Split the project in 3

This commit splits the project in 3 sub-projects:

1. `gargantext-graph-core`: it contains the plain algorithms on graphs;
2. `gargantext-graph-accelerate`: accelerate utilities on graphs;
3. `gargantext-graph-eigin`: eigen utilities on graphs;

.gitignore

@@ -2,3 +2,5 @@
 *~
 *lock
 dist-newstyle
+.DS_Store**
+cabal.project.local

cabal.project

-packages: .
+packages: gargantext-graph-core
+          gargantext-graph-accelerate
+          gargantext-graph-eigen
 
 index-state: 2025-02-17T10:13:39Z
 
@@ -26,16 +28,6 @@ source-repository-package
     location: https://github.com/AccelerateHS/accelerate.git
     tag: 334d05519436bb7f20f9926ec76418f5b8afa359
 
-source-repository-package
-    type: git
-    location: https://github.com/alpmestan/accelerate-arithmetic.git
-    tag: a110807651036ca2228a76507ee35bbf7aedf87a
-
-source-repository-package
-    type: git
-    location: https://gitlab.iscpif.fr/amestanogullari/accelerate-utility.git
-    tag: a3875fe652d3bb5acb522674c22c6c814c1b4ad0
-
 source-repository-package
     type: git
     location: https://github.com/alpmestan/hmatrix.git

cabal.project.freeze

@@ -10,8 +10,6 @@ constraints: any.Cabal ==3.10.3.0,
              any.StateVar ==1.2.2,
              any.accelerate ==1.3.0.0,
              accelerate +bounds-checks -debug -internal-checks -nofib -unsafe-checks,
-             any.accelerate-arithmetic ==1.0.0.1,
-             any.accelerate-utility ==1.0.0.1,
              any.adjunctions ==4.4.2,
              any.aeson ==2.2.3.0,
              aeson +ordered-keymap,

gargantext-graph-accelerate/gargantext-graph-accelerate.cabal

+cabal-version: 1.12
+
+-- This file has been generated from package.yaml by hpack version 0.34.7.
+--
+-- see: https://github.com/sol/hpack
+
+name:           gargantext-graph-accelerate
+version:        0.1.0.0
+description:    Please see the README on GitHub at <https://github.com/githubuser/gargantext-graph#readme>
+homepage:       https://github.com/gargantext/gargantext-graph#readme
+bug-reports:    https://github.com/gargantext/gargantext-graph/issues
+author:         Alexandre Delanoë
+maintainer:     alexandre+dev@delanoe.org
+copyright:      2021 CNRS / Alexandre Delanoë
+license:        AGPL
+license-file:   LICENSE
+build-type:     Simple
+extra-source-files:
+    README.md
+    ChangeLog.md
+
+source-repository head
+  type: git
+  location: https://github.com/gargantext/gargantext-graph
+
+library
+  exposed-modules:
+      Data.Array.Accelerate.Utils
+  other-modules:
+      Paths_gargantext_graph_accelerate
+  hs-source-dirs:
+      src
+  default-extensions:
+      DataKinds
+      FlexibleInstances
+      OverloadedStrings
+  build-depends:
+      accelerate
+    , base >=4.7 && <5
+    , protolude
+  default-language: Haskell2010

src/Data/Array/Accelerate/Utils.hs → gargantext-graph-accelerate/src/Data/Array/Accelerate/Utils.hs

@@ -33,7 +33,6 @@ module Data.Array.Accelerate.Utils
   where
 
 import qualified Data.Foldable as P (foldl1)
-import Debug.Trace (trace)
 import Data.Array.Accelerate
 import Data.Array.Accelerate.Interpreter (run)
 import qualified Protolude as P
@@ -417,14 +416,7 @@ theMatrixInt n = matrix n (dataMatrix n)
                                  ]
 
 
-                 | P.otherwise = P.undefined
-
-{-
-theResult :: Int -> Matrix Double
-theResult n | (P.==) n 2 = let r = 1.6094379124341003 in [ 0, r, r, 0]
-          | P.otherwise = [ 1, 1 ]
--}
-
+                 | P.otherwise = error "undefined"
 
 colMatrix :: Elt e
           => Int -> [e] -> Acc (Array ((Z :. Int) :. Int) e)

gargantext-graph.cabal → gargantext-graph-core/gargantext-graph-core.cabal

@@ -25,8 +25,6 @@ source-repository head
 
 library
   exposed-modules:
-      Data.Array.Accelerate.Utils
-      Data.Eigen.Coeff
       Graph.BAC.Clustering
       Graph.BAC.Proxemy
       Graph.BAC.ProxemyOptim
@@ -48,15 +46,11 @@ library
       FlexibleInstances
       OverloadedStrings
   build-depends:
-      accelerate
-    , accelerate-arithmetic
-    , accelerate-utility
-    , base >=4.7 && <5
+      base >=4.7 && <5
     , bytestring
     , cassava
     , cereal
     , containers
-    , eigen
     , fgl
     , haskell-igraph >=0.6.0
     , hmatrix
@@ -85,15 +79,11 @@ test-suite gargantext-graph-test
   ghc-options: -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       QuickCheck
-    , accelerate
-    , accelerate-arithmetic
-    , accelerate-utility
     , base >=4.7 && <5
     , bytestring
     , cassava
     , cereal
     , containers
-    , eigen
     , fgl
     , gargantext-graph
     , haskell-igraph >=0.10.4

src/Graph/Tools/CSV.hs → gargantext-graph-core/src/Graph/Tools/CSV.hs

@@ -157,10 +157,10 @@ csvDecodeOptions x = defaultDecodeOptions {decDelimiter = delimiter}
     delimiter = fromIntegral $ ord x
 
 ------------------------------------------------------------------------
-data SnapCsv = 
+data SnapCsv =
   SnapCsv { sc_fromNodeId :: Int
           , sc_toNodeId   :: Int
-	  }
+  }
     deriving (Show)
 
 instance FromNamedRecord SnapCsv where

src/Graph/Tools/Random.hs → gargantext-graph-core/src/Graph/Tools/Random.hs

@@ -21,8 +21,6 @@ import Data.Vector hiding (map, uniq)
 import Prelude (read)
 import Protolude
 import Graph.Types
--- import qualified Eigen.SparseMatrix                as SMatrix
--- import qualified Eigen.Matrix                      as DMatrix
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import qualified Data.Set                          as Set
 import qualified Data.Vector                       as Vector

src/Graph/Types.hs → gargantext-graph-core/src/Graph/Types.hs

@@ -15,8 +15,6 @@ module Graph.Types where
 
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import Data.IntMap (IntMap)
--- import qualified Eigen.Matrix as DenseMatrix
--- import Eigen.SparseMatrix (SparseMatrix)
 
 import qualified Data.Matrix.Sparse.Static    as Sparse
 import qualified Data.Vector.Unboxed          as VU
@@ -30,7 +28,7 @@ type Dict = IntMap
 -- | Use the optimized version of Graph
 type Graph a b = DGIP.Gr a b
 
--- | Type for Matrix computation optimizations (with Eigen)
+-- | Type for Matrix computation optimizations
 type MatrixD          n = Dense.L n n
 type MatrixS          n = Sparse.Matrix n n Double
 

gargantext-graph-eigen/gargantext-graph-eigen.cabal

+cabal-version: 1.12
+
+name:           gargantext-graph-eigen
+version:        0.1.0.0
+description:    Please see the README on GitHub at <https://github.com/githubuser/gargantext-graph#readme>
+homepage:       https://github.com/gargantext/gargantext-graph#readme
+bug-reports:    https://github.com/gargantext/gargantext-graph/issues
+author:         Alexandre Delanoë
+maintainer:     alexandre+dev@delanoe.org
+copyright:      2021 CNRS / Alexandre Delanoë
+license:        AGPL
+license-file:   LICENSE
+build-type:     Simple
+extra-source-files:
+    README.md
+    ChangeLog.md
+
+source-repository head
+  type: git
+  location: https://github.com/gargantext/gargantext-graph
+
+library
+  exposed-modules:
+      Data.Eigen.Coeff
+  other-modules:
+      Paths_gargantext_graph_eigen
+  hs-source-dirs:
+      src
+  default-extensions:
+      DataKinds
+      FlexibleInstances
+      OverloadedStrings
+  build-depends:
+      base >=4.7 && <5
+    , eigen
+    , reflection
+  default-language: Haskell2010

src/Data/Eigen/Coeff.hs → gargantext-graph-eigen/src/Data/Eigen/Coeff.hs

@@ -16,7 +16,9 @@ Author: Alp Mestanogullari (Well Typed)
 module Data.Eigen.Coeff (coeffSM, coeffDM)
   where
 
