bin/update-project-dependencies

@@ -16,8 +16,8 @@ fi
 # with the `sha256sum` result calculated on the `cabal.project` and
 # `cabal.project.freeze`. This ensures the files stay deterministic so that CI
 # cache can kick in.
-expected_cabal_project_hash="963418e37a17d4bb67d4b885613144b36d290f612eea80355e82abc7e76b450c"
-expected_cabal_project_freeze_hash="cd52143d3a9d285360b59c6371d3e258552c1bc115bd612024db3de1f7593ff7" 
+expected_cabal_project_hash="7d021a8e3d0b68421e26bdfe4e1da82f6ea26b6c420fc984b3c30c14bc5fea98"
+expected_cabal_project_freeze_hash="553b98aadb35506a305bd740cdd71f5fadc1e6d55d10f91cf39daa6735a63d78"
 
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run

cabal.project

@@ -87,7 +87,7 @@ source-repository-package
 source-repository-package
     type: git
     location: https://gitlab.iscpif.fr/gargantext/gargantext-graph.git
-    tag: a08ceed71b297a811f90cb86c3c61dc0b153036b
+    tag: 316d48b6a89593faaf1f2102e9714cea7e416e56
     subdir: gargantext-graph-core
 
 -- Support for GHC 9.6.x
@@ -99,7 +99,7 @@ source-repository-package
 source-repository-package
     type: git
     location: https://gitlab.iscpif.fr/gargantext/haskell-igraph.git
-    tag: 9f8a2f4a014539826a4eab3215cc70c0813f20cb
+    tag: 05e62da3aa466b7d0608d4918b030dc024119b32
 
 source-repository-package
     type: git

cabal.project.freeze

@@ -25,8 +25,6 @@ constraints: any.Boolean ==0.2.4,
              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 ==2.1.2.1,
              aeson -cffi +ordered-keymap,
@@ -79,6 +77,8 @@ constraints: any.Boolean ==0.2.4,
              any.blaze-builder ==0.4.2.3,
              any.blaze-html ==0.9.2.0,
              any.blaze-markup ==0.8.3.0,
+             any.blaze-textual ==0.2.3.1,
+             blaze-textual -developer -integer-simple +native,
              any.boolexpr ==0.3,
              any.boring ==0.2.2,
              boring +tagged,
@@ -103,6 +103,7 @@ constraints: any.Boolean ==0.2.4,
              cassava-conduit +small_base,
              any.cborg ==0.2.10.0,
              cborg +optimize-gmp,
+             any.cborg-json ==0.2.6.0,
              any.cereal ==0.5.8.3,
              cereal -bytestring-builder,
              any.charset ==0.3.11,
@@ -161,6 +162,8 @@ constraints: any.Boolean ==0.2.4,
              any.dense-linear-algebra ==0.1.0.0,
              any.digest ==0.0.2.1,
              digest -have_arm64_crc32c -have_builtin_prefetch -have_mm_prefetch -have_sse42 -have_strong_getauxval -have_weak_getauxval +pkg-config,
+             any.direct-sqlite ==2.3.29,
+             direct-sqlite +dbstat +fulltextsearch +haveusleep +json1 -mathfunctions -systemlib +urifilenames,
              any.directory ==1.3.8.5,
              any.discrimination ==0.5,
              any.distributive ==0.6.2.1,
@@ -170,7 +173,6 @@ constraints: any.Boolean ==0.2.4,
              any.double-conversion ==2.0.5.0,
              double-conversion -developer +embedded_double_conversion,
              any.easy-file ==0.2.5,
-             any.eigen ==3.3.7.0,
              any.either ==5.0.2,
              any.ekg-core ==0.1.1.8,
              any.ekg-json ==0.1.1.1,
@@ -223,7 +225,7 @@ constraints: any.Boolean ==0.2.4,
              any.haskell-bee ==0.1.0.0,
              any.haskell-bee-pgmq ==0.1.0.0,
              any.haskell-bee-tests ==0.1.0.0,
-             any.haskell-igraph ==0.10.4,
+             any.haskell-igraph ==0.10.4.1,
              any.haskell-lexer ==1.1.2,
              any.haskell-pgmq ==0.1.0.0,
              any.haskell-src-exts ==1.23.1,
@@ -300,7 +302,6 @@ constraints: any.Boolean ==0.2.4,
              any.linear ==1.23,
              linear -herbie +template-haskell,
              any.list-t ==1.0.5.7,
-             any.lockfree-queue ==0.2.4,
              any.logict ==0.8.2.0,
              any.loop ==0.3.0,
              any.lzma ==0.0.1.1,
@@ -460,6 +461,7 @@ constraints: any.Boolean ==0.2.4,
              any.servant-blaze ==0.9.1,
              any.servant-client ==0.20.2,
              any.servant-client-core ==0.20.2,
+             any.servant-conduit ==0.16.1,
              any.servant-ekg ==0.3.1,
              any.servant-openapi3 ==2.0.1.6,
              any.servant-routes ==0.1.0.0,
@@ -487,6 +489,7 @@ constraints: any.Boolean ==0.2.4,
              any.split ==0.2.5,
              any.splitmix ==0.1.1,
              splitmix -optimised-mixer,
+             any.sqlite-simple ==0.4.19.0,
              any.statistics ==0.16.3.0,
              statistics -benchpapi,
              any.stemmer ==0.5.2,
@@ -571,7 +574,6 @@ constraints: any.Boolean ==0.2.4,
              any.uri-encode ==1.5.0.7,
              uri-encode +network-uri -tools,
              any.utf8-string ==1.0.2,
-             any.utility-ht ==0.0.17.2,
              any.uuid ==1.3.16,
              any.uuid-types ==1.0.6,
              any.validity ==0.12.1.0,

gargantext.cabal

@@ -552,7 +552,7 @@ library
     , graphviz ^>= 2999.20.1.0
     , haskell-bee
     , haskell-bee-pgmq
-    , haskell-igraph ^>= 0.10.4
+    , haskell-igraph ^>= 0.10.4.1
     , haskell-pgmq >= 0.1.0.0 && < 0.2
     , haskell-throttle
     , hlcm ^>= 0.2.2

src/Gargantext/Core/Text/Metrics/Count.hs

@@ -138,11 +138,11 @@ occurrences = occurrencesOn _terms_stem
 -- Note: Compared to `occurences`, this is the more elementary function, maybe
 -- it would make more sense to rename this one into `occurences` and the other
 -- into something more descriptive
-countOccurrences :: (Foldable f, Ord a, Num n)
-                 => f a     -- ^ The collection whose items will be counted
-                 -> Map a n -- ^ A map whose keys are items of the input
-                            -- collection, and whose values are the number of
-                            -- times those items appear in the input collection
+countOccurrences :: (Foldable f, Ord a)
+                 => f a       -- ^ The collection whose items will be counted
+                 -> Map a Int -- ^ A map whose keys are items of the input
+                              -- collection, and whose values are the number of
+                              -- times those items appear in the input collection
 countOccurrences collection =
   foldl' (\occurenceMap item -> insertWith (+) item 1 occurenceMap)
          empty

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

@@ -33,7 +33,7 @@ import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness, nodeId2comId, setNodes2
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex, map2mat, mat2map, Index, MatrixShape(..))
 import Gargantext.Core.Viz.Graph.Tools.IGraph (mkGraphUfromEdges, spinglass)
 import Gargantext.Core.Viz.Graph.Types (Attributes(..), BridgenessMethod, Edge(..), Graph(..), MultiPartite(..), Node(..), Partite(..), Strength(..), LegendField(..))
-import Gargantext.Core.Viz.Graph.Utils (edgesFilter, nodesFilter)
+import Gargantext.Core.Viz.Graph.Utils (edgesFilter, filterNodesByCount)
 import Gargantext.Prelude
 import Graph.BAC.ProxemyOptim qualified as BAC
 import Graph.Types (ClusterNode(..))
@@ -189,7 +189,7 @@ data2graph multi labels' occurences bridge conf partitions =
             ]
     -- Remove vertices not connected to any other node, i.e. vertices that have
     -- zero edge joining them to other vertices
-    (bridge', toKeep) = nodesFilter (> 0) bridge
+    (bridge', toKeep) = filterNodesByCount (> 0) bridge
 
