Merge branch 'adinapoli/issue-3' into 'master'

Upgrade nixpkgs, use GHC 9.6.6, make it build with cabal

Closes #3

See merge request !1

.gitignore

 .stack-work/
 *~
 *lock
+dist-newstyle
+.DS_Store**
+cabal.project.local

.gitlab-ci.yml

+image: adinapoli/gargantext:v3.5
+
+variables:
+  STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"
+  STACK_OPTS: "--system-ghc"
+  STORE_DIR: "${CI_PROJECT_DIR}/.cabal"
+  CORENLP: "4.5.4"
+  FF_USE_FASTZIP: "true"
+  ARTIFACT_COMPRESSION_LEVEL: "fast"
+  CACHE_COMPRESSION_LEVEL: "fast"
+
+stages:
+  - cabal
+  - test
+
+cabal:
+  stage: cabal
+  cache:
+    key: cabal.project
+    paths:
+      - dist-newstyle/
+      - .cabal/
+    policy: pull-push
+  script:
+    - nix-shell --run "./bin/update-project-dependencies $STORE_DIR && cabal --store-dir=$STORE_DIR v2-build all --ghc-options='-O0'"
+  allow_failure: false
+
+test:
+  stage: test
+  cache:
+    key: cabal.project
+    paths:
+      - dist-newstyle/
+      - .cabal/
+    policy: pull-push
+  script:
+    - |
+      nix-shell --run "cd /builds/gargantext/haskell-gargantext; $CABAL --store-dir=$STORE_DIR v2-test --test-show-details=streaming --ghc-options='-O0'\""

app/Main.hs

@@ -29,8 +29,6 @@ import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import qualified Data.Matrix.Sparse        as SL
 import qualified Data.Matrix.Sparse.Static as SLS
 
-import Criterion
-import Criterion.Main
 import qualified Data.Vector.Sparse.Static as SLV
 import Graph.Tools.Random (randomAdjacency)
 import Data.Reflection

cabal.project

+packages: gargantext-graph-core
+          gargantext-graph-accelerate
+          gargantext-graph-eigen
+
+index-state: 2025-02-17T10:13:39Z
+
+allow-newer:
+           , *:base
+           , eigen:constraints
+           , eigen:transformers
+           , eigen:primitive
+           , accelerate-utility:accelerate
+           , accelerate-arithmetic:accelerate
+
+source-repository-package
+    type: git
+    location: https://github.com/alpmestan/sparse-linear.git
+    tag: bc6ca8058077b0b5702ea4b88bd4189cfcad267a
+    subdir: sparse-linear
+
+source-repository-package
+    type: git
+    location: https://github.com/chessai/eigen.git
+    tag: 1790fdf9138970dde0dbabf8b270698145a4a88c
+
+source-repository-package
+    type: git
+    location: https://github.com/AccelerateHS/accelerate.git
+    tag: 334d05519436bb7f20f9926ec76418f5b8afa359
+
+source-repository-package
+    type: git
+    location: https://github.com/alpmestan/hmatrix.git
+    tag: b9fca8beee0f23c17a6b2001ec834d071709e6e7
+    subdir: packages/base
+
+source-repository-package
+    type: git
+    location: https://gitlab.iscpif.fr/gargantext/haskell-igraph.git
+    tag: 8c09f4cfa2de2ee7569b3ada508c5302360e8f42