-import Eigen.Internal (Row(..), Col(..), Elem(..))
+import Prelude hiding (pi)
+
+import Eigen.Internal (Row(..), Col(..), Elem)
 import Data.Maybe (fromMaybe)
 import Data.Proxy
 import Data.Reflection

package.yaml

-name:                gargantext-graph
-version:             0.1.0.0
-github:              gargantext/gargantext-graph
-license:             AGPL
-author:              "Alexandre Delanoë"
-maintainer:          "alexandre+dev@delanoe.org"
-copyright:           "2021 CNRS / Alexandre Delanoë"
-
-extra-source-files:
-- README.md
-- ChangeLog.md
-
-# Metadata used when publishing your package
-# synopsis:            Short description of your package
-# category:            Web
-
-# To avoid duplicated efforts in documentation and dealing with the
-# complications of embedding Haddock markup inside cabal files, it is
-# common to point users to the README.md file.
-description:         Please see the README on GitHub at <https://github.com/githubuser/gargantext-graph#readme>
-
-dependencies:
-- accelerate
-- accelerate-arithmetic
-- accelerate-utility
-- base >= 4.7 && < 5
-- bytestring
-- cassava
-- cereal     # (IGraph)
-- containers
-- eigen
-- fgl
-- haskell-igraph >= 0.6.0
-- hmatrix
-- lens
-- pretty-simple
-- protolude
-- reflection
-- sparse-linear
-- singletons
-- string-conversions
-- text
-- vector
-
-default-extensions:
-- DataKinds
-- FlexibleInstances
-- OverloadedStrings
-
-library:
-  source-dirs: src
-
-# executables:
-#   gargantext-graph-exe:
-#     main:                Main.hs
-#     source-dirs:         app
-#     ghc-options:
-#     - -O2
-#     - -threaded
-#     - -rtsopts
-#     - -with-rtsopts=-N
-#     - -fprof-auto
-#     - -Wmissing-signatures
-#     - -Wcompat
-#     dependencies:
-#     - gargantext-graph
-#     - criterion
-
-tests:
-  gargantext-graph-test:
-    main:                Main.hs
-    source-dirs:         test
-    ghc-options:
-    - -threaded
-    - -rtsopts
-    - -with-rtsopts=-N
-    dependencies:
-    - gargantext-graph
-    - hspec
-    - QuickCheck

run

-#!/bin/bash
-
-#~/.local/bin/gargantext-graph-exe $1 +RTS -p # -sstderr
-#time ~/.local/bin/gargantext-graph-exe +RTS -p # -sstderr
-
-
-#for beta in -0.6 -0.5 -0.3 -0.2 -0.1 0.0 0.3 0.4 0.5 0.6 0.7; do
-for beta in 0.0 O.5 1.0 ; do
-  for gc in "gc" ; do
-    echo "$beta,$gc";
-    OUTPUT1=${1%csv}_${beta}_${gc}.txt;
-    OUTPUT2=${1%csv}_${beta}_${gc}.clusters.txt;
-    touch $OUTPUT1;
-    time ~/.local/bin/gargantext-graph-exe $1 $OUTPUT2 $gc $beta >> $OUTPUT1 ;
-  done
-done
-

stack.yaml

@@ -38,9 +38,6 @@ extra-deps:
   commit: b9fca8beee0f23c17a6b2001ec834d071709e6e7
   subdirs:
     - packages/base
-- git: https://github.com/alpmestan/accelerate-arithmetic.git
-  commit: a110807651036ca2228a76507ee35bbf7aedf87a
-- eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
 
 - vector-0.12.3.0
 ghc-options: