csa (empty) → 0.1.0

raw patch · 9 files changed

+346/−0 lines, 9 filesdep +basedep +csadep +hedgehogsetup-changed

Dependencies added: base, csa, hedgehog, hmatrix, tasty, tasty-hedgehog, tasty-hspec

Files

• CHANGELOG.md +7/−0
• LICENSE +14/−0
• README.md +41/−0
• Setup.hs +7/−0
• csa.cabal +62/−0
• library/CSA.hs +63/−0
• package.yaml +50/−0
• stack.yaml +66/−0
• test-suite/Main.hs +36/−0

@@ -0,0 +1,7 @@+# Change log++csa uses [Semantic Versioning][].+The change log is available through the [releases on GitHub][].++[Semantic Versioning]: http://semver.org/spec/v2.0.0.html+[releases on GitHub]: https://github.com/githubuser/csa/releases

@@ -0,0 +1,14 @@+Copyright (C) 2018 Jens Egholm Pedersen++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, see <https://www.gnu.org/licenses/>.

@@ -0,0 +1,41 @@+# Connection-set algebra (CSA) library++A library for constructing connection matrices between two collections of+elements. Inspired by Mikael Djurfeldt's article from 2012 ([Neuroinformatics](https://doi.org/10.1007/s12021-012-9146-1)).++## Introduction+Connection-set algebra is a powerful algebra for describing connections between+two elements.+This library provides a syntax tree for modeling the set operations, as well as+a means to transform the operations into adjacency matrices.++## Installation+This is a library and not an executable.+Clone the repository, enter it and run `stack build` (requires [stack](http://haskellstack.org/)).++## Connection-set algebra (CSA)+Say that you have two nodes that connect to each other.+In a adjacency matrix this can be described as a full connection like so:++        1 2+      + ———+    1 | 1 1+    2 | 1 1++In CSA this is simply an `AllToAll` connection.+Similarly a `OneToOne` connection describes the following adjacency matrix:++        1 2+      + ———+    1 | 1 0+    2 | 0 1++And here is the algebra part: If we say `AllToAll - OneToOne` we get:++        1 2+      + ———+    1 | 0 1+    2 | 1 0++## Contact+Jens Egholm <jensegholm@protonmail.com>

@@ -0,0 +1,7 @@+-- This script is used to build and install your package. Typically you don't+-- need to change it. The Cabal documentation has more information about this+-- file: <https://www.haskell.org/cabal/users-guide/installing-packages.html>.+import qualified Distribution.Simple++main :: IO ()+main = Distribution.Simple.defaultMain

@@ -0,0 +1,62 @@+-- This file has been generated from package.yaml by hpack version 0.28.2.+--+-- see: https://github.com/sol/hpack+--+-- hash: 1af8fc7f9a2c6a29dbc50f13e65b27c78c9af0950a1227bd2edb7758f8a977ed++name:           csa+version:        0.1.0+synopsis:       Connection-set algebra (CSA) library+description:    Library for algebraic connection-set expressions, built on M. Djurfeldt's idea of connection-set algebra [1]. +                .+                 1: Mikael Djurfeldt. The Connection-set Algebra: a formalism for the representation of connectivity structure in neuronal network models, implementations in Python and C++, and their use in simulators, BMC Neuroscience, 2011. https://doi.org/10.1186/1471-2202-12-S1-P80+category:       Algebra+homepage:       https://github.com/volr/csa#readme+bug-reports:    https://github.com/volr/csa/issues+author:         Jens Egholm Pedersen+maintainer:     Jens Egholm Pedersen+license:        GPL+license-file:   LICENSE+build-type:     Simple+cabal-version:  >= 1.10+extra-source-files:+    CHANGELOG.md+    LICENSE+    package.yaml+    README.md+    stack.yaml++source-repository head+  type: git+  location: https://github.com/volr/csa++library+  hs-source-dirs:+      library+  ghc-options: -Wall+  build-depends:+      base >=4.10.0 && <5+    , hmatrix+  exposed-modules:+      CSA+  other-modules:+      Paths_csa+  default-language: Haskell2010++test-suite csa-test-suite+  type: exitcode-stdio-1.0+  main-is: Main.hs+  hs-source-dirs:+      test-suite+  ghc-options: -Wall -rtsopts -threaded -with-rtsopts=-N+  build-depends:+      base >=4.10.0 && <5+    , csa+    , hedgehog+    , hmatrix+    , tasty+    , tasty-hedgehog+    , tasty-hspec+  other-modules:+      Paths_csa+  default-language: Haskell2010

