                                                const igraph_vector_t *newc) {      long int co, nocomps = igraph_vector_ptr_size(comps); @@ -330,12 +327,12 @@     return 1; } -int igraph_i_separators_store(igraph_vector_ptr_t *separators,-                              const igraph_adjlist_t *adjlist,-                              igraph_vector_t *components,-                              igraph_vector_t *leaveout,-                              unsigned long int *mark,-                              igraph_vector_t *sorter) {+static int igraph_i_separators_store(igraph_vector_ptr_t *separators,+                                     const igraph_adjlist_t *adjlist,+                                     igraph_vector_t *components,+                                     igraph_vector_t *leaveout,+                                     unsigned long int *mark,+                                     igraph_vector_t *sorter) {      /* We need to stote N(C), the neighborhood of C, but only if it is      * not already stored among the separators.@@ -387,7 +384,7 @@     return 0; } -void igraph_i_separators_free(igraph_vector_ptr_t *separators) {+static void igraph_i_separators_free(igraph_vector_ptr_t *separators) {     long int i, n = igraph_vector_ptr_size(separators);     for (i = 0; i < n; i++) {         igraph_vector_t *vec = VECTOR(*separators)[i];@@ -557,8 +554,8 @@  #undef UPDATEMARK -int igraph_i_minimum_size_separators_append(igraph_vector_ptr_t *old,-        igraph_vector_ptr_t *new) {+static int igraph_i_minimum_size_separators_append(igraph_vector_ptr_t *old,+                                                   igraph_vector_ptr_t *new) {      long int olen = igraph_vector_ptr_size(old);     long int nlen = igraph_vector_ptr_size(new);@@ -587,9 +584,9 @@     return 0; } -int igraph_i_minimum_size_separators_topkdeg(const igraph_t *graph,-        igraph_vector_t *res,-        long int k) {+static int igraph_i_minimum_size_separators_topkdeg(const igraph_t *graph,+                                                    igraph_vector_t *res,+                                                    long int k) {     long int no_of_nodes = igraph_vcount(graph);     igraph_vector_t deg, order;     long int i;@@ -612,7 +609,7 @@     return 0; } -void igraph_i_separators_stcuts_free(igraph_vector_ptr_t *p) {+static void igraph_i_separators_stcuts_free(igraph_vector_ptr_t *p) {     long int i, n = igraph_vector_ptr_size(p);     for (i = 0; i < n; i++) {         igraph_vector_t *v = VECTOR(*p)[i];
igraph/src/sir.c view
@@ -28,15 +28,16 @@ #include "igraph_psumtree.h" #include "igraph_memory.h" #include "igraph_structural.h"+#include "igraph_interrupt_internal.h"  int igraph_sir_init(igraph_sir_t *sir) {-    igraph_vector_init(&sir->times, 1);+    IGRAPH_CHECK(igraph_vector_init(&sir->times, 1));     IGRAPH_FINALLY(igraph_vector_destroy, &sir->times);-    igraph_vector_int_init(&sir->no_s, 1);+    IGRAPH_CHECK(igraph_vector_int_init(&sir->no_s, 1));     IGRAPH_FINALLY(igraph_vector_int_destroy, &sir->no_s);-    igraph_vector_int_init(&sir->no_i, 1);+    IGRAPH_CHECK(igraph_vector_int_init(&sir->no_i, 1));     IGRAPH_FINALLY(igraph_vector_int_destroy, &sir->no_i);-    igraph_vector_int_init(&sir->no_r, 1);+    IGRAPH_CHECK(igraph_vector_int_init(&sir->no_r, 1));     IGRAPH_FINALLY_CLEAN(3);     return 0; }@@ -55,12 +56,12 @@     igraph_vector_int_destroy(&sir->no_r); } -void igraph_i_sir_destroy(igraph_vector_ptr_t *v) {+static void igraph_i_sir_destroy(igraph_vector_ptr_t *v) {     int i, n = igraph_vector_ptr_size(v);     for (i = 0; i < n; i++) {-        igraph_sir_t *s = VECTOR(*v)[i];-        if (s) {-            igraph_sir_destroy(s);+        if ( VECTOR(*v)[i] ) {+            igraph_sir_destroy( VECTOR(*v)[i]) ;+            igraph_Free( VECTOR(*v)[i] ); /* this also sets the vector_ptr element to NULL */         }     } }@@ -127,16 +128,17 @@         IGRAPH_WARNING("Edge directions are ignored in SIR model");     }     if (beta < 0) {-        IGRAPH_ERROR("Beta must be non-negative in SIR model", IGRAPH_EINVAL);+        IGRAPH_ERROR("The infection rate beta must be non-negative in SIR model", IGRAPH_EINVAL);     }-    if (gamma < 0) {-        IGRAPH_ERROR("Gamma must be non-negative in SIR model", IGRAPH_EINVAL);+    /* With a recovery rate of zero, the simulation would never stop. */+    if (gamma <= 0) {+        IGRAPH_ERROR("The recovery rate gamma must be positive in SIR model", IGRAPH_EINVAL);     }     if (no_sim <= 0) {         IGRAPH_ERROR("Number of SIR simulations must be positive", IGRAPH_EINVAL);     } -    igraph_is_simple(graph, &simple);+    IGRAPH_CHECK(igraph_is_simple(graph, &simple));     if (!simple) {         IGRAPH_ERROR("SIR model only works with simple graphs", IGRAPH_EINVAL);     }@@ -156,7 +158,7 @@         if (!sir) {             IGRAPH_ERROR("Cannot run SIR model", IGRAPH_ENOMEM);         }-        igraph_sir_init(sir);+        IGRAPH_CHECK(igraph_sir_init(sir));         VECTOR(*result)[i] = sir;     } @@ -202,6 +204,8 @@             igraph_real_t r;             long int vchange; +            IGRAPH_ALLOW_INTERRUPTION();+             psum = igraph_psumtree_sum(&tree);             tt = igraph_rng_get_exp(igraph_rng_default(), psum);             r = RNG_UNIF(0, psum);@@ -235,18 +239,10 @@                 }             } -            if (times_v) {-                igraph_vector_push_back(times_v, tt + igraph_vector_tail(times_v));-            }-            if (no_s_v)  {-                igraph_vector_int_push_back(no_s_v, ns);-            }-            if (no_i_v)  {-                igraph_vector_int_push_back(no_i_v, ni);-            }-            if (no_r_v)  {-                igraph_vector_int_push_back(no_r_v, nr);-            }+            IGRAPH_CHECK(igraph_vector_push_back(times_v, tt + igraph_vector_tail(times_v)));+            IGRAPH_CHECK(igraph_vector_int_push_back(no_s_v, ns));+            IGRAPH_CHECK(igraph_vector_int_push_back(no_i_v, ni));+            IGRAPH_CHECK(igraph_vector_int_push_back(no_r_v, nr));          } /* psum > 0 */ 
igraph/src/spanning_trees.c view
@@ -33,10 +33,10 @@ #include "igraph_progress.h" #include "igraph_types_internal.h" -int igraph_i_minimum_spanning_tree_unweighted(const igraph_t *graph,-        igraph_vector_t *result);-int igraph_i_minimum_spanning_tree_prim(const igraph_t *graph,-                                        igraph_vector_t *result, const igraph_vector_t *weights);+static int igraph_i_minimum_spanning_tree_unweighted(const igraph_t *graph,+                                                     igraph_vector_t *result);+static int igraph_i_minimum_spanning_tree_prim(const igraph_t *graph,+                                               igraph_vector_t *result, const igraph_vector_t *weights);  /**  * \ingroup structural@@ -203,8 +203,7 @@ }  -int igraph_i_minimum_spanning_tree_unweighted(const igraph_t* graph,-        igraph_vector_t* res) {+static int igraph_i_minimum_spanning_tree_unweighted(const igraph_t* graph, igraph_vector_t* res) {      long int no_of_nodes = igraph_vcount(graph);     long int no_of_edges = igraph_ecount(graph);@@ -271,8 +270,8 @@     return IGRAPH_SUCCESS; } -int igraph_i_minimum_spanning_tree_prim(const igraph_t* graph,-                                        igraph_vector_t* res, const igraph_vector_t *weights) {+static int igraph_i_minimum_spanning_tree_prim(+        const igraph_t* graph, igraph_vector_t* res, const igraph_vector_t *weights) {      long int no_of_nodes = igraph_vcount(graph);     long int no_of_edges = igraph_ecount(graph);
igraph/src/sparsemat.c view
@@ -320,10 +320,10 @@     return 0; } -int igraph_i_sparsemat_index_rows(const igraph_sparsemat_t *A,-                                  const igraph_vector_int_t *p,-                                  igraph_sparsemat_t *res,-                                  igraph_real_t *constres) {+static int igraph_i_sparsemat_index_rows(const igraph_sparsemat_t *A,+                                         const igraph_vector_int_t *p,+                                         igraph_sparsemat_t *res,+                                         igraph_real_t *constres) {      igraph_sparsemat_t II, II2;     long int nrow = A->cs->m;@@ -358,10 +358,10 @@     return 0; } -int igraph_i_sparsemat_index_cols(const igraph_sparsemat_t *A,-                                  const igraph_vector_int_t *q,-                                  igraph_sparsemat_t *res,-                                  igraph_real_t *constres) {+static int igraph_i_sparsemat_index_cols(const igraph_sparsemat_t *A,+                                         const igraph_vector_int_t *q,+                                         igraph_sparsemat_t *res,+                                         igraph_real_t *constres) {      igraph_sparsemat_t JJ, JJ2;     long int ncol = A->cs->n;@@ -590,6 +590,7 @@     return 0; } +static igraph_bool_t igraph_i_sparsemat_is_symmetric_cc(const igraph_sparsemat_t *A) {     igraph_sparsemat_t t, tt;@@ -619,6 +620,7 @@     return res; } +static igraph_bool_t igraph_i_sparsemat_is_symmetric_triplet(const igraph_sparsemat_t *A) {     igraph_sparsemat_t tmp;@@ -1048,8 +1050,8 @@     return 0; } -int igraph_i_sparsemat_cc(igraph_t *graph, const igraph_sparsemat_t *A,-                          igraph_bool_t directed) {+static int igraph_i_sparsemat_cc(igraph_t *graph, const igraph_sparsemat_t *A,+                                 igraph_bool_t directed) {      igraph_vector_t edges;     long int no_of_nodes = A->cs->m;@@ -1088,8 +1090,8 @@     return 0; } -int igraph_i_sparsemat_triplet(igraph_t *graph, const igraph_sparsemat_t *A,-                               igraph_bool_t directed) {+static int igraph_i_sparsemat_triplet(igraph_t *graph, const igraph_sparsemat_t *A,+                                      igraph_bool_t directed) {      igraph_vector_t edges;     long int no_of_nodes = A->cs->m;@@ -1149,11 +1151,11 @@     } } -int igraph_i_weighted_sparsemat_cc(const igraph_sparsemat_t *A,-                                   igraph_bool_t directed, const char *attr,-                                   igraph_bool_t loops,-                                   igraph_vector_t *edges,-                                   igraph_vector_t *weights) {+static int igraph_i_weighted_sparsemat_cc(const igraph_sparsemat_t *A,+                                          igraph_bool_t directed, const char *attr,+                                          igraph_bool_t loops,+                                          igraph_vector_t *edges,+                                          igraph_vector_t *weights) {      long int no_of_edges = A->cs->p[A->cs->n];     int *p = A->cs->p;@@ -1189,12 +1191,12 @@     return 0; } -int igraph_i_weighted_sparsemat_triplet(const igraph_sparsemat_t *A,-                                        igraph_bool_t directed,-                                        const char *attr,-                                        igraph_bool_t loops,-                                        igraph_vector_t *edges,-                                        igraph_vector_t *weights) {+static int igraph_i_weighted_sparsemat_triplet(const igraph_sparsemat_t *A,+                                               igraph_bool_t directed,+                                               const char *attr,+                                               igraph_bool_t loops,+                                               igraph_vector_t *edges,+                                               igraph_vector_t *weights) {      IGRAPH_UNUSED(A); IGRAPH_UNUSED(directed); IGRAPH_UNUSED(attr);     IGRAPH_UNUSED(loops); IGRAPH_UNUSED(edges); IGRAPH_UNUSED(weights);@@ -1338,8 +1340,8 @@  #undef CHECK -int igraph_i_sparsemat_eye_triplet(igraph_sparsemat_t *A, int n, int nzmax,-                                   igraph_real_t value) {+static int igraph_i_sparsemat_eye_triplet(igraph_sparsemat_t *A, int n, int nzmax,+                                          igraph_real_t value) {     long int i;      IGRAPH_CHECK(igraph_sparsemat_init(A, n, n, nzmax));@@ -1351,8 +1353,8 @@     return 0; } -int igraph_i_sparsemat_eye_cc(igraph_sparsemat_t *A, int n,-                              igraph_real_t value) {+static int igraph_i_sparsemat_eye_cc(igraph_sparsemat_t *A, int n,+                                     igraph_real_t value) {     long int i;      if (! (A->cs = cs_spalloc(n, n, n, /*values=*/ 1, /*triplet=*/ 0)) ) {@@ -1397,8 +1399,8 @@     } } -int igraph_i_sparsemat_diag_triplet(igraph_sparsemat_t *A, int nzmax,-                                    const igraph_vector_t *values) {+static int igraph_i_sparsemat_diag_triplet(igraph_sparsemat_t *A, int nzmax,+                                           const igraph_vector_t *values) {      int i, n = (int) igraph_vector_size(values); @@ -1412,8 +1414,8 @@  } -int igraph_i_sparsemat_diag_cc(igraph_sparsemat_t *A,-                               const igraph_vector_t *values) {+static int igraph_i_sparsemat_diag_cc(igraph_sparsemat_t *A,+                                      const igraph_vector_t *values) {      int i, n = (int) igraph_vector_size(values); @@ -1461,10 +1463,10 @@     } } -int igraph_i_sparsemat_arpack_multiply(igraph_real_t *to,-                                       const igraph_real_t *from,-                                       int n,-                                       void *extra) {+static int igraph_i_sparsemat_arpack_multiply(igraph_real_t *to,+                                              const igraph_real_t *from,+                                              int n,+                                              void *extra) {     igraph_sparsemat_t *A = extra;     igraph_vector_t vto, vfrom;     igraph_vector_view(&vto, to, n);@@ -1481,10 +1483,10 @@     igraph_sparsemat_solve_t method; } igraph_i_sparsemat_arpack_rssolve_data_t; -int igraph_i_sparsemat_arpack_solve(igraph_real_t *to,-                                    const igraph_real_t *from,-                                    int n,-                                    void *extra) {+static int igraph_i_sparsemat_arpack_solve(igraph_real_t *to,+                                           const igraph_real_t *from,+                                           int n,+                                           void *extra) {      igraph_i_sparsemat_arpack_rssolve_data_t *data = extra;     igraph_vector_t vfrom, vto;@@ -1958,8 +1960,8 @@     return 0; } -int igraph_i_sparsemat_as_matrix_cc(igraph_matrix_t *res,-                                    const igraph_sparsemat_t *spmat) {+static int igraph_i_sparsemat_as_matrix_cc(igraph_matrix_t *res,+                                           const igraph_sparsemat_t *spmat) {      int nrow = (int) igraph_sparsemat_nrow(spmat);     int ncol = (int) igraph_sparsemat_ncol(spmat);@@ -1986,8 +1988,8 @@     return 0; } -int igraph_i_sparsemat_as_matrix_triplet(igraph_matrix_t *res,-        const igraph_sparsemat_t *spmat) {+static int igraph_i_sparsemat_as_matrix_triplet(igraph_matrix_t *res,+                                                const igraph_sparsemat_t *spmat) {     int nrow = (int) igraph_sparsemat_nrow(spmat);     int ncol = (int) igraph_sparsemat_ncol(spmat);     int *i = spmat->cs->p;@@ -2201,8 +2203,8 @@     return res; } -int igraph_i_sparsemat_rowsums_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_rowsums_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pi = A->cs->i;     double *px = A->cs->x;@@ -2217,8 +2219,8 @@     return 0; } -int igraph_i_sparsemat_rowsums_cc(const igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_rowsums_cc(const igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int ne = A->cs->p[A->cs->n];     double *px = A->cs->x;     int *pi = A->cs->i;@@ -2254,8 +2256,8 @@     } } -int igraph_i_sparsemat_rowmins_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_rowmins_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pi = A->cs->i;     double *px = A->cs->x;@@ -2273,8 +2275,8 @@     return 0; } -int igraph_i_sparsemat_rowmins_cc(igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_rowmins_cc(igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int