cabal.project.freeze

+active-repositories: hackage.haskell.org:merge
+constraints: any.Cabal ==3.10.3.0,
+             any.Cabal-syntax ==3.10.3.0,
+             any.Glob ==0.10.2,
+             any.HUnit ==1.6.2.0,
+             any.OneTuple ==0.4.2,
+             any.Only ==0.1,
+             any.QuickCheck ==2.15.0.1,
+             QuickCheck -old-random +templatehaskell,
+             any.StateVar ==1.2.2,
+             any.accelerate ==1.3.0.0,
+             accelerate +bounds-checks -debug -internal-checks -nofib -unsafe-checks,
+             any.adjunctions ==4.4.2,
+             any.aeson ==2.2.3.0,
+             aeson +ordered-keymap,
+             any.alex ==3.5.2.0,
+             any.ansi-terminal ==1.1.2,
+             ansi-terminal -example,
+             any.ansi-terminal-types ==1.1,
+             any.array ==0.5.6.0,
+             any.assoc ==1.1.1,
+             assoc -tagged,
+             any.async ==2.2.5,
+             async -bench,
+             any.attoparsec ==0.14.4,
+             attoparsec -developer,
+             any.barbies ==2.1.1.0,
+             any.base ==4.18.2.1,
+             any.base-compat ==0.14.1,
+             any.base-compat-batteries ==0.14.1,
+             any.base-orphans ==0.9.3,
+             any.bifunctors ==5.6.2,
+             bifunctors +tagged,
+             any.binary ==0.8.9.1,
+             any.binary-orphans ==1.0.5,
+             any.bitvec ==1.1.5.0,
+             bitvec +simd,
+             any.boring ==0.2.2,
+             boring +tagged,
+             any.bytestring ==0.11.5.3,
+             any.c2hs ==0.28.8,
+             c2hs +base3 -regression,
+             any.cabal-doctest ==1.0.11,
+             any.call-stack ==0.4.0,
+             any.cassava ==0.5.3.2,
+             any.cereal ==0.5.8.3,
+             cereal -bytestring-builder,
+             any.character-ps ==0.1,
+             any.clock ==0.8.4,
+             clock -llvm,
+             any.code-page ==0.2.1,
+             any.colour ==2.3.6,
+             any.comonad ==5.0.9,
+             comonad +containers +distributive +indexed-traversable,
+             any.concurrent-output ==1.10.21,
+             any.conduit ==1.3.6,
+             any.constraints ==0.14.2,
+             any.containers ==0.6.7,
+             any.contravariant ==1.5.5,
+             contravariant +semigroups +statevar +tagged,
+             any.criterion ==1.6.4.0,
+             criterion -embed-data-files -fast,
+             any.criterion-measurement ==0.2.3.0,
+             criterion-measurement -fast,
+             any.data-default ==0.8.0.0,
+             any.data-default-class ==0.2.0.0,
+             any.data-fix ==0.3.4,
+             any.data-ordlist ==0.4.7.0,
+             any.deepseq ==1.4.8.1,
+             any.dense-linear-algebra ==0.1.0.0,
+             any.directory ==1.3.8.5,
+             any.distributive ==0.6.2.1,
+             distributive +semigroups +tagged,
+             any.dlist ==1.0,
+             dlist -werror,
+             any.double-conversion ==2.0.5.0,
+             double-conversion -developer +embedded_double_conversion,
+             any.eigen ==3.3.7.0,
+             any.erf ==2.0.0.0,
+             any.exceptions ==0.10.7,
+             any.fgl ==5.8.3.0,
+             fgl +containers042,
+             any.filepath ==1.4.300.1,
+             any.formatting ==7.2.0,
+             formatting -no-double-conversion,
+             any.free ==5.2,
+             any.generically ==0.1.1,
+             any.ghc-bignum ==1.3,
+             any.ghc-boot-th ==9.6.6,
+             any.ghc-prim ==0.10.0,
+             any.half ==0.3.2,
+             any.happy ==2.1.5,
+             any.happy-lib ==2.1.5,
+             any.hashable ==1.4.7.0,
+             hashable -arch-native +integer-gmp -random-initial-seed,
+             any.hashtables ==1.4.2,
+             hashtables -bounds-checking -debug -detailed-profiling -portable -sse42 +unsafe-tricks,
+             any.haskell-igraph ==0.10.4,
+             any.haskell-lexer ==1.1.2,
+             any.hedgehog ==1.5,
+             any.hmatrix ==0.20.2,
+             hmatrix -disable-default-paths -no-random_r -openblas,
+             any.hsc2hs ==0.68.10,
+             hsc2hs -in-ghc-tree,
+             any.hspec ==2.11.10,
+             any.hspec-core ==2.11.10,
+             any.hspec-discover ==2.11.10,
+             any.hspec-expectations ==0.8.4,
+             any.indexed-traversable ==0.1.4,
+             any.indexed-traversable-instances ==0.1.2,
+             any.integer-conversion ==0.1.1,
+             any.integer-logarithms ==1.0.4,
+             integer-logarithms -check-bounds +integer-gmp,
+             any.invariant ==0.6.4,
+             any.js-chart ==2.9.4.1,
+             any.kan-extensions ==5.2.6,
+             any.language-c ==0.10.0,
+             language-c +iecfpextension +usebytestrings,
+             any.lens ==5.3.3,