@@ -0,0 +1,63 @@+{-# LANGUAGE DataKinds #-}++{-|+Module: CSA+Description: Connectivity description using connection-set algebra+License: MIT+Maintainer: jensegholm@protonmail.com+Stability: experimental++This module uses connection-set algebra to describe connectivity between+two entities with a scalar ('Double') value. The library build on the concept+of M. Djurfeldt's Connection-Set Algebar [1].+The connection expressions can be compiled to a dependently typed+'AdjacencyMatrix' from the "Numeric.LinearAlgebra.Static" package. Such+a matrix can be used and exported as a regular n-dimensional vector.++Usage:++>>> toAdjacencyMatrix None :: L 2 2+(matrix+ [ 0.0, 0.0+ , 0.0, 0.0 ] :: L 2 2)++>>> toAdjacencyMatrix $ Minus (AllToAll 2) (OneToOne 1) :: L 2 2+(matrix+ [ 1.0, 2.0+ , 2.0, 1.0 ] :: L 2 2)++1: Mikael Djurfeldt. The Connection-set Algebra: a formalism for the+representation of connectivity structure in neuronal network models,+implementations in Python and C++, and their use in simulators,+BMC Neuroscience, 2011. https://doi.org/10.1186/1471-2202-12-S1-P80+-}+module CSA where++import GHC.TypeLits+import Numeric.LinearAlgebra.Static++-- | An adjacency matrix describing connections in a directed graph+type AdjacencyMatrix = L++-- | An expression algebra tree (AST) that describes connections+--   between two elements+data Expr+  = None -- ^ An empty connection (only 0s)+  | AllToAll ℝ -- ^ Full connectivity with the given value+  | OneToOne ℝ -- ^ One-to-one (diagonally) connectivity+  | Mask (ℝ -> ℝ -> ℝ) -- ^ A masked connectivity given by a function+  | Plus Expr Expr -- ^ Addition of two connectivity expressions+  | Minus Expr Expr -- ^ Subtraction of two connectivity expressions++-- | Converts an expression to an adjacency matrix by unrolling the+--   expression tree from left to right+toAdjacencyMatrix+  :: (KnownNat m, KnownNat n) => Expr -- ^ The expression to turn into a 'AdjacencyMatrix'+  -> AdjacencyMatrix m n -- ^ The resulting adjacency matrix+toAdjacencyMatrix expr = case expr of+  None -> build (\_ _ -> 0)+  Mask f -> build f+  OneToOne v -> build (\x y -> if x == y then v else 0)+  AllToAll v -> build (\_ _ -> v)+  Plus left right -> (+) (toAdjacencyMatrix left) (toAdjacencyMatrix right)+  Minus left right -> (-) (toAdjacencyMatrix left) (toAdjacencyMatrix right)

@@ -0,0 +1,50 @@+# This YAML file describes your package. Stack will automatically generate a+# Cabal file when you run `stack build`. See the hpack website for help with+# this file: <https://github.com/sol/hpack>.+name: csa+version: '0.1.0'+github: "volr/csa"+license: GPL+author: "Jens Egholm Pedersen"+maintainer: "Jens Egholm Pedersen"+synopsis: Connection-set algebra (CSA) library+description: "Library for algebraic connection-set expressions, built on+             M. Djurfeldt's idea of connection-set algebra [1].+             \n\n+             1: Mikael Djurfeldt. The Connection-set Algebra: a formalism for the+             representation of connectivity structure in neuronal network models,+             implementations in Python and C++, and their use in simulators,+             BMC Neuroscience, 2011. https://doi.org/10.1186/1471-2202-12-S1-P80"+category: Algebra++extra-source-files:+- CHANGELOG.md+- LICENSE+- package.yaml+- README.md+- stack.yaml++ghc-options: -Wall++library:+  dependencies:+  - base >= 4.10.0 && < 5+  - hmatrix+  source-dirs: library++tests:+  csa-test-suite:+    source-dirs: test-suite+    main: Main.hs+    dependencies:+    - base >= 4.10.0 && < 5+    - csa+    - hmatrix+    - hedgehog+    - tasty+    - tasty-hspec+    - tasty-hedgehog+    ghc-options:+    - -rtsopts+    - -threaded+    - -with-rtsopts=-N