ne;     double *px;     int *pi;@@ -2308,8 +2310,8 @@ }  -int igraph_i_sparsemat_rowmaxs_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_rowmaxs_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pi = A->cs->i;     double *px = A->cs->x;@@ -2327,8 +2329,8 @@     return 0; } -int igraph_i_sparsemat_rowmaxs_cc(igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_rowmaxs_cc(igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int ne;     double *px;     int *pi;@@ -2361,8 +2363,8 @@     } } -int igraph_i_sparsemat_colmins_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_colmins_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pp = A->cs->p;     double *px = A->cs->x;@@ -2380,8 +2382,8 @@     return 0; } -int igraph_i_sparsemat_colmins_cc(igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_colmins_cc(igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int n;     double *px;     int *pp;@@ -2419,8 +2421,8 @@     } } -int igraph_i_sparsemat_colmaxs_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_colmaxs_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pp = A->cs->p;     double *px = A->cs->x;@@ -2438,8 +2440,8 @@     return 0; } -int igraph_i_sparsemat_colmaxs_cc(igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_colmaxs_cc(igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int n;     double *px;     int *pp;@@ -2477,9 +2479,9 @@     } } -int igraph_i_sparsemat_which_min_rows_triplet(igraph_sparsemat_t *A,-        igraph_vector_t *res,-        igraph_vector_int_t *pos) {+static int igraph_i_sparsemat_which_min_rows_triplet(igraph_sparsemat_t *A,+                                                     igraph_vector_t *res,+                                                     igraph_vector_int_t *pos) {     int i;     int *pi = A->cs->i;     int *pp = A->cs->p;@@ -2501,9 +2503,9 @@     return 0; } -int igraph_i_sparsemat_which_min_rows_cc(igraph_sparsemat_t *A,-        igraph_vector_t *res,-        igraph_vector_int_t *pos) {+static int igraph_i_sparsemat_which_min_rows_cc(igraph_sparsemat_t *A,+                                                igraph_vector_t *res,+                                                igraph_vector_int_t *pos) {     int n;     double *px;     int *pp;@@ -2545,9 +2547,9 @@     } } -int igraph_i_sparsemat_which_min_cols_triplet(igraph_sparsemat_t *A,-        igraph_vector_t *res,-        igraph_vector_int_t *pos) {+static int igraph_i_sparsemat_which_min_cols_triplet(igraph_sparsemat_t *A,+                                                     igraph_vector_t *res,+                                                     igraph_vector_int_t *pos) {      int i;     int *pi = A->cs->i;@@ -2570,9 +2572,9 @@     return 0; } -int igraph_i_sparsemat_which_min_cols_cc(igraph_sparsemat_t *A,-        igraph_vector_t *res,-        igraph_vector_int_t *pos) {+static int igraph_i_sparsemat_which_min_cols_cc(igraph_sparsemat_t *A,+                                                igraph_vector_t *res,+                                                igraph_vector_int_t *pos) {     int n, j, p;     double *px;     double *pr;@@ -2612,8 +2614,8 @@     } } -int igraph_i_sparsemat_colsums_triplet(const igraph_sparsemat_t *A,-                                       igraph_vector_t *res) {+static int igraph_i_sparsemat_colsums_triplet(const igraph_sparsemat_t *A,+                                              igraph_vector_t *res) {     int i;     int *pp = A->cs->p;     double *px = A->cs->x;@@ -2628,8 +2630,8 @@     return 0; } -int igraph_i_sparsemat_colsums_cc(const igraph_sparsemat_t *A,-                                  igraph_vector_t *res) {+static int igraph_i_sparsemat_colsums_cc(const igraph_sparsemat_t *A,+                                         igraph_vector_t *res) {     int n = A->cs->n;     double *px = A->cs->x;     int *pp = A->cs->p;@@ -2828,8 +2830,8 @@     return 0; } -int igraph_i_sparsemat_scale_cols_cc(igraph_sparsemat_t *A,-                                     const igraph_vector_t *fact) {+static int igraph_i_sparsemat_scale_cols_cc(igraph_sparsemat_t *A,+                                            const igraph_vector_t *fact) {     int *i = A->cs->i;     igraph_real_t *x = A->cs->x;     int no_of_edges = A->cs->p[A->cs->n];@@ -2848,8 +2850,8 @@     return 0; } -int igraph_i_sparsemat_scale_cols_triplet(igraph_sparsemat_t *A,-        const igraph_vector_t *fact) {+static int igraph_i_sparsemat_scale_cols_triplet(igraph_sparsemat_t *A,+                                                 const igraph_vector_t *fact) {     int *j = A->cs->p;     igraph_real_t *x = A->cs->x;     int no_of_edges = A->cs->nz;
igraph/src/spectral_properties.c view
@@ -27,10 +27,10 @@ #include "config.h" #include <math.h> -int igraph_i_weighted_laplacian(const igraph_t *graph, igraph_matrix_t *res,-                                igraph_sparsemat_t *sparseres,-                                igraph_bool_t normalized,-                                const igraph_vector_t *weights) {+static int igraph_i_weighted_laplacian(const igraph_t *graph, igraph_matrix_t *res,+                                       igraph_sparsemat_t *sparseres,+                                       igraph_bool_t normalized,+                                       const igraph_vector_t *weights) {      igraph_eit_t edgeit;     int no_of_nodes = (int) igraph_vcount(graph);
igraph/src/spmatrix.c view
@@ -24,14 +24,11 @@  #include "igraph_types.h" #include "igraph_spmatrix.h"-#include "igraph_memory.h"-#include "igraph_random.h" #include "igraph_error.h" #include "config.h"  #include <assert.h> #include <string.h>     /* memcpy & co. */-#include <stdlib.h>  /**  * \section igraph_spmatrix_constructor_and_destructor Sparse matrix constructors
igraph/src/st-cuts.c view
@@ -28,18 +28,16 @@ #include "igraph_constants.h" #include "igraph_interface.h" #include "igraph_adjlist.h"-#include "igraph_conversion.h" #include "igraph_constructors.h" #include "igraph_structural.h" #include "igraph_components.h"-#include "igraph_types_internal.h"-#include "config.h" #include "igraph_math.h" #include "igraph_dqueue.h" #include "igraph_visitor.h" #include "igraph_marked_queue.h" #include "igraph_stack.h" #include "igraph_estack.h"+#include "config.h"  /*  * \function igraph_even_tarjan_reduction@@ -244,7 +242,7 @@     igraph_vector_long_t next; } igraph_i_dbucket_t; -int igraph_i_dbucket_init(igraph_i_dbucket_t *buck, long int size) {+static int igraph_i_dbucket_init(igraph_i_dbucket_t *buck, long int size) {     IGRAPH_CHECK(igraph_vector_long_init(&buck->head, size));     IGRAPH_FINALLY(igraph_vector_long_destroy, &buck->head);     IGRAPH_CHECK(igraph_vector_long_init(&buck->next, size));@@ -252,42 +250,42 @@     return 0; } -void igraph_i_dbucket_destroy(igraph_i_dbucket_t *buck) {+static void igraph_i_dbucket_destroy(igraph_i_dbucket_t *buck) {     igraph_vector_long_destroy(&buck->head);     igraph_vector_long_destroy(&buck->next); } -int igraph_i_dbucket_insert(igraph_i_dbucket_t *buck, long int bid,-                            long int elem) {+static int igraph_i_dbucket_insert(igraph_i_dbucket_t *buck, long int bid,+                                   long int elem) {     /* Note: we can do this, since elem is not in any buckets */     VECTOR(buck->next)[elem] = VECTOR(buck->head)[bid];     VECTOR(buck->head)[bid] = elem + 1;     return 0; } -long int igraph_i_dbucket_empty(const igraph_i_dbucket_t *buck,-                                long int bid) {+static long int igraph_i_dbucket_empty(const igraph_i_dbucket_t *buck,+                                       long int bid) {     return VECTOR(buck->head)[bid] == 0; } -long int igraph_i_dbucket_delete(igraph_i_dbucket_t *buck, long int bid) {+static long int igraph_i_dbucket_delete(igraph_i_dbucket_t *buck, long int bid) {     long int elem = VECTOR(buck->head)[bid] - 1;     VECTOR(buck->head)[bid] = VECTOR(buck->next)[elem];     return elem; } -int igraph_i_dominator_LINK(long int v, long int w,-                            igraph_vector_long_t *ancestor) {+static int igraph_i_dominator_LINK(long int v, long int w,+                                   igraph_vector_long_t *ancestor) {     VECTOR(*ancestor)[w] = v + 1;     return 0; }  /* TODO: don't always reallocate path */ -int igraph_i_dominator_COMPRESS(long int v,-                                igraph_vector_long_t *ancestor,-                                igraph_vector_long_t *label,-                                igraph_vector_long_t *semi) {+static int igraph_i_dominator_COMPRESS(long int v,+                                       igraph_vector_long_t *ancestor,+                                       igraph_vector_long_t *label,+                                       igraph_vector_long_t *semi) {     igraph_stack_long_t path;     long int w = v;     long int top, pretop;@@ -319,10 +317,10 @@     return 0; } -long int igraph_i_dominator_EVAL(long int v,-                                 igraph_vector_long_t *ancestor,-                                 igraph_vector_long_t *label,-                                 igraph_vector_long_t *semi) {+static long int igraph_i_dominator_EVAL(long int v,+                                        igraph_vector_long_t *ancestor,+                                        igraph_vector_long_t *label,+                                        igraph_vector_long_t *semi) {     if (VECTOR(*ancestor)[v] == 0) {         return v;     } else {@@ -362,7 +360,7 @@  * \param dom Pointer to an initialized vector or a null pointer. If  *        not a null pointer, then the immediate dominator of each  *        vertex will be stored here. For vertices that are not- *        reachable from the root, \c IGRAPH_NAN is stored here. For+ *        reachable from the root, NaN is stored here. For  *        the root vertex itself, -1 is added.  * \param domtree Pointer to an uninitialized igraph_t, or NULL. If  *        not a null pointer, then the dominator tree is returned@@ -579,7 +577,8 @@     const igraph_vector_t *map; } igraph_i_all_st_cuts_minimal_dfs_data_t; -igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_incb(const igraph_t *graph,+static igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_incb(+        const igraph_t *graph,         igraph_integer_t vid,         igraph_integer_t dist,         void *extra) {@@ -604,7 +603,8 @@     return 0; } -igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_otcb(const igraph_t *graph,+static igraph_bool_t igraph_i_all_st_cuts_minimal_dfs_otcb(+        const igraph_t *graph,         igraph_integer_t vid,         igraph_integer_t dist,         void *extra) {@@ -623,13 +623,13 @@     return 0; } -int igraph_i_all_st_cuts_minimal(const igraph_t *graph,-                                 const igraph_t *domtree,-                                 long int root,-                                 const igraph_marked_queue_t *X,-                                 const igraph_vector_bool_t *GammaX,-                                 const igraph_vector_t *invmap,-                                 igraph_vector_t *minimal) {+static int igraph_i_all_st_cuts_minimal(const igraph_t *graph,+                                        const igraph_t *domtree,+                                        long int root,+                                        const igraph_marked_queue_t *X,+                                        const igraph_vector_bool_t *GammaX,+                                        const igraph_vector_t *invmap,+                                        igraph_vector_t *minimal) {      long int no_of_nodes = igraph_vcount(graph);     igraph_stack_t stack;@@ -684,6 +684,7 @@     return 0; } +/* not 'static' because used in igraph_all_st_cuts.c test program */ int igraph_i_all_st_cuts_pivot(const igraph_t *graph,                                const igraph_marked_queue_t *S,                                const igraph_estack_t *T,@@ -1118,10 +1119,10 @@    zero-indegree vertices. */ -int igraph_i_all_st_mincuts_minimal(const igraph_t *Sbar,-                                    const igraph_vector_bool_t *active,-                                    const igraph_vector_t *invmap,-                                    igraph_vector_t *minimal) {+static int igraph_i_all_st_mincuts_minimal(const igraph_t *Sbar,+                                           const igraph_vector_bool_t *active,+                                           const igraph_vector_t *invmap,+                                           igraph_vector_t *minimal) {      long int no_of_nodes = igraph_vcount(Sbar);     igraph_vector_t indeg;@@ -1169,7 +1170,7 @@      igraph_vector_destroy(&indeg);     igraph_vector_destroy(&neis);-    IGRAPH_FINALLY_CLEAN(3);+    IGRAPH_FINALLY_CLEAN(2);      return 0; }@@ -1178,14 +1179,14 @@     const igraph_vector_bool_t *active; } igraph_i_all_st_mincuts_data_t; -int igraph_i_all_st_mincuts_pivot(const igraph_t *graph,-                                  const igraph_marked_queue_t *S,-                                  const igraph_estack_t *T,-                                  long int source,-                                  long int target,-                                  long int *v,-                                  igraph_vector_t *Isv,-                                  void *arg) {+static int igraph_i_all_st_mincuts_pivot(const igraph_t *graph,+                                         const igraph_marked_queue_t *S,+                                         const igraph_estack_t *T,+                                         long int source,+                                         long int target,+                                         long int *v,+                                         igraph_vector_t *Isv,+                                         void *arg) {      igraph_i_all_st_mincuts_data_t *data = arg;     const igraph_vector_bool_t *active = data->active;@@ -1283,10 +1284,14 @@  * \function igraph_all_st_mincuts  * All minimum s-t cuts of a directed graph  *- * This function lists all minimum edge cuts between two vertices, in a- * directed graph. The implemented algorithm- * is described in JS Provan and DR Shier: A Paradigm for listing- * (s,t)-cuts in graphs, Algorithmica 15, 351--372, 1996.+ * This function lists all edge cuts between two vertices, in a directed graph,+ * with minimum total capacity. Possibly, multiple cuts may have the same total+ * capacity, although there is often only one minimum cut in weighted graphs.+ * It is recommended to supply integer-values capacities. Otherwise, not all+ * minimum cuts may be detected because of numerical roundoff errors.+ * The implemented algorithm is described in JS Provan and DR+ * Shier: A Paradigm for listing (s,t)-cuts in graphs, Algorithmica 15,+ * 351--372, 1996.  *  * \param graph The input graph, it must be directed.  * \param value Pointer to a real number, the value of the minimum cut@@ -1306,8 +1311,9 @@  *        ignored if it is a null pointer.  * \param source The id of the source vertex.  * \param target The id of the target vertex.- * \param capacity Vector of edge capacities. If this is a null- *        pointer, then all edges are assumed to have capacity one.+ * \param capacity Vector of edge capacities. All capacities must be+ *        strictly positive. If this is a null pointer, then all edges+ *        are assumed to have capacity one.  * \return Error code.  *  * Time complexity: O(n(|V|+|E|))+O(F), where |V| is the number of@@ -1358,6 +1364,10 @@     }     if (source == target) {         IGRAPH_ERROR("`source' and 'target' are the same vertex", IGRAPH_EINVAL);+    }+    if (capacity != NULL && igraph_vector_min(capacity) <= 0)+    {+        IGRAPH_ERROR("Not all capacities are strictly positive.", IGRAPH_EINVAL);     }      if (!partition1s) {
igraph/src/statusbar.c view
@@ -21,10 +21,10 @@  */ -#include "config.h" #include "igraph_types.h" #include "igraph_statusbar.h" #include "igraph_error.h"+#include "config.h" #include <stdio.h> #include <stdarg.h> 
igraph/src/structural_properties.c view
