Merge branch 'clusternode-eq-instance' into 'master'

Align side branch with main master

See merge request !2

gargantext-graph.cabal

 cabal-version: 1.12
 
--- This file has been generated from package.yaml by hpack version 0.34.4.
+-- This file has been generated from package.yaml by hpack version 0.34.7.
 --
 -- see: https://github.com/sol/hpack
 
@@ -71,43 +71,6 @@ library
     , vector
   default-language: Haskell2010
 
-executable gargantext-graph-exe
-  main-is: Main.hs
-  other-modules:
-      Paths_gargantext_graph
-  hs-source-dirs:
-      app
-  default-extensions:
-      DataKinds
-      FlexibleInstances
-      OverloadedStrings
-  ghc-options: -O2 -threaded -rtsopts -with-rtsopts=-N -fprof-auto -Wmissing-signatures -Wcompat
-  build-depends:
-      accelerate
-    , accelerate-arithmetic
-    , accelerate-utility
-    , base >=4.7 && <5
-    , bytestring
-    , cassava
-    , cereal
-    , containers
-    , criterion
-    , eigen
-    , fgl
-    , gargantext-graph
-    , haskell-igraph >=0.6.0
-    , hmatrix
-    , lens
-    , pretty-simple
-    , protolude
-    , reflection
-    , singletons
-    , sparse-linear
-    , string-conversions
-    , text
-    , vector
-  default-language: Haskell2010
-
 test-suite gargantext-graph-test
   type: exitcode-stdio-1.0
   main-is: Main.hs

nix/pinned-20.09.nix

+# this version of nixpkgs contains liblapack at ?
+# this version of nixpkgs contains gsl at ?
+import (builtins.fetchGit {
+  # Descriptive name to make the store path easier to identify
+  name = "nixos-20.09";
+  url = "https://github.com/nixos/nixpkgs/";
+  # `git ls-remote https://github.com/nixos/nixpkgs-channels nixos-20.09`
+  ref = "refs/heads/nixos-20.09";
+  rev = "69f3a9705014ce75b0489404210995fb6f29836e";
+})

nix/pinned-21.05.nix

+import (builtins.fetchGit {
+  name = "nixos-21.05";
+  url = "https://github.com/nixos/nixpkgs";
+  ref = "refs/heads/nixos-21.05";
+  rev = "7e9b0dff974c89e070da1ad85713ff3c20b0ca97";
+})

nix/pinned-22.05.nix

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

nix/pkgs.nix

+{ pkgs ? import ./pinned-22.05.nix {} }:
+
+rec {
+  inherit pkgs;
+  ghc = pkgs.haskell.compiler.ghc8104;
+  hsBuildInputs = [
+    ghc
+    pkgs.cabal-install
+  ];
+  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
+  ];
+  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}"
+  '';
+  shell = pkgs.mkShell {
+    name = "gargantext-shell";
+    buildInputs = hsBuildInputs ++ nonhsBuildInputs;
+    inherit shellHook;
+  };
+}

nix/shell.nix

+(import ./pkgs.nix {}).shell

nix/stack-shell.nix

+let ourpkgs = import ./pkgs.nix {};
+    pkgs = ourpkgs.pkgs;
+in
+pkgs.haskell.lib.buildStackProject rec {
+  name = "gargantext";
+  ghc = ourpkgs.ghc;
+  buildInputs = ourpkgs.nonhsBuildInputs;
+  shellHook = ourpkgs.shellHook;
+}

package.yaml

@@ -50,21 +50,21 @@ default-extensions:
 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
+# 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:

src/Data/Array/Accelerate/Utils.hs

@@ -134,7 +134,7 @@ condOrDefault
 condOrDefault theCond def x = permute const zeros filterInd x
   where 
     zeros = fill (shape x) (def)
-    filterInd ix = (cond (theCond ix)) (Just_ ix) Nothing_
+    filterInd ix = cond (theCond ix) (Just_ ix) Nothing_
 
 -----------------------------------------------------------------------
 _runExp :: Elt e => Exp e -> e
@@ -308,7 +308,7 @@ sumRowMin n m = {-trace (P.show $ run m') $-} m'
        $ P.map (\z -> sumRowMin1 n (constant z) m) [0..n-1]
 
 sumRowMin1 :: (Num a, Ord a) => Dim -> Exp Int -> Acc (Matrix a) -> Acc (Vector a)
-sumRowMin1 n x m = {- trace (P.show (run m,run $ transpose m)) $ -} m''
+sumRowMin1 n x m = m''
   where
     m'' = sum $ zipWith min (transpose m) m
     _m'  = zipWith (*) (zipWith (*) (nullOf n (MatCol x)) $ nullOfWithDiag n (MatRow x)) m

src/Graph/Types.hs

@@ -40,4 +40,5 @@ data ClusterNode = ClusterNode
   , cl_community_id :: Int
   } deriving Show
 
-
+instance Eq ClusterNode where
+  ClusterNode n1 c1 == ClusterNode n2 c2 = (n1 == n2) && (c1 == c2)

stack.yaml

-# 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
-#
-# The location of a snapshot can be provided as a file or url. Stack assumes
-# a snapshot provided as a file might change, whereas a url resource does not.
-#
-# resolver: ./custom-snapshot.yaml
-# resolver: https://example.com/snapshots/2018-01-01.yaml
-
 resolver:
-  url: https://raw.githubusercontent.com/commercialhaskell/stackage-snapshots/master/lts/17/10.yaml
-allow-newer: true
-# 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
-#   subdirs:
-#   - auto-update
-#   - wai
+ url: https://raw.githubusercontent.com/commercialhaskell/stackage-snapshots/master/lts/18/28.yaml
+flags:
+    accelerate:
+        debug: false
+extra-package-dbs: []
+skip-ghc-check: true
 packages:
 - .
-  #- '../eigen/'
-  # Dependency packages to be pulled from upstream that are not in the resolver.
-# These entries can reference officially published versions as well as
-# forks / in-progress versions pinned to a git hash. For example:
-#
+
+docker:
+  enable: false
+  #enable: true
+  repo: 'cgenie/stack-build:lts-18.18-garg'
+  #repo: 'cgenie/nixos-stack:latest'
+
+skip-ghc-check: true
+
+nix:
+  enable: false
+  add-gc-roots: true
+  shell-file: nix/stack-shell.nix
+
+allow-newer: true
+
 extra-deps:
-- git: https://github.com/kaizhang/haskell-igraph.git
-  commit: d790e030e6e08b04dc0971221b6054d6700d82e7
-- git: https://gitlab.iscpif.fr/anoe/accelerate.git
-  commit: f5c0e0071ec7b6532f9a9cd3eb33d14f340fbcc9
-- git: https://gitlab.iscpif.fr/anoe/accelerate-utility.git
-  commit: 83ada76e78ac10d9559af8ed6bd4064ec81308e4
+- git: https://github.com/alpmestan/haskell-igraph.git
+  commit: 9f55eb36639c8e0965c8bc539a57738869f33e9a
+- git: https://github.com/alpmestan/accelerate.git
+  commit: 640b5af87cea94b61c7737d878e6f7f2fca5c015
+- git: https://gitlab.iscpif.fr/amestanogullari/accelerate-utility.git
+  commit: a3875fe652d3bb5acb522674c22c6c814c1b4ad0
 - git: https://github.com/alpmestan/sparse-linear.git
   commit: bc6ca8058077b0b5702ea4b88bd4189cfcad267a
   subdirs:
@@ -52,7 +38,8 @@ extra-deps:
   commit: b9fca8beee0f23c17a6b2001ec834d071709e6e7
   subdirs:
     - packages/base
-- accelerate-arithmetic-1.0.0.1@sha256:555639232aa5cad411e89247b27871d09352b987a754230a288c690b6de6d888,2096
+- git: https://github.com/alpmestan/accelerate-arithmetic.git
+  commit: a110807651036ca2228a76507ee35bbf7aedf87a
 - eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
 
 - vector-0.12.3.0
@@ -61,26 +48,7 @@ ghc-options:
   sparse-linear: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
   gargantext-graph: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
 
-
-# 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: ">=2.5"
-#
-# 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
+ghc-options:
+  hmatrix: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
+  sparse-linear: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack
+  gargantext-graph: -O2 -fsimpl-tick-factor=10000 -fdicts-cheap -fdicts-strict -flate-dmd-anal  -fno-state-hack