[FIX] merge

bin/install

@@ -2,4 +2,4 @@
 
 #stack install --nix --profile --test --fast --no-install-ghc --skip-ghc-check
 
-env LANG=C.UTF-8 stack install --nix --test --no-install-ghc --skip-ghc-check
+env LANG=C.UTF-8 stack install --haddock --nix --test --no-install-ghc --skip-ghc-check

cabal.project

 packages: .
 
 allow-newer: base, accelerate, servant, time, classy-prelude
+allow-newer: binary, primitive, vector
 
 -- Patches
 source-repository-package
@@ -61,12 +62,27 @@ source-repository-package
   location: https://gitlab.iscpif.fr/gargantext/crawlers/hal.git
   tag: 020f5f9b308f5c23c925aedf5fb11f8b4728fb19
 
+source-repository-package
+  type: git
+  location: https://gitlab.iscpif.fr/gargantext/crawlers/arxiv-api.git
+  tag: f3e517cc40d92e282c5245b23d253d2ca3f802e5
+
 -- Graphs
 source-repository-package
   type: git
   location: https://github.com/alpmestan/haskell-igraph.git
   tag: 9f55eb36639c8e0965c8bc539a57738869f33e9a
 
+source-repository-package
+  type: git
+  location: https://gitlab.iscpif.fr/gargantext/haskell-infomap.git
+  tag: 6d1d60b952b9b2b272b58fc5539700fd8890ac88
+
+source-repository-package
+  type: git
+  location: https://gitlab.iscpif.fr/gargantext/gargantext-graph.git
+  tag: f41ee8b53c3264e5aa5adc06b2e5b293d2a8c474
+
 -- Data mining
 source-repository-package
   type: git
@@ -116,16 +132,33 @@ source-repository-package
   tag: fc24987d3af348a677748f226e48d64779a694e9
 
 
--- Accelerate
+-- numerical computing
+source-repository-package
+  type: git
+  location: https://github.com/alpmestan/accelerate.git
+  tag: 640b5af87cea94b61c7737d878e6f7f2fca5c015
+
+source-repository-package
+  type: git
+  location: https://gitlab.iscpif.fr/amestanogullari/accelerate-utility.git
+  tag: a3875fe652d3bb5acb522674c22c6c814c1b4ad0
+
 source-repository-package
   type: git
-  location: https://gitlab.iscpif.fr/anoe/accelerate.git
-  tag: f5c0e0071ec7b6532f9a9cd3eb33d14f340fbcc9
+  location: https://github.com/alpmestan/accelerate-arithmetic.git
+  tag: a110807651036ca2228a76507ee35bbf7aedf87a
 
 source-repository-package
   type: git
-  location: https://gitlab.iscpif.fr/anoe/accelerate-utility.git
-  tag: 83ada76e78ac10d9559af8ed6bd4064ec81308e4
+  location: https://github.com/alpmestan/accelerate-llvm.git
+  tag: 944f5a4aea35ee6aedb81ea754bf46b131fce9e3
+  subdir: accelerate-llvm/ accelerate-llvm-native/
+
+source-repository-package
+  type: git
+  location: https://github.com/alpmestan/hmatrix.git
+  tag: b9fca8beee0f23c17a6b2001ec834d071709e6e7
+  subdir: packages/base/
 
 
 -- Wikidata 
@@ -135,7 +168,22 @@ source-repository-package
   tag: 9637a82344bb70f7fa8f02e75db3c081ccd434ce
 
 
+-- numerical computing
+source-repository-package
+  type: git
+  location: https://github.com/alpmestan/sparse-linear.git
+  tag: bc6ca8058077b0b5702ea4b88bd4189cfcad267a
+  subdir: sparse-linear/
+
+
 constraints: unordered-containers==0.2.14.*,
              servant-ekg==0.3.1,
              time==1.9.3,
-             stm==2.5.0.1
+             stm==2.5.0.1,
+             vector==0.12.3.0,
+             eigen==3.3.7.0,
+             cborg==0.2.6.0,
+             primitive==0.7.3.0
+
+package accelerate
+        flags: +debug
\ No newline at end of file

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 1.12
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.5.9.5
+version:        0.0.5.9.5
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data

nix/pkgs.nix

@@ -18,6 +18,7 @@ rec {
     #haskell-language-server
     hlint
     igraph
+    libffi
     liblapack
     lzma
     pcre
@@ -31,8 +32,7 @@ rec {
     expat
     icu
     graphviz
-    libffi
-    llvmPackages_9.llvm
+    llvm_9
   ];
   libPaths = pkgs.lib.makeLibraryPath nonhsBuildInputs;
   shellHook = ''

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

@@ -132,14 +132,11 @@ cooc2graphWith' doPartitions distance threshold strength myCooc = do
         (as, bs) = List.unzip $ Map.keys distanceMap
         n' = Set.size $ Set.fromList $ as <> bs
     bridgeness' = bridgeness (fromIntegral nodesApprox) partitions distanceMap
-    confluence' = Map.empty -- confluence (Map.keys bridgeness') 3 True False
+    confluence' = BAC.computeConfluences 3 (Map.keys bridgeness') True
+               -- confluence (Map.keys bridgeness') 3 True False
   seq bridgeness' $ printDebug "bridgeness OK" ()
-  saveAsFileDebug "/tmp/bridgeness" bridgeness'
-  --seq confluence' $ printDebug "confluence OK" ()
-  --saveAsFileDebug "/tmp/confluence" confluence'
-  let g = data2graph ti diag bridgeness' confluence' partitions
-  --saveAsFileDebug "/tmp/graph" g
-  pure g
+  seq confluence' $ printDebug "confluence OK" ()
+  pure $ data2graph ti diag bridgeness' confluence' partitions
 
 type Reverse = Bool
 

src/Gargantext/Database/Action/Flow.hs

@@ -135,7 +135,7 @@ allDataOrigins = map InternalOrigin API.externalAPIs
 ---------------
 data DataText = DataOld ![NodeId]
               | DataNew !(Maybe Integer, ConduitT () HyperdataDocument IO ())
-              -- | DataNew ![[HyperdataDocument]]
+              --- | DataNew ![[HyperdataDocument]]
 
 -- Show instance is not possible because of IO
 printDataText :: DataText -> IO ()

stack.yaml

@@ -35,7 +35,7 @@ extra-deps:
 - git: https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude.git
   commit: 08096a4913572cf22762fa77613340207ec6d9fd
 - git: https://gitlab.iscpif.fr/gargantext/gargantext-graph.git
-  commit: 13131f5173e2e2ab35b968e53f0feaeee13ad8ac
+  commit: f41ee8b53c3264e5aa5adc06b2e5b293d2a8c474
   # Data Mining Libs
 - git: https://github.com/delanoe/data-time-segment.git
   commit: 10a416b9f6c443866b36479c3441ebb3bcdeb7ef
@@ -100,7 +100,7 @@ extra-deps:
 - git: https://github.com/alpmestan/haskell-igraph.git
   commit: 9f55eb36639c8e0965c8bc539a57738869f33e9a
 - git: https://gitlab.iscpif.fr/gargantext/haskell-infomap.git
-  commit: 76b795c1eaca37f43418d07da9fbdf5f4e7d8f5c
+  commit: 6d1d60b952b9b2b272b58fc5539700fd8890ac88
 
   # Accelerate Linear Algebra and specific instances
 - git: https://github.com/alpmestan/accelerate.git
@@ -110,7 +110,7 @@ extra-deps:
 - git: https://gitlab.iscpif.fr/amestanogullari/accelerate-utility.git
   commit: a3875fe652d3bb5acb522674c22c6c814c1b4ad0
 - git: https://github.com/alpmestan/accelerate-llvm.git
-  commit: 08eaa8ee771dde88b3dcf37a89b31777f1ca4910
+  commit: 944f5a4aea35ee6aedb81ea754bf46b131fce9e3
   subdirs:
     - accelerate-llvm/
     - accelerate-llvm-native/