@@ -0,0 +1,66 @@+# This file was automatically generated by 'stack init'+#+# Some commonly used options have been documented as comments in this file.+# For advanced use and comprehensive documentation of the format, please see:+# https://docs.haskellstack.org/en/stable/yaml_configuration/++# Resolver to choose a 'specific' stackage snapshot or a compiler version.+# A snapshot resolver dictates the compiler version and the set of packages+# to be used for project dependencies. For example:+#+# resolver: lts-3.5+# resolver: nightly-2015-09-21+# resolver: ghc-7.10.2+# resolver: ghcjs-0.1.0_ghc-7.10.2+# resolver:+#  name: custom-snapshot+#  location: "./custom-snapshot.yaml"+resolver: lts-11.13++# User packages to be built.+# Various formats can be used as shown in the example below.+#+# packages:+# - some-directory+# - https://example.com/foo/bar/baz-0.0.2.tar.gz+# - location:+#    git: https://github.com/commercialhaskell/stack.git+#    commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a+# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a+#   extra-dep: true+#  subdirs:+#  - auto-update+#  - wai+#+# A package marked 'extra-dep: true' will only be built if demanded by a+# non-dependency (i.e. a user package), and its test suites and benchmarks+# will not be run. This is useful for tweaking upstream packages.+packages:+- .+# Dependency packages to be pulled from upstream that are not in the resolver+# (e.g., acme-missiles-0.3)+extra-deps: []++# Override default flag values for local packages and extra-deps+# flags: {}++# Extra package databases containing global packages+# extra-package-dbs: []++# Control whether we use the GHC we find on the path+# system-ghc: true+#+# Require a specific version of stack, using version ranges+# require-stack-version: -any # Default+# require-stack-version: ">=1.6"+#+# Override the architecture used by stack, especially useful on Windows+# arch: i386+# arch: x86_64+#+# Extra directories used by stack for building+# extra-include-dirs: [/path/to/dir]+# extra-lib-dirs: [/path/to/dir]+#+# Allow a newer minor version of GHC than the snapshot specifies+# compiler-check: newer-minor

@@ -0,0 +1,36 @@+{-# LANGUAGE DataKinds #-}+{-# LANGUAGE Rank2Types #-}+{-# LANGUAGE TypeOperators #-}++-- | Tests for constructing and manipulating CSA matrices+module Main where++import GHC.TypeLits+import qualified Numeric.LinearAlgebra.Static as LA++import CSA++--import Hedgehog+--import qualified Hedgehog.Gen as Gen+--import qualified Hedgehog.Range as Range+import Test.Tasty+import Test.Tasty.Hspec+--import Test.Tasty.Hedgehog++-- | Test entrypoint+main :: IO ()+main = do+    unitTree <- testSpec "CSA" unitTests+    Test.Tasty.defaultMain unitTree++equal :: (KnownNat m, KnownNat n) => LA.L m n -> LA.L m n -> Bool+equal x y = (LA.extract x) == (LA.extract y)++unitTests :: Spec+unitTests = do+    it "Can construct an empty matrix" $+      LA.size (toAdjacencyMatrix None :: AdjacencyMatrix 2 3) `shouldBe` (2, 3)+    it "Can construct a one-to-one matrix" $+      equal (toAdjacencyMatrix (OneToOne 1) :: AdjacencyMatrix 2 2) (LA.matrix [1, 0, 0, 1] :: LA.L 2 2) `shouldBe` True+    it "Can construct a reverse one-to-one matrix" $+      equal (toAdjacencyMatrix (Minus (AllToAll 1) (OneToOne 1))) (LA.matrix [0, 1, 1, 0] :: LA.L 2 2) `shouldBe` True