+             lens -benchmark-uniplate -dump-splices +inlining -j +test-hunit +test-properties +test-templates +trustworthy,
+             any.lifted-async ==0.10.2.7,
+             any.lifted-base ==0.2.3.12,
+             any.math-functions ==0.3.4.4,
+             math-functions +system-erf +system-expm1,
+             any.microlens ==0.4.13.1,
+             any.microstache ==1.0.3,
+             any.mmorph ==1.2.0,
+             any.monad-control ==1.0.3.1,
+             any.mono-traversable ==1.0.21.0,
+             any.mtl ==2.3.1,
+             any.mtl-compat ==0.2.2,
+             mtl-compat -two-point-one -two-point-two,
+             any.mwc-random ==0.15.2.0,
+             mwc-random -benchpapi,
+             any.network-uri ==2.6.4.2,
+             any.old-locale ==1.0.0.7,
+             any.optparse-applicative ==0.18.1.0,
+             optparse-applicative +process,
+             any.ordered-containers ==0.2.4,
+             any.os-string ==2.0.7,
+             any.parallel ==3.2.2.0,
+             any.parsec ==3.1.16.1,
+             any.pretty ==1.1.3.6,
+             any.pretty-show ==1.10,
+             any.pretty-simple ==4.1.3.0,
+             pretty-simple -buildexample +buildexe,
+             any.prettyprinter ==1.7.1,
+             prettyprinter -buildreadme +text,
+             any.prettyprinter-ansi-terminal ==1.1.3,
+             any.primitive ==0.9.0.0,
+             any.process ==1.6.19.0,
+             any.profunctors ==5.6.2,
+             any.protolude ==0.3.4,
+             any.quickcheck-io ==0.2.0,
+             any.random ==1.2.1.3,
+             any.reflection ==2.1.9,
+             reflection -slow +template-haskell,
+             any.resourcet ==1.3.0,
+             any.rts ==1.0.2,
+             any.safe ==0.3.21,
+             any.safe-exceptions ==0.1.7.4,
+             any.scientific ==0.3.8.0,
+             scientific -integer-simple,
+             any.semialign ==1.3.1,
+             semialign +semigroupoids,
+             any.semigroupoids ==6.0.1,
+             semigroupoids +comonad +containers +contravariant +distributive +tagged +unordered-containers,
+             any.semigroups ==0.20,
+             semigroups +binary +bytestring -bytestring-builder +containers +deepseq +hashable +tagged +template-haskell +text +transformers +unordered-containers,
+             any.singletons ==3.0.4,
+             any.singletons-base ==3.2,
+             any.singletons-th ==3.2,
+             any.sparse-linear ==0.1.0.0,
+             any.split ==0.2.5,
+             any.splitmix ==0.1.1,
+             splitmix -optimised-mixer,
+             any.statistics ==0.16.3.0,
+             statistics -benchpapi,
+             any.stm ==2.5.1.0,
+             any.storable-complex ==0.2.3.0,
+             any.strict ==0.5.1,
+             any.string-conversions ==0.4.0.1,
+             any.syb ==0.7.2.4,
+             any.system-cxx-std-lib ==1.0,
+             any.tagged ==0.8.9,
+             tagged +deepseq +transformers,
+             any.tasty ==1.5.3,
+             tasty +unix,
+             any.template-haskell ==2.20.0.0,
+             any.terminal-size ==0.3.4,
+             any.text ==2.0.2,
+             any.text-iso8601 ==0.1.1,
+             any.text-short ==0.1.6,
+             text-short -asserts,
+             any.tf-random ==0.5,
+             any.th-abstraction ==0.6.0.0,
+             any.th-compat ==0.1.6,
+             any.th-desugar ==1.15,
+             any.th-expand-syns ==0.4.12.0,
+             any.th-lift ==0.8.6,
+             any.th-orphans ==0.13.16,
+             any.th-reify-many ==0.1.10,
+             any.these ==1.2.1,
+             any.time ==1.12.2,
+             any.time-compat ==1.9.8,
+             any.transformers ==0.6.1.0,
+             any.transformers-base ==0.4.6,
+             transformers-base +orphaninstances,
+             any.transformers-compat ==0.7.2,
+             transformers-compat -five +five-three -four +generic-deriving +mtl -three -two,
+             any.unique ==0.0.1,
+             any.unix ==2.8.4.0,
+             any.unliftio-core ==0.2.1.0,
+             any.unordered-containers ==0.2.20,
+             unordered-containers -debug,
+             any.utf8-string ==1.0.2,
+             any.utility-ht ==0.0.17.2,
+             any.uuid-types ==1.0.6,
+             any.vector ==0.13.2.0,
+             vector +boundschecks -internalchecks -unsafechecks -wall,
+             any.vector-algorithms ==0.9.1.0,
+             vector-algorithms +bench +boundschecks -internalchecks -llvm -unsafechecks,
+             any.vector-binary-instances ==0.2.5.2,
+             any.vector-stream ==0.1.0.1,
+             any.vector-th-unbox ==0.2.2,
+             any.void ==0.7.3,
+             void -safe,
+             any.witherable ==0.5,
+             any.wl-pprint-annotated ==0.1.0.1
+index-state: hackage.haskell.org 2025-02-17T10:13:39Z

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
@@ -85,23 +79,20 @@ 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 >=0.6.0
+    , haskell-igraph >=0.10.4
     , hmatrix
     , hspec
     , lens
     , pretty-simple
     , protolude
+    , random
     , reflection
     , singletons
     , sparse-linear

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

nix/pinned-22.05.nix

@@ -2,5 +2,5 @@ import (builtins.fetchGit {
   name = "nixos-22.05";
   url = "https://github.com/nixos/nixpkgs";
   ref = "refs/heads/nixos-22.05";
-  rev = "7e9b0dff974c89e070da1ad85713ff3c20b0ca97";
+  rev = "ce6aa13369b667ac2542593170993504932eb836";
 })

nix/pinned-23.11.nix

+import (builtins.fetchGit {
+  name = "nixos-23.11";
+  url = "https://github.com/nixos/nixpkgs";
+  ref = "refs/heads/nixos-23.11";
+  rev = "057f9aecfb71c4437d2b27d3323df7f93c010b7e";
+})

nix/pinned-25.05.darwin.nix

+import (builtins.fetchTarball "https://github.com/NixOS/nixpkgs/archive/32fb99ba93fea2798be0e997ea331dd78167f814.tar.gz")

nix/pinned-25.05.nix

+import (builtins.fetchTarball "https://github.com/NixOS/nixpkgs/archive/c46290747b2aaf090f48a478270feb858837bf11.tar.gz")

nix/pkgs.nix

-{ pkgs ? import ./pinned-22.05.nix {} }:
+{ pkgs ? import (if builtins.elem builtins.currentSystem ["x86_64-darwin" "aarch64-darwin"]
+                 then ./pinned-25.05.darwin.nix
+                 else ./pinned-25.05.nix) {} }:
 