@@ -1554,7 +1554,7 @@ }  /* Not declared static so that the testsuite can use it, but not part of the public API. */-int igraph_rewire_core(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode, igraph_bool_t use_adjlist) {+int igraph_i_rewire(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode, igraph_bool_t use_adjlist) {     long int no_of_nodes = igraph_vcount(graph);     long int no_of_edges = igraph_ecount(graph);     char message[256];@@ -1785,7 +1785,7 @@ int igraph_rewire(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode) {      igraph_bool_t use_adjlist = n >= REWIRE_ADJLIST_THRESHOLD;-    return igraph_rewire_core(graph, n, mode, use_adjlist);+    return igraph_i_rewire(graph, n, mode, use_adjlist);  } @@ -1915,11 +1915,13 @@     for (i = 0; i < no_of_new_nodes; i++) {         long int old_vid = (long int) VECTOR(*my_vids_new2old)[i];         long int new_vid = i;+        igraph_bool_t skip_loop_edge;          IGRAPH_CHECK(igraph_incident(graph, &nei_edges, old_vid, IGRAPH_OUT));         n = igraph_vector_size(&nei_edges);          if (directed) {+            /* directed graph; this is easier */             for (j = 0; j < n; j++) {                 eid = (igraph_integer_t) VECTOR(nei_edges)[j]; @@ -1933,10 +1935,15 @@                 IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid));             }         } else {+            /* undirected graph. We need to be careful with loop edges as each+             * loop edge will appear twice. We use a boolean flag to skip every+             * second loop edge */+            skip_loop_edge = 0;             for (j = 0; j < n; j++) {                 eid = (igraph_integer_t) VECTOR(nei_edges)[j]; -                if (IGRAPH_FROM(graph, eid) != old_vid) { /* avoid processing edges twice */+                if (IGRAPH_FROM(graph, eid) != old_vid) {+                    /* avoid processing edges twice */                     continue;                 } @@ -1944,9 +1951,18 @@                 if (!to) {                     continue;                 }+                to -= 1; +                if (new_vid == to) {+                    /* this is a loop edge; check whether we need to skip it */+                    skip_loop_edge = !skip_loop_edge;+                    if (skip_loop_edge) {+                        continue;+                    }+                }+                 IGRAPH_CHECK(igraph_vector_push_back(&new_edges, new_vid));-                IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to - 1));+                IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to));                 IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid));             }         }@@ -2540,7 +2556,7 @@  * C[i] = sum( sum( (p[i,q] p[q,j])^2, q in V[i], q != i,j ), j in  * V[], j != i)  * </para></blockquote>- * for a graph of order (ie. number of vertices) N, where proportional+ * for a graph of order (i.e. number of vertices) N, where proportional  * tie strengths are defined as  * <blockquote><para>  * p[i,j]=(a[i,j]+a[j,i]) / sum(a[i,k]+a[k,i], k in V[i], k != i),@@ -2948,7 +2964,7 @@  * \brief Calculates the size of the neighborhood of a given vertex.  *  * The neighborhood of a given order of a vertex includes all vertices- * which are closer to the vertex than the order. Ie. order 0 is+ * which are closer to the vertex than the order. I.e., order 0 is  * always the vertex itself, order 1 is the vertex plus its immediate  * neighbors, order 2 is order 1 plus the immediate neighbors of the  * vertices in order 1, etc.@@ -3074,7 +3090,7 @@  * Calculate the neighborhood of vertices.  *  * The neighborhood of a given order of a vertex includes all vertices- * which are closer to the vertex than the order. Ie. order 0 is+ * which are closer to the vertex than the order. I.e., order 0 is  * always the vertex itself, order 1 is the vertex plus its immediate  * neighbors, order 2 is order 1 plus the immediate neighbors of the  * vertices in order 1, etc.@@ -3085,15 +3101,15 @@  * \param res An initialized pointer vector. Note that the objects  *    (pointers) in the vector will \em not be freed, but the pointer  *    vector will be resized as needed. The result of the calculation- *    will be stored here in \c vector_t objects.+ *    will be stored here in \ref igraph_vector_t objects.  * \param vids The vertices for which the calculation is performed.  * \param order Integer giving the order of the neighborhood.  * \param mode Specifies how to use the direction of the edges if a  *   directed graph is analyzed. For \c IGRAPH_OUT only the outgoing  *   edges are followed, so all vertices reachable from the source- *   vertex in at most \c order steps are included. For \c IGRAPH_IN+ *   vertex in at most \p order steps are included. For \c IGRAPH_IN  *   all vertices from which the source vertex is reachable in at most- *   \c order steps are included. \c IGRAPH_ALL ignores the direction+ *   \p order steps are included. \c IGRAPH_ALL ignores the direction  *   of the edges. This argument is ignored for undirected graphs.  * \param mindist The minimum distance to include a vertex in the counting.  *   If this is one, then the starting vertex is not counted. If this is@@ -3228,7 +3244,7 @@  * Vincent Matossian, thanks Vincent.  * \param graph The input graph.  * \param res Pointer to a pointer vector, the result will be stored- *   here, ie. \c res will contain pointers to \c igraph_t+ *   here, ie. \p res will contain pointers to \c igraph_t  *   objects. It will be resized if needed but note that the  *   objects in the pointer vector will not be freed.  * \param vids The vertices for which the calculation is performed.@@ -3236,9 +3252,9 @@  * \param mode Specifies how to use the direction of the edges if a  *   directed graph is analyzed. For \c IGRAPH_OUT only the outgoing  *   edges are followed, so all vertices reachable from the source- *   vertex in at most \c order steps are counted. For \c IGRAPH_IN+ *   vertex in at most \p order steps are counted. For \c IGRAPH_IN  *   all vertices from which the source vertex is reachable in at most- *   \c order steps are counted. \c IGRAPH_ALL ignores the direction+ *   \p order steps are counted. \c IGRAPH_ALL ignores the direction  *   of the edges. This argument is ignored for undirected graphs.  * \param mindist The minimum distance to include a vertex in the counting.  *   If this is one, then the starting vertex is not counted. If this is@@ -3568,7 +3584,7 @@         igraph_bool_t found = 0;         IGRAPH_VECTOR_INIT_FINALLY(&neis, 0);         for (i = 0; i < vc; i++) {-            igraph_neighbors(graph, &neis, (igraph_integer_t) i, IGRAPH_OUT);+            IGRAPH_CHECK(igraph_neighbors(graph, &neis, (igraph_integer_t) i, IGRAPH_OUT));             n = igraph_vector_size(&neis);             for (j = 0; j < n; j++) {                 if (VECTOR(neis)[j] == i) {@@ -3781,6 +3797,7 @@     return 0; } + /**  * \function igraph_count_multiple  * \brief Count the number of appearances of the edges in a graph.@@ -3801,15 +3818,15 @@  *  * \sa \ref igraph_is_multiple() and \ref igraph_simplify().  *- * Time complexity: O(e*d), e is the number of edges to check and d is the+ * Time complexity: O(E d), E is the number of edges to check and d is the  * average degree (out-degree in directed graphs) of the vertices at the  * tail of the edges.  */ - int igraph_count_multiple(const igraph_t *graph, igraph_vector_t *res, igraph_es_t es) {     igraph_eit_t eit;     long int i;+    igraph_bool_t directed = igraph_is_directed(graph);     igraph_lazy_inclist_t inclist;      IGRAPH_CHECK(igraph_eit_create(graph, es, &eit));@@ -3835,7 +3852,7 @@             }         }         /* for loop edges, divide the result by two */-        if (to == from) {+        if (!directed && to == from) {             VECTOR(*res)[i] /= 2;         }     }@@ -3843,9 +3860,11 @@     igraph_lazy_inclist_destroy(&inclist);     igraph_eit_destroy(&eit);     IGRAPH_FINALLY_CLEAN(2);-    return 0;++    return IGRAPH_SUCCESS; } + /**  * \function igraph_girth  * \brief The girth of a graph is the length of the shortest circle in it.@@ -5968,6 +5987,10 @@         }     } +    igraph_vector_destroy(&edge_neis);+    igraph_vector_destroy(&neis);+    IGRAPH_FINALLY_CLEAN(2);+     if (knnk) {         for (i = 0; i < maxdeg; i++) {             igraph_real_t dh = VECTOR(deghist)[i];@@ -5982,7 +6005,7 @@         IGRAPH_FINALLY_CLEAN(1);     } -    igraph_vector_destroy(&neis);+    igraph_vector_destroy(&strength);     igraph_vector_destroy(&deg);     IGRAPH_FINALLY_CLEAN(2); @@ -5999,39 +6022,54 @@  /**  * \function igraph_avg_nearest_neighbor_degree- * Average nearest neighbor degree.+ * Average neighbor degree.  *- * Calculates the average degree of the neighbors for each vertex, and- * optionally, the same quantity in the function of vertex degree.+ * Calculates the average degree of the neighbors for each vertex (\p knn), and+ * optionally, the same quantity as a function of the vertex degree (\p knnk).  *- * </para><para>For isolate vertices \p knn is set to \c- * IGRAPH_NAN. The same is done in \p knnk for vertex degrees that+ * </para><para>+ * For isolated vertices \p knn is set to NaN.+ * The same is done in \p knnk for vertex degrees that  * don't appear in the graph.  *- * \param graph The input graph, it can be directed but the- *   directedness of the edges is ignored.+ * </para><para>+ * The weighted version computes a weighted average of the neighbor degrees as+ *+ * <code>k_nn_u = 1/s_u sum_v w_uv k_v</code>,+ *+ * where <code>s_u = sum_v w_uv</code> is the sum of the incident edge weights+ * of vertex \c u, i.e. its strength.+ * The sum runs over the neighbors \c v of vertex \c u+ * as indicated by \p mode. <code>w_uv</code> denotes the weighted adjacency matrix+ * and <code>k_v</code> is the neighbors' degree, specified by \p neighbor_degree_mode.+ *+ * </para><para>+ * Reference:+ * A. Barrat, M. Barthélemy, R. Pastor-Satorras, and A. Vespignani,+ * The architecture of complex weighted networks,+ * Proc. Natl. Acad. Sci. USA 101, 3747 (2004).+ * https://dx.doi.org/10.1073/pnas.0400087101+ *+ * \param graph The input graph. It may be directed.  * \param vids The vertices for which the calculation is performed.- * \param mode The neighbors over which is averaged.- * \param neighbor_degree_mode The degree of the neighbors which is- *   averaged.+ * \param mode The type of neighbors to consider in directed graphs.+ *   \c IGRAPH_OUT considers out-neighbors, \c IGRAPH_IN in-neighbors+ *   and \c IGRAPH_ALL ignores edge directions.+ * \param neighbor_degree_mode The type of degree to average in directed graphs.+ *   \c IGRAPH_OUT averages out-degrees, \c IGRAPH_IN averages in-degrees+ *   and \c IGRAPH_ALL ignores edge directions for the degree calculation.  * \param vids The vertices for which the calculation is performed.  * \param knn Pointer to an initialized vector, the result will be- *   stored here. It will be resized as needed. Supply a NULL pointer+ *   stored here. It will be resized as needed. Supply a \c NULL pointer  *   here, if you only want to calculate \c knnk.- * \param knnk Pointer to an initialized vector, the average nearest- *   neighbor degree in the function of vertex degree is stored+ * \param knnk Pointer to an initialized vector, the average+ *   neighbor degree as a function of the vertex degree is stored  *   here. The first (zeroth) element is for degree one vertices,- *   etc. Supply a NULL pointer here if you don't want to calculate+ *   etc. Supply a \c NULL pointer here if you don't want to calculate  *   this.  * \param weights Optional edge weights. Supply a null pointer here- *   for the non-weighted version. The weighted version computes- *   a weighted average of the neighbor degrees, i.e.- *- *    k_nn_i = 1/s_i sum_j w_ij k_j+ *   for the non-weighted version.  *- *   where s_i is the sum of the weights, the sum runs over- *   the neighbors as indicated by \c mode (with appropriate weights)- *   and k_j is the degree, specified by \c neighbor_degree_mode.  * \return Error code.  *  * Time complexity: O(|V|+|E|), linear in the number of vertices and@@ -6493,8 +6531,7 @@  int igraph_contract_vertices(igraph_t *graph,                              const igraph_vector_t *mapping,-                             const igraph_attribute_combination_t-                             *vertex_comb) {+                             const igraph_attribute_combination_t *vertex_comb) {     igraph_vector_t edges;     long int no_of_nodes = igraph_vcount(graph);     long int no_of_edges = igraph_ecount(graph);@@ -6907,15 +6944,22 @@     } } -int igraph_i_is_graphical_degree_sequence_undirected(-    const igraph_vector_t *degrees, igraph_bool_t *res) {+int igraph_i_is_graphical_degree_sequence_undirected(const igraph_vector_t *degrees, igraph_bool_t *res) {     igraph_vector_t work;     long int w, b, s, c, n, k; +    n = igraph_vector_size(degrees);++    /* zero-length sequences are considered graphical */+    if (n == 0) {+        *res = 1;+        return IGRAPH_SUCCESS;+    }+     IGRAPH_CHECK(igraph_vector_copy(&work, degrees));     IGRAPH_FINALLY(igraph_vector_destroy, &work); -    igraph_vector_sort(&work);+    igraph_vector_reverse_sort(&work);      /* This algorithm is outlined in TR-2011-11 of the Egervary Research Group,      * ISSN 1587-4451. The main loop of the algorithm is O(n) but it is dominated@@ -6926,13 +6970,12 @@      * the degrees themselves. w and k are zero-based here; in the technical      * report they are 1-based */     *res = 1;-    n = igraph_vector_size(&work);     w = n - 1; b = 0; s = 0; c = 0;     for (k = 0; k < n; k++) {-        b += VECTOR(*degrees)[k];+        b += VECTOR(work)[k];         c += w;-        while (w > k && VECTOR(*degrees)[w] <= k + 1) {-            s += VECTOR(*degrees)[w];+        while (w > k && VECTOR(work)[w] <= k + 1) {+            s += VECTOR(work)[w];             c -= (k + 1);             w--;         }@@ -6948,7 +6991,7 @@     igraph_vector_destroy(&work);     IGRAPH_FINALLY_CLEAN(1); -    return 0;+    return IGRAPH_SUCCESS; }  typedef struct {
igraph/src/structure_generators.c view
@@ -100,18 +100,18 @@     return 0; } -int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix,-                                igraph_vector_t *edges);-int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix,-                           igraph_vector_t *edges);-int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix,-                             igraph_vector_t *edges);-int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix,-                             igraph_vector_t *edges);-int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix,-                           igraph_vector_t *edges);+static int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix,+                                       igraph_vector_t *edges);+static int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix,+                                  igraph_vector_t *edges);+static int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix,+                                    igraph_vector_t *edges);+static int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix,+                                    igraph_vector_t *edges);+static int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix,+                                  igraph_vector_t *edges); -int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {+static int igraph_i_adjacency_directed(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j, k;@@ -129,7 +129,7 @@     return 0; } -int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {+static int igraph_i_adjacency_max(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j, k;@@ -151,7 +151,7 @@     return 0; } -int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {+static int igraph_i_adjacency_upper(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j, k;@@ -168,7 +168,7 @@     return 0; } -int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {+static int igraph_i_adjacency_lower(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j, k;@@ -185,7 +185,7 @@     return 0; } -int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {+static int igraph_i_adjacency_min(igraph_matrix_t *adjmatrix, igraph_vector_t *edges) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j, k;@@ -311,32 +311,39 @@     return 0; } -int igraph_i_weighted_adjacency_directed(const igraph_matrix_t *adjmatrix,+static int igraph_i_weighted_adjacency_directed(+        const igraph_matrix_t *adjmatrix,         igraph_vector_t *edges,         igraph_vector_t *weights,         igraph_bool_t loops);-int igraph_i_weighted_adjacency_plus(const igraph_matrix_t *adjmatrix,-                                     igraph_vector_t *edges,-                                     igraph_vector_t *weights,-                                     igraph_bool_t loops);-int igraph_i_weighted_adjacency_max(const igraph_matrix_t *adjmatrix,-                                    igraph_vector_t *edges,-                                    igraph_vector_t *weights,-                                    igraph_bool_t loops);-int igraph_i_weighted_adjacency_upper(const igraph_matrix_t *adjmatrix,-                                      igraph_vector_t *edges,-                                      igraph_vector_t *weights,-                                      igraph_bool_t loops);-int igraph_i_weighted_adjacency_lower(const igraph_matrix_t *adjmatrix,-                                      igraph_vector_t *edges,-                                      igraph_vector_t *weights,-                                      igraph_bool_t loops);-int igraph_i_weighted_adjacency_min(const igraph_matrix_t *adjmatrix,-                                    igraph_vector_t *edges,-                                    igraph_vector_t *weights,-                                    igraph_bool_t loops);+static int igraph_i_weighted_adjacency_plus(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops);+static int igraph_i_weighted_adjacency_max(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops);+static int igraph_i_weighted_adjacency_upper(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops);+static int igraph_i_weighted_adjacency_lower(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops);+static int igraph_i_weighted_adjacency_min(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops); -int igraph_i_weighted_adjacency_directed(const igraph_matrix_t *adjmatrix,+static int igraph_i_weighted_adjacency_directed(+        const igraph_matrix_t *adjmatrix,         igraph_vector_t *edges,         igraph_vector_t *weights,         igraph_bool_t loops) {@@ -362,10 +369,11 @@     return 0; } -int igraph_i_weighted_adjacency_plus(const igraph_matrix_t *adjmatrix,-                                     igraph_vector_t *edges,-                                     igraph_vector_t *weights,-                                     igraph_bool_t loops) {+static int igraph_i_weighted_adjacency_plus(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j;@@ -391,10 +399,11 @@     return 0; } -int igraph_i_weighted_adjacency_max(const igraph_matrix_t *adjmatrix,-                                    igraph_vector_t *edges,-                                    igraph_vector_t *weights,-                                    igraph_bool_t loops) {+static int igraph_i_weighted_adjacency_max(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j;@@ -420,10 +429,11 @@     return 0; } -int igraph_i_weighted_adjacency_upper(const igraph_matrix_t *adjmatrix,-                                      igraph_vector_t *edges,-                                      igraph_vector_t *weights,-                                      igraph_bool_t loops) {+static int igraph_i_weighted_adjacency_upper(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j;@@ -445,10 +455,11 @@     return 0; } -int igraph_i_weighted_adjacency_lower(const igraph_matrix_t *adjmatrix,-                                      igraph_vector_t *edges,-                                      igraph_vector_t *weights,-                                      igraph_bool_t loops) {+static int igraph_i_weighted_adjacency_lower(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j;@@ -470,10 +481,11 @@     return 0; } -int igraph_i_weighted_adjacency_min(const igraph_matrix_t *adjmatrix,-                                    igraph_vector_t *edges,-                                    igraph_vector_t *weights,-                                    igraph_bool_t loops) {+static int igraph_i_weighted_adjacency_min(+        const igraph_matrix_t *adjmatrix,+        igraph_vector_t *edges,+        igraph_vector_t *weights,+        igraph_bool_t loops) {      long int no_of_nodes = igraph_matrix_nrow(adjmatrix);     long int i, j;@@ -750,18 +762,31 @@ /**  * \ingroup generators  * \function igraph_lattice- * \brief Creates most kinds of lattices.+ * \brief Arbitrary dimensional square lattices.  *+ * Creates d-dimensional square lattices of the given size. Optionally,+ * the lattice can be made periodic, and the neighbors within a given+ * graph distance can be connected.+ *+ * </para><para>+ * In the zero-dimensional case, the singleton graph is returned.+ *+ * </para><para>+ * The vertices of the resulting graph are ordered such that the+ * index of the vertex at position <code>(i_0, i_1, i_2, ..., i_d)</code>+ * in a lattice of size <code>(n_0, n_1, ..., n_d)</code> will be+ * <code>i_0 + n_0 * i_1 + n_0 * n_1 * i_2 + ...</code>.+ *  * \param graph An uninitialized graph object.  * \param dimvector Vector giving the sizes of the lattice in each of- *        its dimensions. Ie. the dimension of the lattice will be the+ *        its dimensions. The dimension of the lattice will be the  *        same as the length of this vector.  * \param nei Integer value giving the distance (number of steps)  *        within which two vertices will be connected.- * \param directed Boolean, whether to create a directed graph. The- *        direction of the edges is determined by the generation- *        algorithm and is unlikely to suit you, so this isn't a very- *        useful option.+ * \param directed Boolean, whether to create a directed graph. + *        If the \c mutual and \c circular arguments are not set to true,+ *        edges will be directed from lower-index vertices towards+ *        higher-index ones.  * \param mutual Boolean, if the graph is directed this gives whether  *        to create all connections as mutual.  * \param circular Boolean, defines whether the generated lattice is@@ -770,10 +795,10 @@  *         \c IGRAPH_EINVAL: invalid (negative)  *         dimension vector.  *- * Time complexity: if \p nei is less than two then it is O(|V|+|E|) (as+ * Time complexity: If \p nei is less than two then it is O(|V|+|E|) (as  * far as I remember), |V| and |E| are the number of vertices- * and edges in the generated graph. Otherwise it is O(|V|*d^o+|E|), d- * is the average degree of the graph, o is the \p nei argument.+ * and edges in the generated graph. Otherwise it is O(|V|*d^k+|E|), d+ * is the average degree of the graph, k is the \p nei argument.  */ int igraph_lattice(igraph_t *graph, const igraph_vector_t *dimvector,                    igraph_integer_t nei, igraph_bool_t directed, igraph_bool_t mutual,@@ -794,14 +819,14 @@      coords = igraph_Calloc(dims, long int);     if (coords == 0) {-        IGRAPH_ERROR("lattice failed", IGRAPH_ENOMEM);+        IGRAPH_ERROR("Lattice creation failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, coords); /* TODO: hack */+    IGRAPH_FINALLY(igraph_free, coords);     weights = igraph_Calloc(dims, long int);     if (weights == 0) {-        IGRAPH_ERROR("lattice failed", IGRAPH_ENOMEM);+        IGRAPH_ERROR("Lattice creation failed", IGRAPH_ENOMEM);     }-    IGRAPH_FINALLY(free, weights);+    IGRAPH_FINALLY(igraph_free, weights);     if (dims > 0) {         weights[0] = 1;         for (i = 1; i < dims; i++) {@@ -1991,9 +2016,7 @@     32, 33 }; -int igraph_i_famous(igraph_t *graph, const igraph_real_t *data);--int igraph_i_famous(igraph_t *graph, const igraph_real_t *data) {+static int igraph_i_famous(igraph_t *graph, const igraph_real_t *data) {     long int no_of_nodes = (long int) data[0];     long int no_of_edges = (long int) data[1];     igraph_bool_t directed = (igraph_bool_t) data[2];@@ -2110,11 +2133,11 @@  *           vertices and 12 edges.  *   \cli Petersen  *           A 3-regular graph with 10 vertices and 15 edges. It is- *           the smallest hypohamiltonian graph, ie. it is+ *           the smallest hypohamiltonian graph, i.e. it is  *           non-hamiltonian but removing any single vertex from it makes it  *           Hamiltonian.  *   \cli Robertson- *           The unique (4,5)-cage graph, ie. a 4-regular+ *           The unique (4,5)-cage graph, i.e. a 4-regular  *           graph of girth 5. It has 19 vertices and 38 edges.  *   \cli Smallestcyclicgroup  *           A smallest nontrivial graph@@ -2370,7 +2393,7 @@  *             invalid Pr&uuml;fer sequence given  *          \endclist  *- * \sa \ref igraph_tree(), \ref igraph_tree_game()+ * \sa \ref igraph_to_prufer(), \ref igraph_tree(), \ref igraph_tree_game()  *  */ 
igraph/src/sugiyama.c view
@@ -22,7 +22,7 @@  */ -#include "config.h"+#include "igraph_layout.h" #include "igraph_centrality.h" #include "igraph_components.h" #include "igraph_constants.h"@@ -34,6 +34,7 @@ #include "igraph_memory.h" #include "igraph_structural.h" #include "igraph_types.h"+#include "config.h"  #include <limits.h> @@ -157,8 +158,8 @@ /**  * Initializes a layering.  */-int igraph_i_layering_init(igraph_i_layering_t* layering,-                           const igraph_vector_t* membership) {+static int igraph_i_layering_init(igraph_i_layering_t* layering,+                                  const igraph_vector_t* membership) {     long int i, n, num_layers;      if (igraph_vector_size(membership) == 0) {@@ -193,21 +194,21 @@ /**  * Destroys a layering.  */-void igraph_i_layering_destroy(igraph_i_layering_t* layering) {+static void igraph_i_layering_destroy(igraph_i_layering_t* layering) {     igraph_vector_ptr_destroy_all(&layering->layers); }  /**  * Returns the number of layers in a layering.  */-int igraph_i_layering_num_layers(const igraph_i_layering_t* layering) {+static int igraph_i_layering_num_layers(const igraph_i_layering_t* layering) {     return (int) igraph_vector_ptr_size(&layering->layers); }  /**  * Returns the list of vertices in a given layer  */-igraph_vector_t* igraph_i_layering_get(const igraph_i_layering_t* layering,+static igraph_vector_t* igraph_i_layering_get(const igraph_i_layering_t* layering,                                        long int index) {     return (igraph_vector_t*)VECTOR(layering->layers)[index]; }
igraph/src/topology.c view
@@ -31,6 +31,7 @@ #include "igraph_stack.h" #include "igraph_attributes.h" #include "igraph_structural.h"+#include "igraph_isoclasses.h" #include "config.h"  const unsigned int igraph_i_isoclass_3[] = {  0, 1, 1, 3, 1, 5, 6, 7,@@ -689,6 +690,9 @@  * (between 0 and 15), for undirected graph it is only 4. For graphs  * with four vertices it is 218 (directed) and 11 (undirected).  *+ * </para><para>+ * Multi-edges and self-loops are ignored by this function.+ *  * \param graph The graph object.  * \param isoclass Pointer to an integer, the isomorphism class will  *        be stored here.@@ -754,26 +758,31 @@  * \brief Decides whether two graphs are isomorphic  *  * </para><para>- * From Wikipedia: The graph isomorphism problem or GI problem is the- * graph theory problem of determining whether, given two graphs G1- * and G2, it is possible to permute (or relabel) the vertices of one- * graph so that it is equal to the other. Such a permutation is- * called a graph isomorphism.</para>+ * In simple terms, two graphs are isomorphic if they become indistinguishable+ * from each other once their vertex labels are removed (rendering the vertices+ * within each graph indistiguishable). More precisely, two graphs are isomorphic+ * if there is a one-to-one mapping from the vertices of the first one+ * to the vertices of the second such that it transforms the edge set of the+ * first graph into the edge set of the second. This mapping is called+ * an \em isomorphism.  *- * <para>This function decides which graph isomorphism algorithm to be+ * </para><para>Currently, this function supports simple graphs and graphs+ * with self-loops, but does not support multigraphs.+ *+ * </para><para>This function decides which graph isomorphism algorithm to be  * used based on the input graphs. Right now it does the following:  * \olist  * \oli If one graph is directed and the other undirected then an  *    error is triggered.+ * \oli If one of the graphs has multi-edges then an error is triggered.  * \oli If the two graphs does not have the same number of vertices  *    and edges it returns with \c FALSE.  * \oli Otherwise, if the graphs have three or four vertices then an O(1)  *    algorithm is used with precomputed data.  * \oli Otherwise BLISS is used, see \ref igraph_isomorphic_bliss().  * \endolist- * </para>  *- * <para> Please call the VF2 and BLISS functions directly if you need+ * </para><para>Please call the VF2 and BLISS functions directly if you need  * something more sophisticated, e.g. you need the isomorphic mapping.  *  * \param graph1 The first graph.@@ -793,8 +802,15 @@     long int nodes1 = igraph_vcount(graph1), nodes2 = igraph_vcount(graph2);     long int edges1 = igraph_ecount(graph1), edges2 = igraph_ecount(graph2);     igraph_bool_t dir1 = igraph_is_directed(graph1), dir2 = igraph_is_directed(graph2);-    igraph_bool_t loop1, loop2;+    igraph_bool_t loop1, loop2, multi1, multi2; +    IGRAPH_CHECK(igraph_has_multiple(graph1, &multi1));+    IGRAPH_CHECK(igraph_has_multiple(graph2, &multi2));++    if (multi1 || multi2) {+        IGRAPH_ERROR("Isomorphism testing is not implemented for multigraphs", IGRAPH_UNIMPLEMENTED);+    }+     if (dir1 != dir2) {         IGRAPH_ERROR("Cannot compare directed and undirected graphs", IGRAPH_EINVAL);     } else if (nodes1 != nodes2 || edges1 != edges2) {@@ -821,7 +837,8 @@  * Graph isomorphism for 3-4 vertices  *  * This function uses precomputed indices to decide isomorphism- * problems for graphs with only 3 or 4 vertices.+ * problems for graphs with only 3 or 4 vertices. Multi-edges+ * and self-loops are ignored by this function.  * \param graph1 The first input graph.  * \param graph2 The second input graph. Must have the same  *   directedness as \p graph1.@@ -1640,7 +1657,8 @@     void *arg, *carg; } igraph_i_iso_cb_data_t; -igraph_bool_t igraph_i_isocompat_node_cb(const igraph_t *graph1,+static igraph_bool_t igraph_i_isocompat_node_cb(+        const igraph_t *graph1,         const igraph_t *graph2,         const igraph_integer_t g1_num,         const igraph_integer_t g2_num,@@ -1649,7 +1667,8 @@     return data->node_compat_fn(graph1, graph2, g1_num, g2_num, data->carg); } -igraph_bool_t igraph_i_isocompat_edge_cb(const igraph_t *graph1,+static igraph_bool_t igraph_i_isocompat_edge_cb(+        const igraph_t *graph1,         const igraph_t *graph2,         const igraph_integer_t g1_num,         const igraph_integer_t g2_num,@@ -1658,9 +1677,9 @@     return data->edge_compat_fn(graph1, graph2, g1_num, g2_num, data->carg); } -igraph_bool_t igraph_i_isomorphic_vf2(igraph_vector_t *map12,-                                      igraph_vector_t *map21,-                                      void *arg) {+static igraph_bool_t igraph_i_isomorphic_vf2(igraph_vector_t *map12,+                                             igraph_vector_t *map21,+                                             void *arg) {     igraph_i_iso_cb_data_t *data = arg;     igraph_bool_t *iso = data->arg;     IGRAPH_UNUSED(map12); IGRAPH_UNUSED(map21);@@ -1699,11 +1718,11 @@  * \param map12 Pointer to an initialized vector or a NULL pointer. If not  *    a NULL pointer then the mapping from \p graph1 to \p graph2 is  *    stored here. If the graphs are not isomorphic then the vector is- *    cleared (ie. has zero elements).+ *    cleared (i.e. has zero elements).  * \param map21 Pointer to an initialized vector or a NULL pointer. If not  *    a NULL pointer then the mapping from \p graph2 to \p graph1 is  *    stored here. If the graphs are not isomorphic then the vector is- *    cleared (ie. has zero elements).+ *    cleared (i.e. has zero elements).  * \param node_compat_fn A pointer to a function of type \ref  *   igraph_isocompat_t. This function will be called by the algorithm to  *   determine whether two nodes are compatible.@@ -1756,7 +1775,8 @@     return 0; } -igraph_bool_t igraph_i_count_isomorphisms_vf2(const igraph_vector_t *map12,+static igraph_bool_t igraph_i_count_isomorphisms_vf2(+        const igraph_vector_t *map12,         const igraph_vector_t *map21,         void *arg) {     igraph_i_iso_cb_data_t *data = arg;@@ -1828,7 +1848,7 @@     return 0; } -void igraph_i_get_isomorphisms_free(igraph_vector_ptr_t *data) {+static void igraph_i_get_isomorphisms_free(igraph_vector_ptr_t *data) {     long int i, n = igraph_vector_ptr_size(data);     for (i = 0; i < n; i++) {         igraph_vector_t *vec = VECTOR(*data)[i];@@ -1837,7 +1857,8 @@     } } -igraph_bool_t igraph_i_get_isomorphisms_vf2(const igraph_vector_t *map12,+static igraph_bool_t igraph_i_get_isomorphisms_vf2(+        const igraph_vector_t *map12,         const igraph_vector_t *map21,         void *arg) { @@ -1883,11 +1904,11 @@  * \param edge_color2 The edge color vector for the second graph.  * \param maps Pointer vector. On return it is empty if the input graphs  *   are no isomorphic. Otherwise it contains pointers to- *   <type>igraph_vector_t</type> objects, each vector is an+ *   \ref igraph_vector_t objects, each vector is an  *   isomorphic mapping of \p graph2 to \p graph1. Please note that  *   you need to 1) Destroy the vectors via \ref  *   igraph_vector_destroy(), 2) free them via- *   <function>free()</function> and then 3) call \ref+ *   \ref igraph_free() and then 3) call \ref  *   igraph_vector_ptr_destroy() on the pointer vector to deallocate all  *   memory when \p maps is no longer needed.  * \param node_compat_fn A pointer to a function of type \ref@@ -2473,7 +2494,8 @@     return 0; } -igraph_bool_t igraph_i_subisomorphic_vf2(const igraph_vector_t *map12,+static igraph_bool_t igraph_i_subisomorphic_vf2(+        const igraph_vector_t *map12,         const igraph_vector_t *map21,         void *arg) {     igraph_i_iso_cb_data_t *data = arg;@@ -2560,7 +2582,8 @@     return 0; } -igraph_bool_t igraph_i_count_subisomorphisms_vf2(const igraph_vector_t *map12,+static igraph_bool_t igraph_i_count_subisomorphisms_vf2(+        const igraph_vector_t *map12,         const igraph_vector_t *map21,         void *arg) {     igraph_i_iso_cb_data_t *data = arg;@@ -2635,7 +2658,7 @@     return 0; } -void igraph_i_get_subisomorphisms_free(igraph_vector_ptr_t *data) {+static void igraph_i_get_subisomorphisms_free(igraph_vector_ptr_t *data) {     long int i, n = igraph_vector_ptr_size(data);     for (i = 0; i < n; i++) {         igraph_vector_t *vec = VECTOR(*data)[i];@@ -2644,7 +2667,8 @@     } } -igraph_bool_t igraph_i_get_subisomorphisms_vf2(const igraph_vector_t *map12,+static igraph_bool_t igraph_i_get_subisomorphisms_vf2(+        const igraph_vector_t *map12,         const igraph_vector_t *map21,         void *arg) { @@ -2690,11 +2714,11 @@  *   edge-colored.  * \param edge_color2 The edge color vector for the second graph.  * \param maps Pointer vector. On return it contains pointers to- *   <type>igraph_vector_t</type> objects, each vector is an+ *   \ref igraph_vector_t objects, each vector is an  *   isomorphic mapping of \p graph2 to a subgraph of \p graph1. Please note that  *   you need to 1) Destroy the vectors via \ref  *   igraph_vector_destroy(), 2) free them via- *   <function>free()</function> and then 3) call \ref+ *   \ref igraph_free() and then 3) call \ref  *   igraph_vector_ptr_destroy() on the pointer vector to deallocate all  *   memory when \p maps is no longer needed.  * \param node_compat_fn A pointer to a function of type \ref
igraph/src/triangles.c view
@@ -394,7 +394,7 @@  /* This removes loop, multiple edges and edges that point      "backwards" according to the rank vector. */-+/* TODO used in scan.c, add prototype to private header */ int igraph_i_trans4_al_simplify(igraph_adjlist_t *al,                                 const igraph_vector_int_t *rank) {     long int i;
igraph/src/type_indexededgelist.c view
@@ -25,13 +25,13 @@ #include "igraph_interface.h" #include "igraph_attributes.h" #include "igraph_memory.h"-#include <string.h>     /* memset & co. */ #include "config.h"  /* Internal functions */ -int igraph_i_create_start(igraph_vector_t *res, igraph_vector_t *el, igraph_vector_t *index,-                          igraph_integer_t nodes);+static int igraph_i_create_start(+        igraph_vector_t *res, igraph_vector_t *el,+        igraph_vector_t *index, igraph_integer_t nodes);  /**  * \section about_basic_interface@@ -829,8 +829,9 @@  *  */ -int igraph_i_create_start(igraph_vector_t *res, igraph_vector_t *el, igraph_vector_t *iindex,-                          igraph_integer_t nodes) {+static int igraph_i_create_start(+        igraph_vector_t *res, igraph_vector_t *el,+        igraph_vector_t *iindex, igraph_integer_t nodes) {  # define EDGE(i) (VECTOR(*el)[ (long int) VECTOR(*iindex)[(i)] ]) @@ -1018,7 +1019,9 @@  * will be placed here.  * \return Error code. The current implementation always returns with  * success.- * \sa \ref igraph_get_eid() for the opposite operation.+ * \sa \ref igraph_get_eid() for the opposite operation;+ *     \ref IGRAPH_TO(), \ref IGRAPH_FROM() and \ref IGRAPH_OTHER() for+ *     a faster but non-error-checked version.  *  * Added in version 0.2.</para><para>  *
igraph/src/uninit.c view
@@ -1,3 +1,8 @@++/* Defining _GNU_SOURCE enables the GNU extensions fedisableexcept() and feenableexcept()+ * when using glibc. It must be defined before any standard headers are included. */+#define _GNU_SOURCE 1+#include <fenv.h> #include <stdio.h> #include <string.h> #include <stdlib.h>@@ -253,9 +258,7 @@ #ifdef __GLIBC__ #define IEEE0_done -#if ((__GLIBC__>=2) && (__GLIBC_MINOR__>=2))-#define _GNU_SOURCE 1-#include <fenv.h>+#if ((__GLIBC__ > 2) || ((__GLIBC__ == 2) && (__GLIBC_MINOR__ >= 2)))  static void   ieee0(Void)         
igraph/src/utils.cc view
@@ -23,6 +23,7 @@  namespace bliss { +#if 0 void print_permutation(FILE* const fp, 		  const unsigned int N,@@ -88,6 +89,7 @@     fprintf(fp, ")");   } }+#endif  bool is_permutation(const unsigned int N, const unsigned int* perm)
igraph/src/vector_ptr.c view
@@ -37,12 +37,12 @@  * (<type>igraph_vector_ptr_t</type>)  *  * <para>The \type igraph_vector_ptr_t data type is very similar to- * the \type igraph_vector_t type, but it stores generic pointers instead of+ * the \ref igraph_vector_t type, but it stores generic pointers instead of  * real numbers.</para>  *- * <para>This type has the same space complexity as \type+ * <para>This type has the same space complexity as \ref  * igraph_vector_t, and most implemented operations work the same way- * as for \type igraph_vector_t. </para>+ * as for \ref igraph_vector_t.</para>  *  * <para>This type is mostly used to pass to or receive from a set of  * graphs to some \a igraph functions, such as \ref@@ -160,7 +160,7 @@  *  * If an item destructor is set for this pointer vector, this function will  * first call the destructor on all elements of the vector and then- * free all the elements using free(). If an item destructor is not set,+ * free all the elements using \ref igraph_free(). If an item destructor is not set,  * the elements will simply be freed.  *  * \param v Pointer to the pointer vector whose elements will be freed.@@ -254,7 +254,7 @@  * \brief Gives the number of elements in the pointer vector.  *  * \param v The pointer vector object.- * \return The size of the object, ie. the number of pointers stored.+ * \return The size of the object, i.e. the number of pointers stored.  *  * Time complexity: O(1).  */@@ -273,7 +273,7 @@  * </para><para>  * This function resizes a pointer to vector to zero length. Note that  * the pointed objects are \em not deallocated, you should call- * free() on them, or make sure that their allocated memory is freed+ * \ref igraph_free() on them, or make sure that their allocated memory is freed  * in some other way, you'll get memory leaks otherwise. If you have  * set up an item destructor earlier, the destructor will be called  * on every element.@@ -537,7 +537,7 @@  * Sometimes it is necessary to sort the pointers in the vector based on  * the property of the element being referenced by the pointer. This  * function allows us to sort the vector based on an arbitrary external- * comparison function which accepts two \c void* pointers \c p1 and \c p2+ * comparison function which accepts two <type>void *</type> pointers \c p1 and \c p2  * and returns an integer less than, equal to or greater than zero if the  * first argument is considered to be respectively less than, equal to, or  * greater than the second. \c p1 and \c p2 will point to the pointer in the
igraph/src/walktrap.cpp view
@@ -55,18 +55,12 @@  #include "walktrap_graph.h" #include "walktrap_communities.h"-#include <ctime>-#include <set>-#include <cstdlib>-#include <iostream>-#include <fstream>  #include "igraph_community.h" #include "igraph_components.h" #include "igraph_interface.h" #include "igraph_interrupt_internal.h" -using namespace std; using namespace igraph::walktrap;  /**@@ -75,12 +69,12 @@  * This function is the implementation of the Walktrap community  * finding algorithm, see Pascal Pons, Matthieu Latapy: Computing  * communities in large networks using random walks,- * http://arxiv.org/abs/physics/0512106+ * https://arxiv.org/abs/physics/0512106  *  * </para><para>  * Currently the original C++ implementation is used in igraph,- * see http://www-rp.lip6.fr/~latapy/PP/walktrap.html- * I'm grateful to Matthieu Latapy and Pascal Pons for providing this+ * see https://www-complexnetworks.lip6.fr/~latapy/PP/walktrap.html+ * We are grateful to Matthieu Latapy and Pascal Pons for providing this  * source code.  *  * </para><para>
igraph/src/walktrap_communities.cpp view
@@ -54,12 +54,11 @@ // see readme.txt for more details  #include "walktrap_communities.h"-#include <cstdlib>-#include <iostream>-#include <cmath>+#include "config.h" #include <algorithm>+#include <cmath> -#include "config.h"+using namespace std;  namespace igraph { 
igraph/src/walktrap_graph.cpp view
@@ -53,14 +53,10 @@ //----------------------------------------------------------------------------- // see readme.txt for more details -#include <iostream>-#include <fstream>-#include <sstream>-#include <algorithm>-#include <cstring>      // strlen #include "walktrap_graph.h"- #include "igraph_interface.h"+#include <algorithm>+#include <cstring>      // strlen  using namespace std; 
igraph/src/walktrap_heap.cpp view
@@ -54,11 +54,7 @@ // see readme.txt for more details  #include "walktrap_heap.h"-#include <cstdlib>-#include <iostream> --using namespace std; using namespace igraph::walktrap;  void Neighbor_heap::move_up(int index) {
igraph/src/zeroin.c view
@@ -79,6 +79,7 @@  ************************************************************************  */ +#include "igraph_nongraph.h" #include "igraph_types.h" #include "igraph_interrupt_internal.h" 
− igraph/src/zeta.c 
@@ -1,154 +0,0 @@-/* specfunc/zeta.c- * - * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2004 Gerard Jungman- * - * This program is free software; you can redistribute it and/or modify- * it under the terms of the GNU General Public License as published by- * the Free Software Foundation; either version 3 of the License, or (at- * your option) any later version.- * - * This program is distributed in the hope that it will be useful, but- * WITHOUT ANY WARRANTY; without even the implied warranty of- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU- * General Public License for more details.- * - * You should have received a copy of the GNU General Public License- * along with this program; if not, write to the Free Software- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.- */--/* Author:  G. Jungman */--/* This file was taken from the GNU Scientific Library. Some modifications- * were done in order to make it independent from the rest of GSL- */--/*-#include <config.h>-#include <gsl/gsl_math.h>-#include <gsl/gsl_errno.h>-#include <gsl/gsl_sf_elementary.h>-#include <gsl/gsl_sf_exp.h>-#include <gsl/gsl_sf_gamma.h>-#include <gsl/gsl_sf_pow_int.h>-#include <gsl/gsl_sf_zeta.h>--#include "error.h"--#include "chebyshev.h"-#include "cheb_eval.c"-*/--#include <math.h>-#include <stdio.h>-#include "error.h"--/*-*-*-*-*-*-*-*-*-*- From gsl_machine.h -*-*-*-*-*-*-*-*-*-*-*-*-*/--#define GSL_LOG_DBL_MIN   (-7.0839641853226408e+02)-#define GSL_LOG_DBL_MAX    7.0978271289338397e+02-#define GSL_DBL_EPSILON        2.2204460492503131e-16--/*-*-*-*-*-*-*-*-*-* From gsl_sf_result.h *-*-*-*-*-*-*-*-*-*-*-*/--struct gsl_sf_result_struct {-  double val;-  double err;-};-typedef struct gsl_sf_result_struct gsl_sf_result;--/*-*-*-*-*-*-*-*-*-*-*-* Private Section *-*-*-*-*-*-*-*-*-*-*-*/--/* coefficients for Maclaurin summation in hzeta()- * B_{2j}/(2j)!- */-static double hzeta_c[15] = {-  1.00000000000000000000000000000,-  0.083333333333333333333333333333,- -0.00138888888888888888888888888889,-  0.000033068783068783068783068783069,- -8.2671957671957671957671957672e-07,-  2.0876756987868098979210090321e-08,- -5.2841901386874931848476822022e-10,-  1.3382536530684678832826980975e-11,- -3.3896802963225828668301953912e-13,-  8.5860620562778445641359054504e-15,- -2.1748686985580618730415164239e-16,-  5.5090028283602295152026526089e-18,- -1.3954464685812523340707686264e-19,-  3.5347070396294674716932299778e-21,- -8.9535174270375468504026113181e-23-};--/*-*-*-*-*-*-*-*-*-*-*-* Functions with Error Codes *-*-*-*-*-*-*-*-*-*-*-*/--static int gsl_sf_hzeta_e(const double s, const double q, gsl_sf_result * result)-{-  /* CHECK_POINTER(result) */--  if(s <= 1.0 || q <= 0.0) {-	PLFIT_ERROR("s must be larger than 1.0 and q must be larger than zero", PLFIT_EINVAL);-  }-  else {-    const double max_bits = 54.0;-    const double ln_term0 = -s * log(q);  --    if(ln_term0 < GSL_LOG_DBL_MIN + 1.0) {-	  PLFIT_ERROR("underflow", PLFIT_UNDRFLOW);-    }-    else if(ln_term0 > GSL_LOG_DBL_MAX - 1.0) {-	  PLFIT_ERROR("overflow", PLFIT_OVERFLOW);-    }-    else if((s > max_bits && q < 1.0) || (s > 0.5*max_bits && q < 0.25)) {-      result->val = pow(q, -s);-      result->err = 2.0 * GSL_DBL_EPSILON * fabs(result->val);-      return PLFIT_SUCCESS;-    }-    else if(s > 0.5*max_bits && q < 1.0) {-      const double p1 = pow(q, -s);-      const double p2 = pow(q/(1.0+q), s);-      const double p3 = pow(q/(2.0+q), s);-      result->val = p1 * (1.0 + p2 + p3);-      result->err = GSL_DBL_EPSILON * (0.5*s + 2.0) * fabs(result->val);-      return PLFIT_SUCCESS;-    }-    else {-      /* Euler-Maclaurin summation formula -       * [Moshier, p. 400, with several typo corrections]-       */-      const int jmax = 12;-      const int kmax = 10;-      int j, k;-      const double pmax  = pow(kmax + q, -s);-      double scp = s;-      double pcp = pmax / (kmax + q);-      double ans = pmax*((kmax+q)/(s-1.0) + 0.5);--      for(k=0; k<kmax; k++) {-        ans += pow(k + q, -s);-      }--      for(j=0; j<=jmax; j++) {-        double delta = hzeta_c[j+1] * scp * pcp;-        ans += delta;-        if(fabs(delta/ans) < 0.5*GSL_DBL_EPSILON) break;-        scp *= (s+2*j+1)*(s+2*j+2);-        pcp /= (kmax + q)*(kmax + q);-      }--      result->val = ans;-      result->err = 2.0 * (jmax + 1.0) * GSL_DBL_EPSILON * fabs(ans);-      return PLFIT_SUCCESS;-    }-  }-}--/*-*-*-*-*-*-*-*-*-* Functions w/ Natural Prototypes *-*-*-*-*-*-*-*-*-*-*/--double gsl_sf_hzeta(const double s, const double a)-{-  gsl_sf_result result;-  gsl_sf_hzeta_e(s, a, &result);-  return result.val;-}-
− include/bytestring.h 
@@ -1,111 +0,0 @@-#ifndef HASKELL_IGRAPH_BYTESTRING-#define HASKELL_IGRAPH_BYTESTRING--#include "igraph.h"--typedef struct bytestring_t {-  unsigned long int len;-  char *value;-} bytestring_t;--typedef struct bsvector_t {-  bytestring_t **data;-  long int len;-} bsvector_t;--#define BSVECTOR_INIT_FINALLY(v, size) \-  do { IGRAPH_CHECK(bsvector_init(v, size)); \-  IGRAPH_FINALLY( (igraph_finally_func_t*) bsvector_destroy, v); } while (0)--/**- * \define STR- * Indexing string vectors- *- * This is a macro which allows to query the elements of a string vector in- * simpler way than \ref igraph_strvector_get(). Note this macro cannot be- * used to set an element, for that use \ref igraph_strvector_set().- * \param sv The string vector- * \param i The the index of the element.- * \return The element at position \p i.- *- * Time complexity: O(1).- */-#define BS(sv,i) ((const bytestring_t *)((sv).data[(i)]))--int bsvector_init(bsvector_t *sv, long int len);--void bsvector_destroy(bsvector_t *sv);--void bsvector_get(const bsvector_t *sv, long int idx, bytestring_t **value);--int bsvector_set(bsvector_t *sv, long int idx, const bytestring_t *value);--void bsvector_remove_section(bsvector_t *v, long int from, long int to);--void bsvector_remove(bsvector_t *v, long int elem);--/*-void bsvector_move_interval(bsvector_t *v, long int begin,-				   long int end, long int to) {-  long int i;-  assert(v != 0);-  assert(v->data != 0);-  for (i=to; i<to+end-begin; i++) {-    if (v->data[i] != 0) {-      destroy_bytestring(v->data[i]);-    }-  }-  for (i=0; i<end-begin; i++) {-    if (v->data[begin+i] != 0) {-      size_t len=strlen(v->data[begin+i])+1;-      v->data[to+i]=igraph_Calloc(len, char);-      memcpy(v->data[to+i], v->data[begin+i], sizeof(char)*len);-    }-  }-}-*/--int bsvector_copy(bsvector_t *to, const bsvector_t *from);--int bsvector_append(bsvector_t *to, const bsvector_t *from);--void bsvector_clear(bsvector_t *sv);--int bsvector_resize(bsvector_t* v, long int newsize);--/**- * \ingroup strvector- * \function igraph_strvector_permdelete- * \brief Removes elements from a string vector (for internal use)- */--void bsvector_permdelete(bsvector_t *v, const igraph_vector_t *index,-				long int nremove);--/**- * \ingroup strvector- * \function igraph_strvector_remove_negidx- * \brief Removes elements from a string vector (for internal use)- */--void bsvector_remove_negidx(bsvector_t *v, const igraph_vector_t *neg,-				   long int nremove);--int bsvector_index(const bsvector_t *v, bsvector_t *newv,-                   const igraph_vector_t *idx);--long int bsvector_size(const bsvector_t *sv);--bytestring_t* new_bytestring(int n);--void destroy_bytestring(bytestring_t* str);--char* bytestring_to_char(bytestring_t* from);--bytestring_t* char_to_bytestring(char* from);--igraph_strvector_t* bsvector_to_strvector(bsvector_t* from);--bsvector_t* strvector_to_bsvector(igraph_strvector_t* from);--#endif
− include/haskell_attributes.h 
@@ -1,218 +0,0 @@-#ifndef HASKELL_IGRAPH_ATTRIBUTE-#define HASKELL_IGRAPH_ATTRIBUTE--#include "igraph.h"-#include "bytestring.h"--#include <string.h>--igraph_bool_t igraph_haskell_attribute_find(const igraph_vector_ptr_t *ptrvec,-				       const char *name, long int *idx);--typedef struct igraph_haskell_attributes_t {-  igraph_vector_ptr_t gal;-  igraph_vector_ptr_t val;-  igraph_vector_ptr_t eal;-} igraph_haskell_attributes_t;--int igraph_haskell_attributes_copy_attribute_record(igraph_attribute_record_t **newrec,-					       const igraph_attribute_record_t *rec);---int igraph_haskell_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr);--void igraph_haskell_attribute_destroy(igraph_t *graph);--void igraph_haskell_attribute_copy_free(igraph_haskell_attributes_t *attr);--int igraph_haskell_attribute_copy(igraph_t *to, const igraph_t *from,-			     igraph_bool_t ga, igraph_bool_t va, igraph_bool_t ea);--int igraph_haskell_attribute_add_vertices(igraph_t *graph, long int nv,-				     igraph_vector_ptr_t *nattr);--void igraph_haskell_attribute_permute_free(igraph_vector_ptr_t *v);--int igraph_haskell_attribute_permute_vertices(const igraph_t *graph,-					 igraph_t *newgraph,-					 const igraph_vector_t *idx);--int igraph_haskell_attribute_combine_vertices(const igraph_t *graph,-			 igraph_t *newgraph,-			 const igraph_vector_ptr_t *merges,-			 const igraph_attribute_combination_t *comb);--int igraph_haskell_attribute_add_edges(igraph_t *graph, const igraph_vector_t *edges,-				 igraph_vector_ptr_t *nattr);--int igraph_haskell_attribute_permute_edges(const igraph_t *graph,-				      igraph_t *newgraph,-				      const igraph_vector_t *idx);--int igraph_haskell_attribute_combine_edges(const igraph_t *graph,-			 igraph_t *newgraph,-			 const igraph_vector_ptr_t *merges,-			 const igraph_attribute_combination_t *comb);--int igraph_haskell_attribute_get_info(const igraph_t *graph,-				 igraph_strvector_t *gnames,-				 igraph_vector_t *gtypes,-				 igraph_strvector_t *vnames,-				 igraph_vector_t *vtypes,-				 igraph_strvector_t *enames,-				 igraph_vector_t *etypes);--igraph_bool_t igraph_haskell_attribute_has_attr(const igraph_t *graph,-					 igraph_attribute_elemtype_t type,-					 const char *name);--int igraph_haskell_attribute_gettype(const igraph_t *graph,-			      igraph_attribute_type_t *type,-			      igraph_attribute_elemtype_t elemtype,-			      const char *name);--int igraph_haskell_attribute_get_numeric_graph_attr(const igraph_t *graph,-					      const char *name,-					      igraph_vector_t *value);--int igraph_haskell_attribute_get_bool_graph_attr(const igraph_t *graph,-					    const char *name,-					    igraph_vector_bool_t *value);--int igraph_haskell_attribute_get_string_graph_attr(const igraph_t *graph,-					     const char *name,-					     igraph_strvector_t *value_);--int igraph_haskell_attribute_get_numeric_vertex_attr(const igraph_t *graph,-					      const char *name,-					      igraph_vs_t vs,-					      igraph_vector_t *value);--int igraph_haskell_attribute_get_bool_vertex_attr(const igraph_t *graph,-					     const char *name,-					     igraph_vs_t vs,-					     igraph_vector_bool_t *value);--int igraph_haskell_attribute_get_string_vertex_attr(const igraph_t *graph,-					     const char *name,-					     igraph_vs_t vs,-					     igraph_strvector_t *value_);--int igraph_haskell_attribute_get_numeric_edge_attr(const igraph_t *graph,-					    const char *name,-					    igraph_es_t es,-					    igraph_vector_t *value);--int igraph_haskell_attribute_get_string_edge_attr(const igraph_t *graph,-					   const char *name,-					   igraph_es_t es,-					   igraph_strvector_t *value_);--int igraph_haskell_attribute_get_bool_edge_attr(const igraph_t *graph,-					   const char *name,-					   igraph_es_t es,-					   igraph_vector_bool_t *value);--igraph_real_t igraph_haskell_attribute_GAN(const igraph_t *graph, const char *name);--igraph_bool_t igraph_haskell_attribute_GAB(const igraph_t *graph, const char *name);--const bytestring_t* igraph_haskell_attribute_GAS(const igraph_t *graph, const char *name);--igraph_real_t igraph_haskell_attribute_VAN(const igraph_t *graph, const char *name,-				      igraph_integer_t vid);--igraph_bool_t igraph_haskell_attribute_VAB(const igraph_t *graph, const char *name,-				    igraph_integer_t vid);--const bytestring_t* igraph_haskell_attribute_VAS(const igraph_t *graph, const char *name,-				    igraph_integer_t vid);--igraph_real_t igraph_haskell_attribute_EAN(const igraph_t *graph, const char *name,-				      igraph_integer_t eid);--igraph_bool_t igraph_haskell_attribute_EAB(const igraph_t *graph, const char *name,-				    igraph_integer_t eid);--const bytestring_t* igraph_haskell_attribute_EAS(const igraph_t *graph, const char *name,-				    igraph_integer_t eid);--int igraph_haskell_attribute_VANV(const igraph_t *graph, const char *name,-			   igraph_vs_t vids, igraph_vector_t *result);--int igraph_haskell_attribute_VABV(const igraph_t *graph, const char *name,-			   igraph_vs_t vids, igraph_vector_bool_t *result);--int igraph_haskell_attribute_EANV(const igraph_t *graph, const char *name,-			   igraph_es_t eids, igraph_vector_t *result);--int igraph_haskell_attribute_EABV(const igraph_t *graph, const char *name,-			   igraph_es_t eids, igraph_vector_bool_t *result);--int igraph_haskell_attribute_VASV(const igraph_t *graph, const char *name,-			   igraph_vs_t vids, igraph_strvector_t *result);--int igraph_haskell_attribute_EASV(const igraph_t *graph, const char *name,-			   igraph_es_t eids, igraph_strvector_t *result);--int igraph_haskell_attribute_list(const igraph_t *graph,-			   igraph_strvector_t *gnames, igraph_vector_t *gtypes,-			   igraph_strvector_t *vnames, igraph_vector_t *vtypes,-			   igraph_strvector_t *enames, igraph_vector_t *etypes);--int igraph_haskell_attribute_GAN_set(igraph_t *graph, const char *name,-			      igraph_real_t value);--int igraph_haskell_attribute_GAB_set(igraph_t *graph, const char *name,-			      igraph_bool_t value);--int igraph_haskell_attribute_GAS_set(igraph_t *graph, const char *name,-			      const bytestring_t *value);--int igraph_haskell_attribute_VAN_set(igraph_t *graph, const char *name,-			      igraph_integer_t vid, igraph_real_t value);--int igraph_haskell_attribute_VAB_set(igraph_t *graph, const char *name,-			      igraph_integer_t vid, igraph_bool_t value);--int igraph_haskell_attribute_VAS_set(igraph_t *graph, const char *name,-			      igraph_integer_t vid, const bytestring_t *value);--int igraph_haskell_attribute_EAN_set(igraph_t *graph, const char *name,-			      igraph_integer_t eid, igraph_real_t value);--int igraph_haskell_attribute_EAB_set(igraph_t *graph, const char *name,-			      igraph_integer_t eid, igraph_bool_t value);--int igraph_haskell_attribute_EAS_set(igraph_t *graph, const char *name,-			      igraph_integer_t eid, const bytestring_t *value);--int igraph_haskell_attribute_VAN_setv(igraph_t *graph, const char *name,-			       const igraph_vector_t *v);--int igraph_haskell_attribute_VAB_setv(igraph_t *graph, const char *name,-			       const igraph_vector_bool_t *v);--int igraph_haskell_attribute_VAS_setv(igraph_t *graph, const char *name,-			       const bsvector_t *sv);--int igraph_haskell_attribute_EAN_setv(igraph_t *graph, const char *name,-			       const igraph_vector_t *v);--int igraph_haskell_attribute_EAB_setv(igraph_t *graph, const char *name,-			       const igraph_vector_bool_t *v);--int igraph_haskell_attribute_EAS_setv(igraph_t *graph, const char *name,-			       const bsvector_t *sv);--void igraph_haskell_attribute_free_rec(igraph_attribute_record_t *rec);--void igraph_haskell_attribute_remove_g(igraph_t *graph, const char *name);--void igraph_haskell_attribute_remove_v(igraph_t *graph, const char *name);--void igraph_haskell_attribute_remove_e(igraph_t *graph, const char *name);--void igraph_haskell_attribute_remove_all(igraph_t *graph, igraph_bool_t g,-				  igraph_bool_t v, igraph_bool_t e);-#endif
− include/haskell_igraph.h 
@@ -1,8 +0,0 @@-#ifndef HASKELL_IGRAPH-#define HASKELL_IGRAPH--#include "igraph.h"--void haskelligraph_init();--#endif
src/IGraph/Algorithms.hs view
@@ -2,7 +2,7 @@     ( module IGraph.Algorithms.Structure     , module IGraph.Algorithms.Community     , module IGraph.Algorithms.Clique---    , module IGraph.Algorithms.Layout+    , module IGraph.Algorithms.Layout     , module IGraph.Algorithms.Motif     , module IGraph.Algorithms.Generators     , module IGraph.Algorithms.Isomorphism@@ -12,7 +12,7 @@ import IGraph.Algorithms.Structure import IGraph.Algorithms.Community import IGraph.Algorithms.Clique---import IGraph.Algorithms.Layout+import IGraph.Algorithms.Layout import IGraph.Algorithms.Motif import IGraph.Algorithms.Generators import IGraph.Algorithms.Isomorphism
src/IGraph/Algorithms/Centrality.chs view
@@ -4,19 +4,21 @@     , betweenness     , eigenvectorCentrality     , pagerank+    , hubScore+    , authorityScore     ) where  import           Control.Monad import           Data.Serialize            (Serialize) import Data.List (foldl') import           System.IO.Unsafe          (unsafePerformIO)-import Data.Maybe import Data.Singletons (SingI)  import Foreign import Foreign.C.Types  import           IGraph+import IGraph.Internal.C2HS {#import IGraph.Internal #} {#import IGraph.Internal.Constants #} @@ -140,4 +142,44 @@     , castPtr `Ptr Vector'     , castPtr `Ptr Vector'     , id `Ptr ()'+    } -> `CInt' void- #}++-- | Kleinberg's hub scores.+hubScore :: Graph d v e+         -> Bool -- ^ scale result such that \(\left|max\ centrality\right|=1\)+         -> ([Double],Double) -- ^ (eigenvector,eigenvalue)+hubScore graph scale = unsafePerformIO $+  allocaVector $ \vector ->+  alloca $ \value ->+  allocaArpackOpt $ \options -> do+    igraphHubScore (_graph graph) vector value scale nullPtr options+    liftM2 (,) (toList vector) (peekFloatConv value)+{-# INLINE igraphHubScore #-}+{#fun igraph_hub_score as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    , castPtr `Ptr CDouble'+    , `Bool'+    , castPtr `Ptr Vector'+    , castPtr `Ptr ArpackOpt'+    } -> `CInt' void- #}++-- | Kleinberg's authority scores.+authorityScore :: Graph d v e+               -> Bool -- ^ scale result such that \(\left|max\ centrality\right|=1\)+               -> ([Double],Double) -- ^ (eigenvector,eigenvalue)+authorityScore graph scale = unsafePerformIO $+  allocaVector $ \vector ->+  alloca $ \value ->+  allocaArpackOpt $ \options -> do+    igraphAuthorityScore (_graph graph) vector value scale nullPtr options+    liftM2 (,) (toList vector) (peekFloatConv value)+{-# INLINE igraphAuthorityScore #-}+{#fun igraph_authority_score as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    , castPtr `Ptr CDouble'+    , `Bool'+    , castPtr `Ptr Vector'+    , castPtr `Ptr ArpackOpt'     } -> `CInt' void- #}
src/IGraph/Algorithms/Clique.chs view
@@ -6,10 +6,7 @@     , cliqueNumber     ) where -import Control.Applicative ((<$>)) import System.IO.Unsafe (unsafePerformIO)--import qualified Foreign.Ptr as C2HSImp import Foreign  import IGraph@@ -18,6 +15,7 @@  #include "haskell_igraph.h" +-- | Find all or some cliques in a graph. cliques :: Graph d v e         -> (Int, Int)  -- ^ Minimum and maximum size of the cliques to be returned.                        -- No bound will be used if negative or zero@@ -27,12 +25,16 @@     (map.map) truncate <$> toLists vptr {#fun igraph_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr', `Int', `Int' } -> `CInt' void- #} +-- | Finds the largest clique(s) in a graph.+-- Time complexity: O(3^(|V|/3)) worst case. largestCliques :: Graph d v e -> [[Int]] largestCliques gr = unsafePerformIO $ allocaVectorPtr $ \vptr -> do     igraphLargestCliques (_graph gr) vptr     (map.map) truncate <$> toLists vptr {#fun igraph_largest_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr' } -> `CInt' void- #} +-- | Find all maximal cliques of a graph. Time complexity: O(d(n-d)3^(d/3))+-- worst case, d is the degeneracy of the graph. maximalCliques :: Graph d v e                -> (Int, Int)  -- ^ Minimum and maximum size of the cliques to be returned.                               -- No bound will be used if negative or zero@@ -42,6 +44,9 @@     (map.map) truncate <$> toLists vpptr {#fun igraph_maximal_cliques as ^ { `IGraph', castPtr `Ptr VectorPtr', `Int', `Int' } -> `CInt' void- #} +-- | Find the clique number of the graph. The clique number of a graph is+-- the size of the largest clique.+-- Time complexity: O(3^(|V|/3)) worst case. cliqueNumber :: Graph d v e -> Int cliqueNumber gr = unsafePerformIO $ igraphCliqueNumber $ _graph gr {#fun igraph_clique_number as ^
src/IGraph/Algorithms/Community.chs view
@@ -2,11 +2,12 @@ {-# LANGUAGE RecordWildCards #-} {-# LANGUAGE DataKinds #-} module IGraph.Algorithms.Community-    ( modularity-    , findCommunity+    ( findCommunity     , CommunityMethod(..)-    , defaultLeadingEigenvector-    , defaultSpinglass+    , leadingEigenvector+    , spinglass+    , leiden+    , modularity     ) where  import           Data.Function             (on)@@ -14,37 +15,53 @@ import Data.List.Ordered (nubSortBy) import           Data.Ord (comparing) import           System.IO.Unsafe          (unsafePerformIO)+import           Data.Serialize            (Serialize)  import           Foreign import           Foreign.C.Types  import           IGraph+import           IGraph.Random import IGraph.Internal.C2HS {#import IGraph.Internal #} {#import IGraph.Internal.Constants #}  #include "haskell_igraph.h" -modularity :: Graph d v e-           -> [[Int]]   -- ^ Communities.-           -> Maybe [Double] -- ^ Weights-           -> Double-modularity gr clusters ws-    | length nds /= length (concat clusters) = error "Duplicated nodes"-    | nds /= nodes gr = error "Some nodes were not given community assignments"-    | otherwise = unsafePerformIO $ withList membership $ \membership' ->-        withListMaybe ws (igraphModularity (_graph gr) membership')+-- | Detecting community structure.+findCommunity :: (Serialize v, Serialize e)+              => Graph 'U v e+              -> Maybe (Node -> v -> Double)  -- ^ Function to assign node weights+              -> Maybe (e -> Double)  -- ^ Function to assign edge weights+              -> CommunityMethod  -- ^ Community finding algorithms+              -> Gen+              -> IO [[Int]]+findCommunity gr getNodeW getEdgeW method _ = allocaVector $ \result ->+    withListMaybe ew $ \ew' -> do+        case method of+            LeadingEigenvector n -> allocaArpackOpt $ \arpack ->+                igraphCommunityLeadingEigenvector (_graph gr) ew' nullPtr result+                                                  n arpack nullPtr False+                                                  nullPtr nullPtr nullPtr+                                                  nullFunPtr nullPtr+            Spinglass{..} -> igraphCommunitySpinglass (_graph gr) ew' nullPtr nullPtr result+                                     nullPtr _nSpins False _startTemp+                                     _stopTemp _coolFact+                                     IgraphSpincommUpdateConfig _gamma+                                     IgraphSpincommImpOrig 1.0+            Leiden{..} -> do+                _ <- withListMaybe nw $ \nw' -> igraphCommunityLeiden+                    (_graph gr) ew' nw' _resolution _beta False result nullPtr+                return ()+        fmap ( map (fst . unzip) . groupBy ((==) `on` snd)+              . sortBy (comparing snd) . zip [0..] ) $ toList result   where-    (membership, nds) = unzip $ nubSortBy (comparing snd) $ concat $-        zipWith f [0 :: Int ..] clusters-      where-        f i xs = zip (repeat i) xs-{#fun igraph_modularity as ^-    { `IGraph'-    , castPtr `Ptr Vector'-	, alloca- `Double' peekFloatConv*-	, castPtr `Ptr Vector'-    } -> `CInt' void- #}+    ew = case getEdgeW of+        Nothing -> Nothing+        Just f -> Just $ map (f . snd) $ labEdges gr+    nw = case getNodeW of+        Nothing -> Nothing+        Just f -> Just $ map (uncurry f) $ labNodes gr  data CommunityMethod =       LeadingEigenvector@@ -57,38 +74,44 @@         , _coolFact  :: Double  -- ^ the cooling factor for the simulated annealing         , _gamma     :: Double  -- ^ the gamma parameter of the algorithm.         }+    | Leiden+        { _resolution :: Double+        , _beta :: Double+        } -defaultLeadingEigenvector :: CommunityMethod-defaultLeadingEigenvector = LeadingEigenvector 10000+-- | Default parameters for the leading eigenvector algorithm.+leadingEigenvector :: CommunityMethod+leadingEigenvector = LeadingEigenvector 10000 -defaultSpinglass :: CommunityMethod-defaultSpinglass = Spinglass+-- | Default parameters for the spin-glass algorithm.+spinglass :: CommunityMethod+spinglass = Spinglass     { _nSpins = 25     , _startTemp = 1.0     , _stopTemp = 0.01     , _coolFact = 0.99     , _gamma = 1.0 } -findCommunity :: Graph 'U v e-              -> Maybe [Double]   -- ^ node weights-              -> CommunityMethod  -- ^ Community finding algorithms-              -> [[Int]]-findCommunity gr ws method = unsafePerformIO $ allocaVector $ \result ->-    withListMaybe ws $ \ws' -> do-        case method of-            LeadingEigenvector n -> allocaArpackOpt $ \arpack ->-                igraphCommunityLeadingEigenvector (_graph gr) ws' nullPtr result-                                                  n arpack nullPtr False-                                                  nullPtr nullPtr nullPtr-                                                  nullFunPtr nullPtr-            Spinglass{..} -> igraphCommunitySpinglass (_graph gr) ws' nullPtr nullPtr result-                                     nullPtr _nSpins False _startTemp-                                     _stopTemp _coolFact-                                     IgraphSpincommUpdateConfig _gamma-                                     IgraphSpincommImpOrig 1.0--        fmap ( map (fst . unzip) . groupBy ((==) `on` snd)-              . sortBy (comparing snd) . zip [0..] ) $ toList result+-- | Default parameters for the leiden algorithm.+-- 1 / 2m sum_ij (A_ij - gamma n_i n_j)d(s_i, s_j), where+-- m is the total edge weight,+-- A_ij is the weight of edge (i, j),+-- gamma is the so-called resolution parameter,+-- n_i is the node weight of node i,+-- s_i is the cluster of node i and+-- d(x, y) = 1 if and only if x = y and 0 otherwise.+-- By setting n_i = k_i, the degree of node i, and dividing gamma by 2m,+-- you effectively obtain an expression for modularity.+-- Hence, the standard modularity will be optimized when you supply the degrees+-- as node_weights and by supplying as a resolution parameter 1.0/(2*m), with m the number of edges.+--+-- RBConfigurationVertexPartition: supplying the degrees as node weights, and+-- a resolution parameter 1.0/(2*m), with m the number of edges.+-- CPM: +leiden :: CommunityMethod+leiden = Leiden+    { _resolution = 1+    , _beta = 0.01 }  {#fun igraph_community_spinglass as ^     { `IGraph'@@ -124,6 +147,18 @@     , id `Ptr ()'     } -> `CInt' void- #} +{#fun igraph_community_leiden as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    , castPtr `Ptr Vector'+    , `Double'+    , `Double'+    , `Bool'+    , castPtr `Ptr Vector'+    , alloca- `Int' peekIntConv*+    , id `Ptr CDouble'+    } -> `CInt' void- #}+ type T = FunPtr ( Ptr ()                 -> CLong                 -> CDouble@@ -132,3 +167,30 @@                 -> Ptr ()                 -> Ptr ()                 -> IO CInt)++-- | Calculate the modularity of a graph with respect to some vertex types.+modularity :: Serialize e+           => Graph d v e+           -> Maybe (e -> Double)  -- ^ Function to assign edge weights+           -> [[Int]]   -- ^ Communities.+           -> Double+modularity gr getEdgeW clusters+    | length nds /= length (concat clusters) = error "Duplicated nodes"+    | nds /= nodes gr = error "Some nodes were not given community assignments"+    | otherwise = unsafePerformIO $ withList membership $ \membership' ->+        withListMaybe ws (igraphModularity (_graph gr) membership')+  where+    (membership, nds) = unzip $ nubSortBy (comparing snd) $ concat $+        zipWith f [0 :: Int ..] clusters+      where+        f i xs = zip (repeat i) xs+    ws = case getEdgeW of+        Nothing -> Nothing+        Just f -> Just $ map (f . snd) $ labEdges gr+{#fun igraph_modularity as ^+    { `IGraph'+    , castPtr `Ptr Vector'+	, alloca- `Double' peekFloatConv*+	, castPtr `Ptr Vector'+    } -> `CInt' void- #}+
src/IGraph/Algorithms/Generators.chs view
@@ -5,6 +5,7 @@     ( full     , star     , ring+    , zacharyKarate     , ErdosRenyiModel(..)     , erdosRenyiGame     , degreeSequenceGame@@ -35,7 +36,7 @@      -> Bool  -- ^ Whether to include self-edges (loops)      -> Graph d () () full n hasLoop = unsafePerformIO $ do-    igraphInit+    _ <- igraphInit     gr <- igraphFull n directed hasLoop     initializeNullAttribute gr     return $ Graph gr M.empty@@ -52,7 +53,7 @@ star :: Int    -- ^ The number of nodes      -> Graph 'U () () star n = unsafePerformIO $ do-    igraphInit+    _ <- igraphInit     gr <- igraphStar n IgraphStarUndirected 0     initializeNullAttribute gr     return $ Graph gr M.empty@@ -66,7 +67,7 @@ -- | Creates a ring graph, a one dimensional lattice. ring :: Int -> Graph 'U () () ring n = unsafePerformIO $ do-    igraphInit+    _ <- igraphInit     gr <- igraphRing n False False True     initializeNullAttribute gr     return $ Graph gr M.empty@@ -78,6 +79,20 @@     , `Bool'     } -> `CInt' void- #} +-- | Zachary's karate club+zacharyKarate :: Graph 'U () ()+zacharyKarate = mkGraph (replicate 34 ()) $ map (\(a, b) -> ((a-1,b-1),())) es+  where+    es = [ (2,1),(3,1),(3,2),(4,1),(4,2),(4,3),(5,1),(6,1),(7,1),(7,5),(7,6)+         , (8,1),(8,2),(8,3),(8,4),(9,1),(9,3),(10,3),(11,1),(11,5),(11,6)+         , (12,1),(13,1),(13,4),(14,1),(14,2),(14,3),(14,4),(17,6),(17,7)+         , (18,1),(18,2),(20,1),(20,2),(22,1),(22,2),(26,24),(26,25)+         , (28,3),(28,24),(28,25),(29,3),(30,24),(30,27),(31,2),(31,9)+         , (32,1),(32,25),(32,26),(32,29),(33,3),(33,9),(33,15),(33,16)+         , (33,19),(33,21),(33,23),(33,24),(33,30),(33,31),(33,32)+         , (34,9),(34,10),(34,14),(34,15),(34,16),(34,19),(34,20),(34,21)+         , (34,23),(34,24),(34,27),(34,28),(34,29),(34,30),(34,31),(34,32),(34,33) ]+ data ErdosRenyiModel = GNP Int Double  -- ^ G(n,p) graph, every possible edge is                                        -- included in the graph with probability p.                      | GNM Int Int   -- ^ G(n,m) graph, m edges are selected@@ -90,7 +105,7 @@                -> Gen                -> IO (Graph d () ()) erdosRenyiGame model self _ = do-    igraphInit+    _ <- igraphInit     gr <- case model of         GNP n p -> igraphErdosRenyiGame IgraphErdosRenyiGnp n p directed self         GNM n m -> igraphErdosRenyiGame IgraphErdosRenyiGnm n (fromIntegral m)@@ -112,7 +127,7 @@                    -> Gen                    -> IO (Graph 'D () ()) degreeSequenceGame out_deg in_deg _ = do-    igraphInit+    _ <- igraphInit     withList out_deg $ \out_deg' ->         withList in_deg $ \in_deg' -> do             gr <- igraphDegreeSequenceGame out_deg' in_deg' IgraphDegseqSimple
src/IGraph/Algorithms/Isomorphism.chs view
@@ -1,8 +1,8 @@ {-# LANGUAGE ForeignFunctionInterface #-} {-# LANGUAGE ScopedTypeVariables #-} module IGraph.Algorithms.Isomorphism-    ( getSubisomorphisms-    , isomorphic+    ( isomorphic+    , getSubisomorphisms     , isoclassCreate     , isoclass3     , isoclass4@@ -20,6 +20,17 @@  #include "haskell_igraph.h" +-- | Determine whether two graphs are isomorphic.+isomorphic :: Graph d v1 e1+           -> Graph d v2 e2+           -> Bool+isomorphic g1 g2 = unsafePerformIO $ alloca $ \ptr -> do+    _ <- igraphIsomorphic (_graph g1) (_graph g2) ptr+    x <- peek ptr+    return (x /= 0)+{-# INLINE isomorphic #-}+{#fun igraph_isomorphic as ^ { `IGraph', `IGraph', id `Ptr CInt' } -> `CInt' void- #}+ getSubisomorphisms :: Graph d v1 e1  -- ^ graph to be searched in                    -> Graph d v2 e2   -- ^ smaller graph                    -> [[Int]]@@ -43,16 +54,6 @@     , id `FunPtr (Ptr IGraph -> Ptr IGraph -> CInt -> CInt -> Ptr () -> IO CInt)'     , id `Ptr ()'     } -> `CInt' void- #}---- | Determine whether two graphs are isomorphic.-isomorphic :: Graph d v1 e1-           -> Graph d v2 e2-           -> Bool-isomorphic g1 g2 = unsafePerformIO $ alloca $ \ptr -> do-    _ <- igraphIsomorphic (_graph g1) (_graph g2) ptr-    x <- peek ptr-    return (x /= 0)-{#fun igraph_isomorphic as ^ { `IGraph', `IGraph', id `Ptr CInt' } -> `CInt' void- #}  -- | Creates a graph from the given isomorphism class. -- This function is implemented only for graphs with three or four vertices.
+ src/IGraph/Algorithms/Layout.chs view
@@ -0,0 +1,120 @@+{-# LANGUAGE ForeignFunctionInterface #-}+module IGraph.Algorithms.Layout+    ( layout+    , LayoutMethod(..)+    , kamadaKawai+    , lgl+    ) where++import           Data.Maybe             (isJust, fromMaybe)+import           Foreign                (nullPtr)+import           System.IO.Unsafe          (unsafePerformIO)+import IGraph++import Foreign+import IGraph.Random+{#import IGraph.Internal #}++#include "haskell_igraph.h"++layout :: Graph d v e -> LayoutMethod -> Gen -> [(Double, Double)]+layout gr method _ = unsafePerformIO $ case method of+    Random -> allocaMatrix $ \mat -> do+        igraphLayoutRandom gptr mat+        getResult mat++    KamadaKawai seed niter kkconst epsilon -> do+        let f mat = igraphLayoutKamadaKawai gptr mat (isJust seed) niter+                epsilon (fromMaybe (fromIntegral $ nNodes gr) kkconst) nullPtr+                nullPtr nullPtr nullPtr nullPtr+        case seed of+            Nothing -> allocaMatrix $ \mat -> do+                f mat+                getResult mat+            Just s -> withRowLists ((\(x,y) -> [x,y]) $ unzip s) $ \mat -> do+                f mat+                getResult mat++    LGL niter delta area coolexp repulserad cellsize -> allocaMatrix $ \mat -> do+        igraphLayoutLgl gptr mat niter (delta n) (area n) coolexp+            (repulserad n) (cellsize n) (-1)+        getResult mat+  where+    n = nNodes gr+    gptr = _graph gr+    getResult mat = (\[x, y] -> zip x y) <$> toColumnLists mat++data LayoutMethod =+    Random +  | KamadaKawai { kk_seed      :: Maybe [(Double, Double)]+                , kk_nIter     :: Int+                , kk_const     :: Maybe Double  -- ^ The Kamada-Kawai vertex attraction constant+                , kk_epsilon   :: Double+                }   -- ^ The Kamada-Kawai algorithm. Time complexity: O(|V|)+                    -- for each iteration, after an O(|V|^2 log|V|)+                    -- initialization step. +  | LGL { lgl_nIter      :: !Int+        , lgl_maxdelta   :: (Int -> Double)  -- ^ The maximum length of the move allowed+        -- for a vertex in a single iteration. A reasonable default is the number of vertices.+        , lgl_area       :: (Int -> Double)  -- ^ This parameter gives the area+        -- of the square on which the vertices will be placed. A reasonable+        -- default value is the number of vertices squared.+        , lgl_coolexp    :: !Double  -- ^ The cooling exponent. A reasonable default value is 1.5.+        , lgl_repulserad :: (Int -> Double) -- ^ Determines the radius at which+        -- vertex-vertex repulsion cancels out attraction of adjacent vertices.+        -- A reasonable default value is area times the number of vertices.+        , lgl_cellsize   :: (Int -> Double)+        }++-- | Default parameters for the Kamada-Kawai algorithm.+kamadaKawai :: LayoutMethod+kamadaKawai = KamadaKawai+    { kk_seed = Nothing+    , kk_nIter = 10+    , kk_const = Nothing+    , kk_epsilon = 0 }++-- | Default parameters for the LGL algorithm.+lgl :: LayoutMethod+lgl = LGL+    { lgl_nIter = 100+    , lgl_maxdelta = \x -> fromIntegral x+    , lgl_area = area+    , lgl_coolexp = 1.5+    , lgl_repulserad = \x -> fromIntegral x * area x+    , lgl_cellsize = \x -> area x ** 0.25+    }+  where+    area x = fromIntegral $ x * x++-- | Places the vertices uniform randomly on a plane.+{#fun igraph_layout_random as ^+    { `IGraph'+    , castPtr `Ptr Matrix'+    } -> `CInt' void- #}++{#fun igraph_layout_kamada_kawai as ^+    { `IGraph'                    -- ^ Graph+    , castPtr `Ptr Matrix'        -- ^ Pointer to the result matrix+    , `Bool'                      -- ^ Whether to use the seed+    , `Int'                       -- ^ The maximum number of iterations to perform+    , `Double'                    -- ^ epsilon+    , `Double'                    -- ^ kkconst+    , castPtr `Ptr Vector'        -- ^ edges weights+    , castPtr `Ptr Vector'+    , castPtr `Ptr Vector'+    , castPtr `Ptr Vector'+    , castPtr `Ptr Vector'+    } -> `CInt' void- #}++{# fun igraph_layout_lgl as ^+    { `IGraph'+    , castPtr `Ptr Matrix'+    , `Int'+    , `Double'+    , `Double'+    , `Double'+    , `Double'+    , `Double'+    , `Int'+    } -> `CInt' void- #}
src/IGraph/Algorithms/Motif.chs view
@@ -1,7 +1,8 @@ {-# LANGUAGE ForeignFunctionInterface #-} {-# LANGUAGE DataKinds #-} module IGraph.Algorithms.Motif-    ( triad+    ( dyadCensus+    , triad     , triadCensus     ) where @@ -10,10 +11,26 @@ import Foreign  import IGraph+import IGraph.Internal.C2HS {#import IGraph.Internal #}  #include "haskell_igraph.h" +-- | Dyad census means classifying each pair of vertices of a directed graph+-- into three categories: mutual, there is an edge from a to b and also+-- from b to a; asymmetric, there is an edge either from a to b or+-- from b to a but not the other way; null, no edges between a and b.+dyadCensus :: Graph 'D v e -> (Int, Int, Int)+dyadCensus = unsafePerformIO . igraphDyadCensus . _graph+{-# INLINE dyadCensus #-}++{#fun igraph_dyad_census as ^+    { `IGraph'+    , alloca- `Int' peekIntConv*+    , alloca- `Int' peekIntConv*+    , alloca- `Int' peekIntConv*+    } -> `CInt' void- #}+ -- | Every triple of vertices in a directed graph -- 003: A, B, C, the empty graph. -- 012: A->B, C, a graph with a single directed edge.@@ -54,16 +71,18 @@          ]     make :: [(Int, Int)] -> Graph 'D () ()     make xs = mkGraph (replicate 3 ()) $ zip xs $ repeat ()+{-# INLINE triad #-} -triadCensus :: (Ord v, Read v) => Graph d v e -> [Int]+-- | Calculating the triad census means classifying every triple of vertices+-- in a directed graph. A triple can be in one of 16 states listed in `triad`.+triadCensus :: (Ord v, Read v) => Graph 'D v e -> [Int] triadCensus gr = unsafePerformIO $ allocaVector $ \result -> do     igraphTriadCensus (_graph gr) result     map truncate <$> toList result---- motifsRandesu-+{-# INLINE triadCensus #-} {#fun igraph_triad_census as ^ { `IGraph'                                , castPtr `Ptr Vector' } -> `CInt' void- #} +-- motifsRandesu {#fun igraph_motifs_randesu as ^ { `IGraph', castPtr `Ptr Vector', `Int'                                  , castPtr `Ptr Vector' } -> `CInt' void- #}
src/IGraph/Algorithms/Structure.chs view
@@ -3,20 +3,31 @@ module IGraph.Algorithms.Structure     ( -- * Shortest Path Related Functions       shortestPath+    , averagePathLength+    , diameter+    , eccentricity+    , radius+      -- * Graph Components     , inducedSubgraph     , isConnected     , isStronglyConnected     , decompose+    , articulationPoints+    , bridges+      -- * Topological Sorting, Directed Acyclic Graphs     , isDag     , topSort     , topSortUnsafe+      -- * Other Operations+    , density+    , reciprocity+      -- * Auxiliary types+    , Neimode(IgraphOut,IgraphIn,IgraphAll) -- not IgraphTotal     ) where  import           Control.Monad import           Data.Serialize            (Serialize)-import Data.List (foldl') import           System.IO.Unsafe          (unsafePerformIO)-import Data.Maybe import Data.Singletons (SingI)  import Foreign@@ -29,14 +40,6 @@  #include "haskell_igraph.h" -{#fun igraph_shortest_paths as ^-    { `IGraph'-    , castPtr `Ptr Matrix'-    , castPtr %`Ptr VertexSelector'-    , castPtr %`Ptr VertexSelector'-    , `Neimode'-    } -> `CInt' void- #}- -- Calculates and returns a single unweighted shortest path from a given vertex -- to another one. If there are more than one shortest paths between the two -- vertices, then an arbitrary one is returned.@@ -53,6 +56,7 @@         Just f -> withList (map (f . snd) $ labEdges gr) $ \ws ->             igraphGetShortestPathDijkstra (_graph gr) path nullPtr s t ws IgraphOut     map truncate <$> toList path+{-# INLINE shortestPath #-} {#fun igraph_get_shortest_path as ^     { `IGraph'     , castPtr `Ptr Vector'@@ -71,13 +75,88 @@     , `Neimode'     } -> `CInt' void- #} +-- | Calculates the average shortest path length between all vertex pairs.+averagePathLength :: SingI d+                  => Graph d v e+                  -> Bool     -- ^ if unconnected,+                              -- include only connected pairs (True)+                              -- or return number if vertices (False)+                  -> Double+averagePathLength graph unconn =+  cFloatConv $ igraphAveragePathLength (_graph graph) (isDirected graph) unconn+{-# INLINE igraphAveragePathLength #-}+{#fun pure igraph_average_path_length as ^+    { `IGraph'+    , alloca- `CDouble' peek*+    , `Bool'+    , `Bool'+    } -> `CInt' void- #}++-- | Calculates the diameter of a graph (longest geodesic).+diameter :: SingI d+         => Graph d v e+         -> Bool     -- ^ if unconnected,+                     -- return largest component diameter (True)+                     -- or number of vertices (False)+         -> (Int, [Node])+diameter graph unconn = unsafePerformIO $+  alloca $ \pres ->+  allocaVector $ \path -> do+    igraphDiameter (_graph graph) pres nullPtr nullPtr path (isDirected graph) unconn+    liftM2 (,) (peekIntConv pres) (toNodes path)+{-# INLINE igraphDiameter #-}+{#fun igraph_diameter as ^+    { `IGraph'+    , castPtr `Ptr CInt'+    , castPtr `Ptr CInt'+    , castPtr `Ptr CInt'+    , castPtr `Ptr Vector'+    , `Bool'+    , `Bool'+    } -> `CInt' void- #}++-- | Eccentricity of some vertices.+eccentricity :: Graph d v e+             -> Neimode -- ^ 'IgraphOut' to follow edges' direction,+                        -- 'IgraphIn' to reverse it, 'IgraphAll' to ignore+             -> [Node]  -- ^ vertices for which to calculate eccentricity+             -> [Double]+eccentricity graph mode vids = unsafePerformIO $+  allocaVector $ \res ->+  withVerticesList vids $ \vs -> do+    igraphEccentricity (_graph graph) res vs mode+    toList res+{-# INLINE igraphEccentricity #-}+{#fun igraph_eccentricity as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    , castPtr %`Ptr VertexSelector'+    , `Neimode'+    } -> `CInt' void- #}++-- | Radius of a graph.+radius :: Graph d v e+       -> Neimode -- ^ 'IgraphOut' to follow edges' direction,+                  -- 'IgraphIn' to reverse it, 'IgraphAll' to ignore+       -> Double+radius graph mode = cFloatConv $ igraphRadius (_graph graph) mode+{-# INLINE igraphRadius #-}+{#fun pure igraph_radius as ^+    { `IGraph'+    , alloca- `CDouble' peek*+    , `Neimode'+    } -> `CInt' void- #}++-- | Creates a subgraph induced by the specified vertices. This function collects+-- the specified vertices and all edges between them to a new graph. inducedSubgraph :: (Ord v, Serialize v)                 => Graph d v e-                -> [Int]+                -> [Node]                 -> Graph d v e inducedSubgraph gr nds = unsafePerformIO $ withVerticesList nds $ \vs ->     igraphInducedSubgraph (_graph gr) vs IgraphSubgraphCreateFromScratch >>=         (\g -> return $ Graph g $ mkLabelToId g)+{-# INLINE inducedSubgraph #-} {#fun igraph_induced_subgraph as ^     { `IGraph'     , allocaIGraph- `IGraph' addIGraphFinalizer*@@ -88,10 +167,11 @@ -- | Decides whether the graph is weakly connected. isConnected :: Graph d v e -> Bool isConnected gr = igraphIsConnected (_graph gr) IgraphWeak+{-# INLINE isConnected #-}  isStronglyConnected :: Graph 'D v e -> Bool isStronglyConnected gr = igraphIsConnected (_graph gr) IgraphStrong-+{-# INLINE isStronglyConnected #-} {#fun pure igraph_is_connected as ^     { `IGraph'     , alloca- `Bool' peekBool*@@ -116,7 +196,28 @@     , `Int'     } -> `CInt' void- #} +-- | Find the articulation points in a graph.+articulationPoints :: Graph d v e -> [Node]+articulationPoints gr = unsafePerformIO $ allocaVector $ \res -> do+  igraphArticulationPoints (_graph gr) res+  toNodes res+{-#INLINE igraphArticulationPoints #-}+{#fun igraph_articulation_points as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    } -> `CInt' void- #} +-- ^ Find all bridges in a graph.+bridges :: Graph d v e -> [Edge]+bridges gr = unsafePerformIO $ allocaVector $ \res -> do+  igraphBridges (_graph gr) res+  map (getEdgeByEid gr) <$> toNodes res+{-# INLINE igraphBridges #-}+{#fun igraph_bridges as ^+    { `IGraph'+    , castPtr `Ptr Vector'+    } -> `CInt' void- #}+ -- | Checks whether a graph is a directed acyclic graph (DAG) or not. isDag :: Graph d v e -> Bool isDag = igraphIsDag . _graph@@ -124,11 +225,14 @@     { `IGraph'     , alloca- `Bool' peekBool*     } -> `CInt' void- #}+{-# INLINE isDag #-} --- | Calculate a possible topological sorting of the graph.+-- | Calculate a possible topological sorting of the graph. Raise error if the+-- graph is not acyclic. topSort :: Graph d v e -> [Node] topSort gr | isDag gr = topSortUnsafe gr            | otherwise = error "the graph is not acyclic"+{-# INLINE topSort #-}  -- | Calculate a possible topological sorting of the graph. If the graph is not -- acyclic (it has at least one cycle), a partial topological sort is returned.@@ -138,8 +242,37 @@     map truncate <$> toList res   where     n = nNodes gr+{-# INLINE topSortUnsafe #-} {#fun igraph_topological_sorting as ^     { `IGraph'     , castPtr `Ptr Vector'     , `Neimode'     } -> `CInt' void- #}++-- | Calculate the density of a graph.+density :: Graph d v e+        -> Bool -- ^ whether to include loops+        -> Double -- ^ the ratio of edges to possible edges+density gr loops = unsafePerformIO $ alloca $ \res -> do+  igraphDensity (_graph gr) res loops+  peek res+{-# INLINE igraphDensity #-}+{#fun igraph_density as ^+    { `IGraph'+    , castPtr `Ptr Double'+    , `Bool'+    } -> `CInt' void -#}++-- | Calculates the reciprocity of a directed graph.+reciprocity :: Graph d v e+            -> Bool -- ^ whether to ignore loop edges+            -> Double -- ^ the proportion of mutual connections+reciprocity gr ignore_loops = unsafePerformIO $ alloca $ \res -> do+  igraphReciprocity (_graph gr) res ignore_loops IgraphReciprocityDefault+  peek res+{#fun igraph_reciprocity as ^+    { `IGraph'+    , castPtr `Ptr Double'+    , `Bool'+    , `Reciprocity'+    } -> `CInt' void -#}
src/IGraph/Internal.chs view
@@ -8,6 +8,7 @@     , withList     , withListMaybe     , toList+    , toNodes     , igraphVectorNull     , igraphVectorFill     , igraphVectorE@@ -192,6 +193,10 @@         igraphVectorCopyTo vec ptr         map realToFrac <$> peekArray n ptr {-# INLINE toList #-}++toNodes :: Ptr Vector -> IO [Node]+toNodes = fmap (map truncate) . toList+{-# INLINE toNodes #-}  {#fun igraph_vector_copy_to as ^ { castPtr `Ptr Vector', id `Ptr CDouble' } -> `()' #} 
src/IGraph/Internal/Constants.chs view
@@ -41,3 +41,6 @@  {#enum igraph_degseq_t as Degseq {underscoreToCase}     deriving (Show, Read, Eq) #}++{#enum igraph_reciprocity_t as Reciprocity {underscoreToCase}+    deriving (Show, Read, Eq) #}
src/IGraph/Mutable.hs view
@@ -23,7 +23,7 @@ import           Data.List                      (foldl', delete) import           Data.Primitive.MutVar import           Data.Serialize                 (Serialize, encode)-import           Data.Singletons.Prelude        (Sing, SingI, fromSing, sing)+import           Data.Singletons (Sing, SingI, fromSing, sing) import           Foreign                        hiding (new)  import           IGraph.Internal
src/IGraph/Types.hs view
@@ -13,12 +13,13 @@ {-# LANGUAGE TypeFamilies           #-} {-# LANGUAGE TypeOperators          #-} {-# LANGUAGE UndecidableInstances   #-}+{-# LANGUAGE StandaloneKindSignatures #-}  module IGraph.Types where  import           Data.Serialize          (Serialize)-import           Data.Singletons.Prelude import           Data.Singletons.TH+import Prelude.Singletons import           GHC.Generics            (Generic)  $(singletons [d|
stack.yaml view
@@ -1,4 +1,4 @@ packages:     - '.' -resolver: lts-15.0+resolver: lts-24.2
tests/Test/Algorithms.hs view
@@ -1,4 +1,5 @@ {-# LANGUAGE DataKinds #-}+{-# LANGUAGE TypeApplications #-} module Test.Algorithms     ( tests     ) where@@ -6,6 +7,7 @@ import           Control.Arrow import           Control.Monad.ST import           Data.List+import Control.Monad import qualified Data.Matrix.Unboxed as M import           Test.Tasty import           Test.Tasty.HUnit@@ -20,9 +22,19 @@     [ graphIsomorphism     , motifTest     , cliqueTest+    , averagePathTest+    , diameterTest+    , eccentricityTest+    , radiusTest     , subGraphs     , decomposeTest+    , articulationTest+    , bridgeTest+    , communityTest     , pagerankTest+    , kleinbergTest+    , densityTest+    , reciprocityTest     ]  graphIsomorphism :: TestTree@@ -55,6 +67,37 @@         [2,3,4], [2,4,5] ]     c4 = [[1, 2, 3, 4], [1, 2, 4, 5]] +averagePathTest :: TestTree+averagePathTest = testGroup "Average path lengths"+    [ testCase "clique" $ averagePathLength (full @'U 10 False) True @?= 1+    , testCase "star" $ averagePathLength (star 10) True @?~ 1.8+    , testCase "ring" $ averagePathLength (ring 11) True @?= 3+    ]++diameterTest :: TestTree+diameterTest = testGroup "Diameters"+    [ testCase "clique" $ fst (diameter (full @'U 10 False) True)  @?= 1+    , testCase "star"   $ fst (diameter (star 10)          False) @?= 2+    , testCase "ring"   $ fst (diameter (ring 10)          False) @?= 5+    ]++eccentricityTest :: TestTree+eccentricityTest = testGroup "Eccentricity"+    [ testCase "clique" $+        eccentricity (full @'U 10 False) IgraphAll [0..9] @?= replicate 10 1+    , testCase "star" $+        eccentricity (star 10) IgraphAll [0..9] @?= (1 : replicate 9 2)+    , testCase "ring" $+        eccentricity (ring 10) IgraphAll [0..9] @?= replicate 10 5+    ]++radiusTest :: TestTree+radiusTest = testGroup "Radius"+    [ testCase "clique" $ radius (full @'U 10 False) IgraphAll @?= 1+    , testCase "star" $ radius (star 10) IgraphAll @?= 1+    , testCase "ring" $ radius (ring 10) IgraphAll @?= 5+    ]+ subGraphs :: TestTree subGraphs = testGroup "generate induced subgraphs"     [ testCase "" $ test case1 ]@@ -83,15 +126,71 @@     ]   where     es = [ (0,1), (1,2), (2,0)-		 , (3,4), (4,5), (5,6)-		 , (8,9), (9,10) ]+         , (3,4), (4,5), (5,6)+         , (8,9), (9,10) ]     gr = mkGraph (replicate 11 ()) $ zip es $ repeat () :: Graph 'U () () +articulationTest :: TestTree+articulationTest = testCase "Articulation points" $+  articulationPoints (star 3) @?= [0]++bridgeTest :: TestTree+bridgeTest = testCase "Bridges" $ edgeLab g <$> bridges g @?= ["bridge"]+  where g = fromLabeledEdges @'U+            [ (("a","b"),"ab") , (("b","c"),"bc") , (("c","a"),"ca")+            , (("i","j"),"ij") , (("j","k"),"jk") , (("k","i"),"ki")+            , (("a","i"),"bridge")+            ]++communityTest :: TestTree+communityTest = testGroup "Community"+    [ consistency, consistency2 ]+  where+    consistency = testCase "Consistency" $ do+        rs <- replicateM 50 $ withSeed 134 $ findCommunity zacharyKarate Nothing Nothing spinglass+        all (== head rs) rs @=? True+    consistency2 = testCase "Consistency -- leiden" $ do+        rs <- replicateM 50 $ withSeed 234 $ findCommunity zacharyKarate Nothing Nothing leiden+        True @=? all (== head rs) rs+    gr = mkGraph (replicate 10 ()) $ map (\(i,j) -> ((i,j),()))+        [ (0, 1), (0, 2), (0, 3), (0, 4), (1, 2), (1, 3), (1, 4), (2, 3), (2, 4)+        , (3, 4), (5, 6), (5, 7), (5, 8), (5, 9), (6, 7), (6, 8), (6, 9), (7, 8)+        , (7, 9), (8, 9), (0, 5) ] :: Graph 'U () ()+ pagerankTest :: TestTree pagerankTest = testGroup "PageRank"-    [ testCase "case 1" $ ranks @=? ranks' ]+    [ consistency+    , testCase "case 1" $ ranks @=? ranks' ]   where+    consistency = testCase "Consistency" $ +        pagerank gr 0.85 Nothing Nothing @=?+        pagerank gr 0.85 Nothing Nothing     gr = star 11     ranks = [0.47,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05]     ranks' = map ((/100) . fromIntegral . round. (*100)) $         pagerank gr 0.85 Nothing Nothing++kleinbergTest :: TestTree+kleinbergTest = testGroup "Kleinberg"+    [ testCase "Hub score" $+        fst (hubScore (full @'U 16 False) True) @?= replicate 16 1+    , testCase "Authority score" $+        fst (authorityScore (ring 4) False) @?= replicate 4 0.5+    ]++densityTest :: TestTree+densityTest = testGroup "Density"+    [ testCase "clique" $ density (full @'U 16 False) False @?= 1+    , testCase "ring" $ density (ring 9) False @?= 1/4+    ]++reciprocityTest :: TestTree+reciprocityTest = testGroup "Reciprocity"+    [ testCase "clique" $ reciprocity (full @'D 10 False) False @?= 1+    , testCase "ring" $ reciprocity g False @?= 0+    ]+  where g = fromLabeledEdges @'D [(("a","b"),()),(("b","c"),()),(("c","a"),())]++-- approximate equality helper+(@?~) :: (Ord n,Fractional n) => n -> n -> Assertion+a @?~ b = assertBool "" $ abs (b-a) < 1/65536