diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -2,7 +2,13 @@
# Changelog for ELynx
-## Version 0.3.2; in development
+## Unreleased changes
+
+
+## Version 0.3.2
+
+- Remove llvm dependency.
+- Move away from hpack.
## Version 0.3.1
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.3.1.
+Version: 0.3.2.
Reproducible evolution made easy.
@@ -90,9 +90,9 @@
slynx --help | head -n -16
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] COMMAND
@@ -136,9 +136,9 @@
slynx concatenate --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
Concatenate sequences found in input files.
@@ -157,9 +157,9 @@
slynx examine --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
@@ -179,9 +179,9 @@
slynx filter-rows --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]
[--shorter-than LENGTH] [--standard-characters]
@@ -202,9 +202,9 @@
slynx filter-columns --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE
[--standard-chars DOUBLE]
@@ -226,9 +226,9 @@
slynx simulate --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
[-m|--mixture-model MODEL] [-e|--edm-file NAME]
@@ -305,9 +305,9 @@
slynx sub-sample --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
(-n|--number-of-sites INT)
@@ -335,9 +335,9 @@
slynx translate --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
(-u|--universal-code CODE)
@@ -360,9 +360,9 @@
tlynx --help | head -n -16
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] COMMAND
@@ -399,9 +399,9 @@
tlynx compare --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
[-f|--newick-format FORMAT] NAMES
@@ -428,9 +428,9 @@
tlynx examine --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
Compute summary statistics of phylogenetic trees.
@@ -452,9 +452,9 @@
tlynx simulate --help
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE]
[-M|--condition-on-mrca] [-l|--lambda DOUBLE]
@@ -491,9 +491,9 @@
elynx --help | head -n -16
- ELynx Suite version 0.3.1.
+ ELynx Suite version 0.3.2.
Developed by Dominik Schrempf.
- Compiled on August 3, 2020, at 12:12 pm, UTC.
+ Compiled on August 17, 2020, at 14:19 pm, UTC.
Usage: elynx COMMAND
Validate and redo past ELynx analyses
diff --git a/elynx-tree.cabal b/elynx-tree.cabal
--- a/elynx-tree.cabal
+++ b/elynx-tree.cabal
@@ -1,13 +1,6 @@
-cabal-version: 2.2
-
--- This file has been generated from package.yaml by hpack version 0.34.2.
---
--- see: https://github.com/sol/hpack
---
--- hash: 5876c21cdef387a8327af59315c4809662b893bf5daeb4f5e60874063f34384f
-
+cabal-version: 2.2
name: elynx-tree
-version: 0.3.1
+version: 0.3.2
synopsis: Handle phylogenetic trees
description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at .
category: Bioinformatics
@@ -19,6 +12,7 @@
license: GPL-3.0-or-later
license-file: LICENSE
build-type: Simple
+
extra-source-files:
README.md
ChangeLog.md
@@ -62,7 +56,7 @@
Paths_elynx_tree
hs-source-dirs:
src
- ghc-options: -Wall -fllvm
+ ghc-options: -Wall
build-depends:
aeson
, attoparsec
@@ -97,7 +91,7 @@
Paths_elynx_tree
hs-source-dirs:
test
- ghc-options: -Wall -fllvm
+ ghc-options: -Wall
build-depends:
QuickCheck
, attoparsec
@@ -116,7 +110,7 @@
Paths_elynx_tree
hs-source-dirs:
bench
- ghc-options: -Wall -fllvm
+ ghc-options: -Wall
build-depends:
base >=4.7 && <5
, bytestring
diff --git a/src/ELynx/Data/Tree/Phylogeny.hs b/src/ELynx/Data/Tree/Phylogeny.hs
--- a/src/ELynx/Data/Tree/Phylogeny.hs
+++ b/src/ELynx/Data/Tree/Phylogeny.hs
@@ -324,7 +324,7 @@
instance FromJSON Phylo
-- | Branch length label.
-
+--
-- For conversion, see 'phyloToLengthTree' and 'lengthToPhyloTree'.
newtype Length = Length {fromLength :: BranchLength}
deriving (Read, Show, Eq, Ord, Generic, NFData)
@@ -426,7 +426,7 @@
cleanSupport :: BranchSupport -> Tree Phylo a -> Tree Support a
cleanSupport maxSup (Node (Phylo _ s) l xs) = Node (Support $ fromMaybe maxSup s) l $ map (cleanSupport maxSup) xs
--- TODO: Change name. Strict is reserved for "not lazy".
+-- XXX: Probably change name. Strict is reserved for "not lazy".
-- | Strict branch label for phylogenetic trees.
data PhyloStrict = PhyloStrict
diff --git a/src/ELynx/Simulate/PointProcess.hs b/src/ELynx/Simulate/PointProcess.hs
--- a/src/ELynx/Simulate/PointProcess.hs
+++ b/src/ELynx/Simulate/PointProcess.hs
@@ -48,12 +48,17 @@
)
import System.Random.MWC
+-- Require near critical process if birth and death rates are closer than this value.
epsNearCriticalPointProcess :: Double
epsNearCriticalPointProcess = 1e-5
+-- Also the distribution of origins needs a Tailor expansion for near critical values.
+--
+-- TODO: Check why the two epsilons are chosen differently.
epsNearCriticalTimeOfOrigin :: Double
epsNearCriticalTimeOfOrigin = 1e-8
+-- Require critical process if birth and death rates are closer than this value.
eps :: Double
eps = 1e-12