     edges = [ Edge { edge_source = show s
                    , edge_hidden = Nothing
@@ -264,7 +264,7 @@ getCoord ACP labels m n = to2d $ maybe (panic "Graph.Tools no coordinate") ident
 
 -- | KamadaKawai Layout
 -- TODO TEST: check labels, nodeId and coordinates
-layout :: Map (Int, Int) Double -> Int -> Gen -> (Double, Double)
+layout :: Map (Int, Int) Double -> Int -> Gen s -> (Double, Double)
 layout m n gen = maybe (panic "") identity $ Map.lookup n $ coord
   where
     coord :: (Map Int (Double,Double))

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

@@ -55,8 +55,7 @@ spinglassAux :: (Serialize v, Serialize e, Show v)
              => Int             -- ^ Random seed
              -> IG.Graph 'U v e -- ^ Input graph
              -> IO [[v]]        -- ^ List of clusters, in the form of lists of vertex labels
-spinglassAux seed graph = do
-  gen <- IG.withSeed seed pure -- initialize random generator
+spinglassAux seed graph = IG.withSeed seed $ \gen -> do -- initialize random generator
   rawClusters <- IG.findCommunity graph Nothing Nothing IG.spinglass gen -- perform clustering
   -- The clusters we get are composed of vertex IDs corresponding to the internal
   -- representation of IGraph graphs, so we need to retrieve the vertex labels:

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

@@ -81,8 +81,17 @@ edgesFilter m = Map.fromList $ catMaybes results
     keys    = Set.toList $ Set.fromList (x <> y)
     (x,y)   = unzip $ Map.keys m
 
-nodesFilter :: (Show a, Show b, Ord a, Ord b, Num b) => (b -> Bool) -> Map (a,a) b -> (Map (a,a) b, Set a)
-nodesFilter f m = (m', toKeep)
+-- | Filter nodes depending on how many times they (co)occur.
+-- More specifically, for a given value `x :: a`, this sums all entries in the
+-- map that have `x` as a value, and then it filters by applying `f` to the sum.
+-- Warning: This counts the value at `(x, x)` twice.
+filterNodesByCount :: (Show node, Ord node)
+                   => (Int -> Bool) -- ^ Filtering function
+                   -> Map (node, node) b   -- ^ Input map
+                   -> (Map (node, node) b, Set node)
+                   -- ^ The map without the filtered out nodes, and the set of
+                   -- remaining nodes
+filterNodesByCount f m = (m', toKeep)
   where
     m' = Map.filterWithKey (\(a,b) _ -> Set.member a toKeep && Set.member b toKeep) m
     toKeep = Set.fromList

stack.yaml

@@ -170,7 +170,7 @@
   git: "https://gitlab.iscpif.fr/gargantext/crawlers/pubmed.git"
   subdirs:
   - .
-- commit: a08ceed71b297a811f90cb86c3c61dc0b153036b
+- commit: 316d48b6a89593faaf1f2102e9714cea7e416e56
   git: "https://gitlab.iscpif.fr/gargantext/gargantext-graph.git"
   subdirs:
   - "gargantext-graph-core"
@@ -190,7 +190,7 @@
   git: "https://gitlab.iscpif.fr/gargantext/haskell-gargantext-prelude"
   subdirs:
   - .
-- commit: 9f8a2f4a014539826a4eab3215cc70c0813f20cb
+- commit: 05e62da3aa466b7d0608d4918b030dc024119b32
   git: "https://gitlab.iscpif.fr/gargantext/haskell-igraph.git"
   subdirs:
   - .