 rec {
   inherit pkgs;
-  ghc = pkgs.haskell.compiler.ghc8104;
+  ghc = pkgs.haskell.compiler.ghc966;
+  igraph_0_10_4 = pkgs.igraph.overrideAttrs (finalAttrs: previousAttrs: {
+    version = "0.10.4";
+
+    src = pkgs.fetchFromGitHub {
+      owner = "igraph";
+      repo = "igraph";
+      rev = "0.10.4";
+      hash = "sha256-LsTOxUktGZcp46Ec9QH3+9C+VADMYTZZCjKF1gp36xk=";
+    };
+
+    postPatch = ''
+      echo "0.10.4" > IGRAPH_VERSION
+    '';
+
+    outputs = [ "dev" "out" "doc" ];
+
+    buildInputs = [
+      pkgs.arpack
+      pkgs.blas
+      pkgs.glpk
+      pkgs.gmp
+      pkgs.lapack
+      pkgs.libxml2
+      pkgs.plfit
+    ] ++ pkgs.lib.optionals pkgs.stdenv.cc.isClang [
+      pkgs.llvmPackages.openmp
+    ];
+
+    cmakeFlags = [
+      "-DIGRAPH_USE_INTERNAL_BLAS=OFF"
+      "-DIGRAPH_USE_INTERNAL_LAPACK=OFF"
+      "-DIGRAPH_USE_INTERNAL_ARPACK=OFF"
+      "-DIGRAPH_USE_INTERNAL_GLPK=OFF"
+      "-DIGRAPH_USE_INTERNAL_GMP=OFF"
+      "-DIGRAPH_USE_INTERNAL_PLFIT=OFF"
+      "-DIGRAPH_GLPK_SUPPORT=ON"
+      "-DIGRAPH_GRAPHML_SUPPORT=OFF"
+      "-DIGRAPH_OPENMP_SUPPORT=ON"
+      "-DIGRAPH_ENABLE_LTO=AUTO"
+      "-DIGRAPH_ENABLE_TLS=ON"
+      "-DBUILD_SHARED_LIBS=ON"
+    ];
+
+    doCheck = false;
+
+    postInstall = ''
+      mkdir -p "$out/share"
+      cp -r doc "$out/share"
+    '';
+
+    postFixup = previousAttrs.postFixup + ''
+      echo "Copying files where they belong .."
+      CUR_DIR=$PWD
+      cd "$dev/include/igraph" && cp *.h ../
+      cd $CUR_DIR
+    '';
+
+  });
   hsBuildInputs = [
     ghc
     pkgs.cabal-install
+    pkgs.blas
+    pkgs.lapack
   ];
   nonhsBuildInputs = with pkgs; [
-    bzip2
-    czmq
-    docker-compose
-    git
-    gmp
-    gsl
-    #haskell-language-server
-    hlint
-    igraph
-    libffi
-    liblapack
-    lzma
-    pcre
-    pkgconfig
-    postgresql
-    xz
-    zlib
-    blas
-    gfortran7
-    #    gfortran7.cc.lib
-    expat
-    icu
-    graphviz
-    llvm_9
-  ];
+    igraph_0_10_4
+  ] ++ ( lib.optionals stdenv.isDarwin [
+       darwin.apple_sdk.frameworks.Accelerate
+       ]);
   libPaths = pkgs.lib.makeLibraryPath nonhsBuildInputs;
   shellHook = ''
-    export LD_LIBRARY_PATH="${pkgs.gfortran7.cc.lib}:${libPaths}:$LD_LIBRARY_PATH"
-    export LIBRARY_PATH="${pkgs.gfortran7.cc.lib}:${libPaths}"
+    export LD_LIBRARY_PATH="${pkgs.gfortran.cc.lib}:${libPaths}:$LD_LIBRARY_PATH"
+    export LIBRARY_PATH="${pkgs.gfortran.cc.lib}:${libPaths}"
   '';
   shell = pkgs.mkShell {
-    name = "gargantext-shell";
+    name = "igraph-shell";
     buildInputs = hsBuildInputs ++ nonhsBuildInputs;
     inherit shellHook;
   };

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
-

shell.nix

+{ pkgs ? import ./nix/pkgs.nix {} }:
+let
+  myBuildInputs = [
+    pkgs.pkgs.docker-compose
+    pkgs.pkgs.haskell-language-server
+    pkgs.pkgs.stack
+  ];
+in
+pkgs.pkgs.mkShell {
+  name = pkgs.shell.name;
+  shellHook = pkgs.shell.shellHook;
+  buildInputs = pkgs.shell.buildInputs ++ myBuildInputs;
+}

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: