Merge branch 'dev' into 184-dev-add-nlp-to-gargantext-ini

bin/gargantext_tmux

@@ -4,4 +4,4 @@ tmux new -d -s gargantext './server' \; \
             split-window -h -d 'cd ./purescript-gargantext ; ./server' \; \
             select-pane -t 1 \; \
             split-window -d    'cd deps/nlp/CoreNLP ; ./startServer.sh' \; \
-            split-window -d    'cd deps/nlp/spacy-server ; source env/bin/activate ; ./server' \; \
+            split-window -d    'cd deps/nlp/spacy-server ; docker-compose up' \; \

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 1.12
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.9.7.4
+version: 0.0.6.9.8.1
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -45,6 +45,7 @@ library
       Gargantext.API.Node.Share
       Gargantext.API.Prelude
       Gargantext.Core
+      Gargantext.Core.NLP
       Gargantext.Core.Methods.Similarities
       Gargantext.Core.NLP
       Gargantext.Core.NodeStory

nix/pkgs.nix

@@ -3,6 +3,61 @@
 rec {
   inherit pkgs;
   ghc = pkgs.haskell.compiler.ghc8107;
+  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 = [ "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=ON"
+      "-DIGRAPH_OPENMP_SUPPORT=ON"
+      "-DIGRAPH_ENABLE_LTO=AUTO"
+      "-DIGRAPH_ENABLE_TLS=ON"
+      "-DBUILD_SHARED_LIBS=ON"
+    ];
+
+    postInstall = ''
+      mkdir -p "$out/share"
+      cp -r doc "$out/share"
+    '';
+
+    postFixup = previousAttrs.postFixup + ''
+      CUR_DIR=$PWD
+      cd "$out/include/igraph" && cp *.h ../
+      cd $CUR_DIR
+    '';
+
+  });
   hsBuildInputs = [
     ghc
     pkgs.cabal-install
@@ -16,9 +71,8 @@ rec {
     gsl
     #haskell-language-server
     hlint
-    igraph
     libffi
-    liblapack
+    lapack
     lzma
     pcre
     pkgconfig
@@ -32,6 +86,7 @@ rec {
     icu
     graphviz
     llvm_9
+    igraph_0_10_4
   ] ++ ( lib.optionals stdenv.isDarwin [
        darwin.apple_sdk.frameworks.Accelerate
        ]);

package.yaml

@@ -6,7 +6,7 @@ name: gargantext
 #         | | | +-----  Layers * : New versions with API additions
 #         | | | | +---  Layers * : New versions without API breaking changes
 #         | | | | |
-version: '0.0.6.9.7.4'
+version: '0.0.6.9.8.1'
 synopsis: Search, map, share
 description: Please see README.md
 category: Data
@@ -70,6 +70,7 @@ library:
   - Gargantext.API.Node.Share
   - Gargantext.API.Prelude
   - Gargantext.Core
+  - Gargantext.Core.NLP
   - Gargantext.Core.Methods.Similarities
   - Gargantext.Core.NodeStory
   - Gargantext.Core.Text

src/Gargantext/Core/Viz/Graph/Tools.hs

@@ -117,12 +117,11 @@ cooc2graphWith' :: Partitions
                 -> Strength
                 -> HashMap (NgramsTerm, NgramsTerm) Int
                 -> IO Graph
-cooc2graphWith' _doPartitions _bridgenessMethod multi similarity@Conditional threshold strength myCooc = do
+cooc2graphWith' _doPartitions _bridgenessMethod multi similarity threshold strength myCooc = do
   let (distanceMap, diag, ti) = doSimilarityMap similarity threshold strength myCooc
   distanceMap `seq` diag `seq` ti `seq` return ()
 
   partitions <- if (Map.size distanceMap > 0)
-      -- then recursiveClustering doPartitions distanceMap
       then recursiveClustering' (spinglass' 1) distanceMap
       else panic $ Text.unlines [ "[Gargantext.C.V.Graph.Tools] Similarity Matrix is empty"
                                 , "Maybe you should add more Map Terms in your list"
@@ -133,35 +132,7 @@ cooc2graphWith' _doPartitions _bridgenessMethod multi similarity@Conditional thr
   let
     !confluence' = BAC.computeConfluences 3 (Map.keys distanceMap) True
     !bridgeness' = bridgeness (Bridgeness_Recursive partitions 1.0 similarity) distanceMap
-{-
-    !bridgeness' = if bridgenessMethod == BridgenessMethod_Basic
-                      then bridgeness (Bridgeness_Basic partitions 1.0) distanceMap
-                      else bridgeness (Bridgeness_Advanced similarity confluence') distanceMap
--}
-  pure $ data2graph multi ti diag bridgeness' confluence' (setNodes2clusterNodes $ List.concat partitions)
 
-cooc2graphWith' _doPartitions _bridgenessMethod multi similarity@Distributional threshold strength myCooc = do
-  let (distanceMap, diag, ti) = doSimilarityMap Distributional threshold strength myCooc
-  distanceMap `seq` diag `seq` ti `seq` return ()
-
-  partitions <- if (Map.size distanceMap > 0)
-      --then recursiveClustering doPartitions distanceMap
-      then recursiveClustering' (spinglass' 1) distanceMap
-      else panic $ Text.unlines [ "[Gargantext.C.V.Graph.Tools] Similarity Matrix is empty"
-                                , "Maybe you should add more Map Terms in your list"
-                                , "Tutorial: TODO"
-                                ]
-  length partitions `seq` return ()
-
-  let
-    !confluence' = BAC.computeConfluences 3 (Map.keys distanceMap) True
-    !bridgeness' = bridgeness (Bridgeness_Recursive partitions 1.0 similarity) distanceMap
-{-
-    !bridgeness' = if bridgenessMethod == BridgenessMethod_Basic
-                      then bridgeness (Bridgeness_Basic partitions 1.0) distanceMap
-                      else bridgeness (Bridgeness_Advanced Distributional confluence') distanceMap
-  pure $ data2graph multi ti diag bridgeness' confluence' partitions
--}
   pure $ data2graph multi ti diag bridgeness' confluence' (setNodes2clusterNodes $ List.concat partitions)
 
 
@@ -239,7 +210,6 @@ nodeTypeWith (MultiPartite (Partite s1 t1) (Partite _s2 t2)) t =
      then t1
      else t2
 
-
 data2graph :: MultiPartite
            -> Map NgramsTerm Int
            -> Map (Int, Int) Occurrences

src/Gargantext/Core/Viz/Phylo.hs

@@ -201,6 +201,7 @@ data PhyloSubConfig =
                  , _sc_timeUnit       :: TimeUnit
                  , _sc_clique         :: Cluster
                  , _sc_exportFilter   :: Double
+                 , _sc_defaultMode    :: Bool
                  }
   deriving (Show,Generic,Eq)
 

stack.yaml

@@ -102,7 +102,8 @@ extra-deps:
 #- git: https://github.com/alpmestan/haskell-igraph.git
 #  commit: 9f55eb36639c8e0965c8bc539a57738869f33e9a
 - git: https://gitlab.iscpif.fr/gargantext/haskell-igraph.git
-  commit: 03c8885d0166255ed7bf0b624a07610ea68ec02c
+  # 0.10.4-rc1
+  commit: 2a28524134b68421f30f6e97961063018f814a82
 - git: https://gitlab.iscpif.fr/gargantext/haskell-infomap.git
   commit: 6d1d60b952b9b2b272b58fc5539700fd8890ac88