Merge branch 'dev' into 548-dev-node-url-share

.gitlab-ci.yml

 # Optimising CI speed by using tips from https://blog.nimbleways.com/let-s-make-faster-gitlab-ci-cd-pipelines/
-image: adinapoli/gargantext:v3.3
+image: adinapoli/gargantext:v3.4
 
 variables:
   STACK_ROOT: "${CI_PROJECT_DIR}/.stack-root"
@@ -37,7 +37,7 @@ cabal:
       - .cabal/
     policy: pull-push
   script:
-    - nix-shell --run "./bin/update-project-dependencies $CABAL_STORE_DIR && cabal --store-dir=$CABAL_STORE_DIR v2-build --flags test-crypto --ghc-options='-O0 -fclear-plugins'"
+    - nix-shell --run "./bin/update-project-dependencies $CABAL_STORE_DIR && cabal --store-dir=$CABAL_STORE_DIR v2-build --flags 'test-crypto no-phylo-debug-logs' --ghc-options='-O0 -fclear-plugins'"
   allow_failure: false
 
 bench:

CHANGELOG.md

+## Version 0.0.6.9.9.9.8.1 [RELEASE CANDIDATE 007]
+
+* [FRONT][FEAT][Make `esc` key close current popup window (#640)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/640)
+* [FRONT][FIX][Inconsistency in naming nodes (#641)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/641)
+* [FRONT][FIX][Remove All language](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/merge_requests/261)
+
+## Version 0.0.6.9.9.9.8 [RELEASE CANDIDATE 007]
+
+* [BACK][DEPS][wikiparsec fork (#320)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/320)
+* [BACK][TEST][Output of `toPhylo` & co non-deterministic? (#329)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/329)
+
 ## Version 0.0.6.9.9.9.7.3 [RELEASE CANDIDATE 007]
 
 * [FRONT][FIX][[Forest] Tree node focus: find a way to focus on the current node in the forest layout layout (#556)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/556)

bin/update-project-dependencies

@@ -18,8 +18,8 @@ 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="3bfa2552464823ff4f1d892e9dc2778a9cbf1a153a6639ec9caf87e6d9c75a7b"
-expected_cabal_project_freeze_hash="2c8960ffcf1b94aa11a3543e3b5facd2db5af19569fecaec4bc0ab4c1edd22a5"
+expected_cabal_project_hash="96be39a29bab66851278db07974dc3c61e7f807aefc3a3e9d50a9eb269706ef0"
+expected_cabal_project_freeze_hash="a88c2d091ee6223b64fb5dd38e71ab8379710a2aa716d2467f318789e4d75589"
 
 cabal --store-dir=$STORE_DIR v2-build --dry-run
 cabal2stack --system-ghc --allow-newer --resolver lts-21.17 --resolver-file devops/stack/lts-21.17.yaml -o stack.yaml

cabal.project

@@ -46,11 +46,6 @@ source-repository-package
     location: https://github.com/adinapoli/text16-compat.git
     tag: 85533b5d597e6fc5498411b4bcfc76380ec80d71
 
-source-repository-package
-    type: git
-    location: https://github.com/adinapoli/wikiparsec.git
-    tag: b3519a0351ae9515497680571f76200c24dedb53
-
 source-repository-package
     type: git
     location: https://github.com/alpmestan/accelerate-arithmetic.git

cabal.project.freeze

@@ -9,7 +9,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.JuicyPixels ==3.3.8,
              JuicyPixels -mmap,
              any.KMP ==0.2.0.0,
-             any.List ==0.6.2,
              any.MissingH ==1.4.3.0,
              MissingH +network--ge-3_0_0,
              any.MonadRandom ==0.6,
@@ -69,7 +68,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.base64 ==0.4.2.4,
              any.base64-bytestring ==1.2.1.0,
              any.basement ==0.0.16,
-             any.basic-prelude ==0.7.0,
              any.bifunctors ==5.5.15,
              bifunctors +semigroups +tagged,
              any.bimap ==0.5.0,
@@ -106,12 +104,10 @@ constraints: any.Cabal ==3.8.1.0,
              any.cereal ==0.5.8.3,
              cereal -bytestring-builder,
              any.charset ==0.3.10,
-             any.chunked-data ==0.3.1,
              any.cipher-aes ==0.2.11,
              cipher-aes +support_aesni,
              any.citeproc ==0.8.1,
              citeproc -executable -icu,
-             any.classy-prelude ==1.5.0.3,
              any.clock ==0.8.4,
              clock -llvm,
              any.cmdargs ==0.10.22,
@@ -183,7 +179,6 @@ constraints: any.Cabal ==3.8.1.0,
              distributive +semigroups +tagged,
              any.dlist ==1.0,
              dlist -werror,
-             any.dlist-instances ==0.1.1.1,
              any.doclayout ==0.4.0.1,
              any.doctemplates ==0.11,
              any.double-conversion ==2.0.4.2,
@@ -205,7 +200,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.extra ==1.7.14,
              any.fail ==4.9.0.0,
              any.fast-logger ==3.2.2,
-             any.fast-tagsoup ==1.0.14,
              any.fclabels ==2.0.5.1,
              any.fgl ==5.8.0.0,
              fgl +containers042,
@@ -263,8 +257,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.haskell-src-exts ==1.23.1,
              any.haskell-src-meta ==0.8.12,
              any.hedgehog ==1.2,
-             any.hexpat ==0.20.13,
-             hexpat -bundle,
              any.hgal ==2.0.0.2,
              any.hlcm ==0.2.2,
              any.hlint ==3.5,
@@ -334,7 +326,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.json-stream ==0.4.5.3,
              json-stream -conduit,
              any.kan-extensions ==5.2.5,
-             any.keys ==3.12.3,
              any.language-c ==0.9.2,
              language-c -allwarnings +iecfpextension +usebytestrings,
              any.lens ==5.2.3,
@@ -378,7 +369,6 @@ constraints: any.Cabal ==3.8.1.0,
              monad-loops +base4,
              any.monad-time ==0.4.0.0,
              any.mono-traversable ==1.0.15.3,
-             any.mono-traversable-instances ==0.1.1.0,
              any.monoid-extras ==0.6.2,
              any.morpheus-graphql ==0.24.3,
              any.morpheus-graphql-app ==0.24.3,
@@ -392,7 +382,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.mtl ==2.2.2,
              any.mtl-compat ==0.2.2,
              mtl-compat -two-point-one -two-point-two,
-             any.mutable-containers ==0.3.4.1,
              any.mwc-random ==0.15.0.2,
              any.natural-transformation ==0.4,
              any.network ==3.1.4.0,
@@ -434,8 +423,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.path-io ==1.8.1,
              path-io -dev,
              any.pem ==0.2.4,
-             any.pointed ==5.0.4,
-             pointed +comonad +containers +kan-extensions +semigroupoids +semigroups +stm +tagged +transformers +unordered-containers,
              any.polyparse ==1.13,
              any.port-utils ==0.2.1.0,
              any.postgres-options ==0.2.1.0,
@@ -495,7 +482,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.rts ==1.0.2,
              any.safe ==0.3.19,
              any.safe-exceptions ==0.1.7.4,
-             any.say ==0.1.0.1,
              any.scientific ==0.3.7.0,
              scientific -bytestring-builder -integer-simple,
              any.securemem ==0.1.10,
@@ -570,8 +556,6 @@ constraints: any.Cabal ==3.8.1.0,
              streaming-commons -use-bytestring-builder,
              any.strict ==0.5,
              any.string-conversions ==0.4.0.1,
-             any.stringsearch ==0.3.6.6,
-             stringsearch -base3 +base4,
              any.swagger2 ==2.8.7,
              any.syb ==0.7.2.4,
              any.system-cxx-std-lib ==1.0,
@@ -601,10 +585,8 @@ constraints: any.Cabal ==3.8.1.0,
              any.text-conversions ==0.3.1.1,
              any.text-format ==0.3.2.1,
              text-format -developer,
-             any.text-icu ==0.8.0.4,
              any.text-metrics ==0.3.2,
              text-metrics -dev,
-             any.text-regex-replace ==0.1.1.5,
              any.text-short ==0.1.5,
              text-short -asserts,
              any.text-show ==3.10.4,
@@ -648,7 +630,6 @@ constraints: any.Cabal ==3.8.1.0,
              unicode-collation -doctests -executable,
              any.unicode-data ==0.4.0.1,
              unicode-data -ucd2haskell,
-             any.unicode-show ==0.1.1.1,
              any.unicode-transforms ==0.4.0.1,
              unicode-transforms -bench-show -dev -has-icu -has-llvm -use-gauge,
              any.uniplate ==1.6.13,
@@ -679,8 +660,6 @@ constraints: any.Cabal ==3.8.1.0,
              any.vector-algorithms ==0.9.0.1,
              vector-algorithms +bench +boundschecks -internalchecks -llvm +properties -unsafechecks,
              any.vector-binary-instances ==0.2.5.2,
-             any.vector-instances ==3.4.2,
-             vector-instances +hashable,
              any.vector-th-unbox ==0.2.2,
              any.void ==0.7.3,
              void -safe,
@@ -697,8 +676,6 @@ constraints: any.Cabal ==3.8.1.0,
              warp +allow-sendfilefd -network-bytestring -warp-debug +x509,
              any.websockets ==0.12.7.3,
              websockets -example,
-             any.wikiparsec ==2.1.0,
-             wikiparsec +library-only,
              any.witherable ==0.4.2,
              any.wl-pprint-annotated ==0.1.0.1,
              any.wl-pprint-text ==1.2.0.2,

gargantext.cabal

@@ -5,7 +5,7 @@ cabal-version: 3.4
 -- see: https://github.com/sol/hpack
 
 name:           gargantext
-version: 0.0.6.9.9.9.7.3
+version: 0.0.6.9.9.9.8.1
 synopsis:       Search, map, share
 description:    Please see README.md
 category:       Data
@@ -36,8 +36,19 @@ data-files:
     test-data/ngrams/simple.json
     test-data/ngrams/simple.csv
     test-data/phylo/bpa_phylo_test.json
-    test-data/phylo/open_science.json
+    test-data/phylo/cleopatre.golden.json
+    test-data/phylo/nadal.golden.json
+    test-data/phylo/nadal_docslist.golden.json
+    test-data/phylo/nadal_ngramslist.golden.json
     test-data/phylo/issue-290-small.golden.json
+    test-data/phylo/open_science.json
+    test-data/phylo/small-phylo.golden.json
+    test-data/phylo/small_phylo_docslist.csv
+    test-data/phylo/small_phylo_ngramslist.csv
+    test-data/phylo/GarganText_DocsList-nodeId-187481.csv
+    test-data/phylo/GarganText_NgramsList-nodeId-187482.csv
+    test-data/phylo/187481.json
+    test-data/phylo/phylo2dot2json.golden.json
     test-data/stemming/lancaster.txt
     test-data/test_config.ini
     gargantext-cors-settings.toml
@@ -186,6 +197,7 @@ library
       Gargantext.Core.Viz.Phylo
       Gargantext.Core.Viz.Phylo.API
       Gargantext.Core.Viz.Phylo.API.Tools
+      Gargantext.Core.Viz.Phylo.Example
       Gargantext.Core.Viz.Phylo.PhyloExport
       Gargantext.Core.Viz.Phylo.PhyloMaker
       Gargantext.Core.Viz.Phylo.PhyloTools
@@ -351,7 +363,6 @@ library
       Gargantext.Core.Viz.Graph.Tools.Infomap
       Gargantext.Core.Viz.Graph.Utils
       Gargantext.Core.Viz.LegacyPhylo
-      Gargantext.Core.Viz.Phylo.Example
       Gargantext.Core.Viz.Phylo.Legacy.LegacyMain
       Gargantext.Core.Viz.Phylo.TemporalMatching
       Gargantext.Data.HashMap.Strict.Utils
@@ -614,6 +625,7 @@ library
     , timezone-series ^>= 0.1.13
     , transformers ^>= 0.5.6.2
     , transformers-base ^>= 0.4.6
+    , tree-diff
     , tomland >= 1.3.3.2
     , tuple ^>= 0.3.0.2
     , unordered-containers ^>= 0.2.16.0
@@ -629,7 +641,6 @@ library
     , wai-websockets ^>= 3.0.1.2
     , warp ^>= 3.3.20
     , websockets ^>= 0.12.7.3
-    , wikiparsec ^>= 1.2.0
     , wreq ^>= 0.5.3.3
     , xml-conduit ^>= 1.9.1.3
     , xml-types ^>= 0.3.8
@@ -844,6 +855,7 @@ test-suite garg-test-tasty
   main-is: drivers/tasty/Main.hs
   other-modules:
       Test.API.Routes
+      Common
       Test.API.Setup
       Test.Core.Similarity
       Test.Core.Text
@@ -879,11 +891,12 @@ test-suite garg-test-tasty
       Test.Utils.Jobs
       Paths_gargantext
   hs-source-dirs:
-      test
+      test bin/gargantext-phylo/Phylo
   ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       QuickCheck ^>= 2.14.2
     , aeson ^>= 1.5.6.0
+    , aeson-pretty ^>= 0.8.9
     , aeson-qq
     , async ^>= 2.2.4
     , boolexpr ^>= 0.2
@@ -892,6 +905,8 @@ test-suite garg-test-tasty
     , conduit ^>= 1.3.4.2
     , containers ^>= 0.6.5.1
     , crawlerArxiv
+    , cryptohash
+    , directory
     , duckling ^>= 0.2.0.0
     , extra ^>= 1.7.9
     , fast-logger ^>= 3.0.5
@@ -932,6 +947,7 @@ test-suite garg-test-tasty
     , servant-server
     , shelly >= 1.9 && < 2
     , stm ^>= 2.5.0.1
+    , split
     , tasty ^>= 1.4.2.1
     , tasty-golden
     , tasty-hspec

nix/pkgs.nix

@@ -14,7 +14,16 @@ rec {
                 })
            else pkgs.haskell.compiler.ghc947;
   cabal_install_3_10_1_0 = pkgs.haskell.lib.compose.justStaticExecutables pkgs.haskell.packages.ghc947.cabal-install;
-  graphviz = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
+  graphviz_dev = pkgs.graphviz.overrideAttrs (finalAttrs: previousAttrs: {
+    version = "11.0.0~dev";
+    src = pkgs.fetchFromGitLab {
+      owner = "graphviz";
+      repo = "graphviz";
+      rev = "f3ec849249ef9cb824feb7f97449d7159e1dcb4e"; # head as of 2024-03-25, see gargantext#329
+      hash = "sha256-s86IqWz6zeKbcRqpV3cVQBVviHbhUSX1U8GVuJBfjC4=";
+    };
+  });
+  graphviz = graphviz_dev.overrideAttrs (finalAttrs: previousAttrs: {
                 # Increase the YY_BUF_SIZE, see https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/290#note_9015
                 patches = [
                             (pkgs.fetchpatch {

src/Gargantext/Core/Types/Phylo.hs

@@ -19,6 +19,7 @@ Phylomemy was first described in Chavalarias, D., Cointet, J.-P., 2013. Phylomem
 .
 -}
 
+{-# LANGUAGE DeriveAnyClass     #-}
 {-# LANGUAGE DerivingStrategies #-}
 {-# LANGUAGE LambdaCase         #-}
 {-# LANGUAGE TemplateHaskell    #-}
@@ -41,6 +42,7 @@ import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
 import Gargantext.Prelude
 import Test.QuickCheck
 import Test.QuickCheck.Instances.Text()
+import Data.TreeDiff
 
 ------------------------------------------------------------------------
 -- | Phylo datatype descriptor of a phylomemy
@@ -121,7 +123,7 @@ data GraphData =
     , _gd_objects       :: [ObjectData]
     , _gd_strict        :: Bool
     , _gd_data          :: GraphDataData
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 data GraphDataData =
   GraphDataData {
@@ -149,7 +151,7 @@ data GraphDataData =
   , _gdd_ratio             :: Text
   , _gdd_splines           :: Text
   , _gdd_style             :: Text
-  } deriving (Show, Eq, Generic)
+  } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON GraphDataData where
   toJSON GraphDataData{..} = object [
@@ -214,7 +216,7 @@ data ObjectData =
   | BranchToNode !GvId !NodeCommonData !BranchToNodeData
   | PeriodToNode !GvId !NodeCommonData !PeriodToNodeData
   | Layer        !GvId !GraphDataData  !LayerData
-  deriving (Show, Eq, Generic)
+  deriving (Show, Eq, Generic, ToExpr)
 
 data GroupToNodeData
   = GroupToNodeData
@@ -234,7 +236,7 @@ data GroupToNodeData
     , _gtn_support    :: Text
     , _gtn_to         :: Text
     , _gtn_weight     :: Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON GroupToNodeData where
   toJSON GroupToNodeData{..} = object [
@@ -290,7 +292,7 @@ data BranchToNodeData
     , _btn_fontsize  :: Text
     , _btn_size      :: Text
     , _btn_style     :: Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON BranchToNodeData where
   toJSON BranchToNodeData{..} = object [
@@ -329,7 +331,7 @@ data PeriodToNodeData
     , _ptn_strFrom  :: Maybe Text
     , _ptn_strTo    :: Maybe Text
     , _ptn_to       :: Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON PeriodToNodeData where
   toJSON PeriodToNodeData{..} = object [
@@ -352,7 +354,7 @@ instance FromJSON PeriodToNodeData where
 data LayerData
   = LayerData {
     _ld_nodes :: [Int]
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON LayerData where
   toJSON LayerData{..} = object [
@@ -373,7 +375,7 @@ data NodeCommonData =
   , _nd_pos      :: !Text
   , _nd_shape    :: !Text
   , _nd_width    :: !Text
-  } deriving (Show, Eq, Generic)
+  } deriving (Show, Eq, Generic, ToExpr)
 
 instance ToJSON NodeCommonData where
   toJSON NodeCommonData{..} = object [
@@ -404,17 +406,18 @@ data EdgeCommonData =
   , _ed_pos   :: !Text
   , _ed_tail  :: !Int
   , _ed_width :: !Text
-  } deriving (Show, Eq, Generic)
+  } deriving (Show, Eq, Generic, ToExpr)
 
 newtype GvId = GvId { _GvId :: Int }
-  deriving (Show, Eq, Generic)
+  deriving stock (Show, Eq, Generic)
+  deriving anyclass ToExpr
 
 data EdgeData
   = GroupToAncestor !GvId !EdgeCommonData !GroupToAncestorData
   | GroupToGroup    !GvId !EdgeCommonData !GroupToGroupData
   | BranchToGroup   !GvId !EdgeCommonData !BranchToGroupData
   | PeriodToPeriod  !GvId !EdgeCommonData
-  deriving (Show, Eq, Generic)
+  deriving (Show, Eq, Generic, ToExpr)
 
 data GroupToAncestorData
   = GroupToAncestorData
@@ -422,20 +425,20 @@ data GroupToAncestorData
     , _gta_lbl       :: !Text
     , _gta_penwidth  :: !Text
     , _gta_style     :: !Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 data GroupToGroupData
   = GroupToGroupData
     { _gtg_constraint :: !Text
     , _gtg_lbl        :: !Text
     , _gtg_penwidth   :: !Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 data BranchToGroupData
   = BranchToGroupData
     { _btg_arrowhead :: !Text
     , _btg_style :: Maybe Text
-    } deriving (Show, Eq, Generic)
+    } deriving (Show, Eq, Generic, ToExpr)
 
 -- | JSON instances
 instance ToJSON GvId where

src/Gargantext/Core/Viz/Phylo/API.hs

@@ -39,7 +39,6 @@ import Gargantext.Prelude
 import Network.HTTP.Media ((//), (/:))
 import Prelude qualified
 import Servant
-import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary (Arbitrary, arbitrary)
 import Web.HttpApiData (readTextData)
 import Gargantext.Database.Query.Table.Node.Error
@@ -195,10 +194,6 @@ putPhylo = undefined
 
 
 -- | Instances
--- instance Arbitrary Phylo             where arbitrary     = elements [phylo]
-instance Arbitrary PhyloGroup        where arbitrary     = elements []
--- instance Arbitrary PhyloView         where arbitrary     = elements [phyloView]
--- instance Arbitrary PhyloConfig       where arbitrary     = elements []
 instance FromHttpApiData DisplayMode where parseUrlPiece = readTextData
 instance FromHttpApiData ExportMode  where parseUrlPiece = readTextData
 instance FromHttpApiData Filiation   where parseUrlPiece = readTextData

src/Gargantext/Core/Viz/Phylo/PhyloExport.hs

@@ -179,7 +179,7 @@ toBid g bs =
 
 exportToDot :: Phylo -> PhyloExport -> DotGraph DotId
 exportToDot phylo export =
-  trace ("\n-- | Convert " <> show(length $ export ^. export_branches) <> " branches and "
+  tracePhylo ("\n-- | Convert " <> show(length $ export ^. export_branches) <> " branches and "
           <> show(length $ export ^. export_groups) <> " groups "
           <> show(length $ nub $ concat $ map (^. phylo_groupNgrams) $ export ^. export_groups)
           <> " terms to a dot file\n\n"

src/Gargantext/Core/Viz/Phylo/PhyloMaker.hs

@@ -192,7 +192,7 @@ findSeaLadder phylo = case getSeaElevation phylo of
 
 appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] ->  Map Int Double -> PhyloGroup) -> Scale -> Map (Date,Date) [a] -> Phylo -> Phylo
 appendGroups f lvl m phylo =
-  trace ("\n" <> "-- | Append "
+  tracePhylo ("\n" <> "-- | Append "
          <> show (length $ concat $ elems m)
          <> " groups to scale "
          <> show (lvl) <> "\n" :: Text)
@@ -241,10 +241,10 @@ clusterToGroup fis pId pId' lvl idx coocs rootsCount = PhyloGroup pId pId' lvl i
 indexDates' :: Map (Date,Date) [Document] -> Map (Date,Date) (Text,Text)
 indexDates' m = map (\docs ->
   let ds = map (\d -> date' d) docs
-      f = if (null ds)
+      f = if (null ds || all T.null ds)
             then ""
             else toFstDate ds
-      l = if (null ds)
+      l = if (null ds || all T.null ds)
             then ""
             else toLstDate ds
    in (f,l)) m
@@ -381,7 +381,7 @@ docsToTimeScaleCooc docs fdt =
         mCooc' = fromList
                $ map (\t -> (t,empty))
                $ toTimeScale (map date docs) 1
-    in  trace ("\n" <> "-- | Build the coocurency matrix for "
+    in  tracePhylo ("\n" <> "-- | Build the coocurency matrix for "
                <> show (length $ keys mCooc')
                <> " unit of time" <> "\n" :: Text)
        $ unionWith sumCooc mCooc mCooc'
@@ -407,7 +407,7 @@ groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(da
 groupDocsByPeriod' f pds docs =
   let docs'    = groupBy (\d d' -> f d == f d') $ sortOn f docs
       periods  = parMap rpar (inPeriode f docs') pds
-   in trace ("\n" <> "-- | Group "
+   in tracePhylo ("\n" <> "-- | Group "
              <> show(length docs)
              <> " docs by "
              <> show(length pds) <> " periods" <> "\n" :: Text)
@@ -426,7 +426,7 @@ groupDocsByPeriod _ _   [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents
 groupDocsByPeriod f pds es =
   let periods  = parMap rpar (inPeriode f es) pds
 
-  in  trace ("\n" <> "-- | Group "
+  in  tracePhylo ("\n" <> "-- | Group "
              <> show(length es) <> " docs by "
              <> show(length pds) <> " periods" <> "\n" :: Text)
     $ fromList $ zip pds periods
@@ -483,7 +483,7 @@ docsToTimeScaleNb :: [Document] -> Map Date Double
 docsToTimeScaleNb docs =
     let docs' = fromListWith (+) $ map (\d -> (date d,1)) docs
         time  = fromList $ map (\t -> (t,0)) $ toTimeScale (keys docs') 1
-    in  trace ("\n" <> "-- | Group "
+    in  tracePhylo ("\n" <> "-- | Group "
                <> show(length docs)
                <> " docs by "
                <> show(length time)
@@ -539,9 +539,9 @@ initPhylo docs conf =
                  then defaultPhyloParam { _phyloParam_config = setDefault conf timeScale (length docs) }
                  else defaultPhyloParam { _phyloParam_config = conf }
         periods = toPeriods (D.sort $ D.nub $ map date docs) (getTimePeriod timeScale) (getTimeStep timeScale)
-    in trace ("\n" <> "-- | Init a phylo out of "
+    in tracePhylo ("\n" <> "-- | Init a phylo out of "
               <> show(length docs) <> " docs \n" :: Text)
-       $ trace ("\n" <> "-- | lambda "
+       $ tracePhylo ("\n" <> "-- | lambda "
                 <> show(_qua_granularity $ phyloQuality $ _phyloParam_config params) :: Text) 
        $ Phylo foundations
                docsSources

src/Gargantext/Core/Viz/Phylo/PhyloTools.hs

@@ -30,7 +30,6 @@ import Data.Vector (Vector, elemIndex)
 import Data.Vector qualified as Vector
 import Gargantext.Core.Viz.Phylo
 import Gargantext.Prelude hiding (empty)
-import Prelude (read)
 import Text.Printf
 
 ------------
@@ -160,7 +159,7 @@ toFstDate ds = snd
              $ head' "firstDate"
              $ sortOn fst
              $ map (\d ->
-                      let d' = read (filter (\c -> notElem c ['U','T','C',' ',':','-']) $ unpack d)::Int
+                      let d' = fromMaybe (error "toFstDate") $ readMaybe (filter (\c -> notElem c ['U','T','C',' ',':','-']) $ unpack d)::Int
                        in (d',d)) ds
 
 toLstDate :: [Text] -> Text
@@ -169,7 +168,7 @@ toLstDate ds = snd
              $ reverse
              $ sortOn fst
              $ map (\d ->
-                      let d' = read (filter (\c -> notElem c ['U','T','C',' ',':','-']) $ unpack d)::Int
+                      let d' = fromMaybe (error "toLstDate") $ readMaybe (filter (\c -> notElem c ['U','T','C',' ',':','-']) $ unpack d)::Int
                        in (d',d)) ds
 
 

stack.yaml

@@ -5,7 +5,6 @@
 - "MissingH-1.4.3.0"
 - "Unique-0.4.7.8"
 - "dependent-sum-0.7.1.0"
-- "fast-tagsoup-1.0.14"
 - "fclabels-2.0.5.1"
 - "full-text-search-0.2.1.4"
 - "fullstop-0.1.4"
@@ -83,10 +82,6 @@
   git: "https://github.com/adinapoli/text16-compat.git"
   subdirs:
   - .
-- commit: b3519a0351ae9515497680571f76200c24dedb53
-  git: "https://github.com/adinapoli/wikiparsec.git"
-  subdirs:
-  - .
 - commit: a110807651036ca2228a76507ee35bbf7aedf87a
   git: "https://github.com/alpmestan/accelerate-arithmetic.git"
   subdirs:
@@ -347,8 +342,6 @@ flags:
     portable: false
     sse42: false
     "unsafe-tricks": true
-  hexpat:
-    bundle: false
   hlint:
     "ghc-lib": true
     gpl: true
@@ -461,16 +454,6 @@ flags:
     dev: false
   "path-io":
     dev: false
-  pointed:
-    comonad: true
-    containers: true
-    "kan-extensions": true
-    semigroupoids: true
-    semigroups: true
-    stm: true
-    tagged: true
-    transformers: true
-    "unordered-containers": true
   "postgresql-libpq":
     "use-pkg-config": false
   "pretty-simple":
@@ -551,9 +534,6 @@ flags:
     "optimised-mixer": false
   "streaming-commons":
     "use-bytestring-builder": false
-  stringsearch:
-    base3: false
-    base4: true
   tagged:
     deepseq: true
     transformers: true
@@ -635,8 +615,6 @@ flags:
     llvm: false
     properties: true
     unsafechecks: false
-  "vector-instances":
-    hashable: true
   void:
     safe: false
   "wai-app-static":
@@ -653,8 +631,6 @@ flags:
     x509: true
   websockets:
     example: false
-  wikiparsec:
-    "library-only": true
   wreq:
     aws: false
     developer: false

test-data/phylo/GarganText_NgramsList-187482.csv

+status	label	forms
+candidate	%	
+candidate	-	
+map	accompagnement	
+map	activités	
+map	adaptation	
+map	addiction	
+map	addictions	conduites addictives
+map	adolescence	
+map	adolescent	
+map	adolescent girls	
+map	adolescent outcomes	
+map	adolescent substance use	
+map	adolescents	adolescence|&|adolescent|&|adolescent girls|&|adolescent outcomes|&|adolescent substance use|&|nombreux adolescents|&|teenagers|&|young adolescents
+map	aide	
+map	alcool	
+candidate	an	
+candidate	analyse	
+map	analyse qualitative	
+candidate	année	
+candidate	années	année
+map	anorexie mentale	
+candidate	ans	an
+map	anxiogène	
+map	anxiété	
+stop	apparition	
+candidate	apprentissage	
+map	approche intégrative	
+map	approche systémique	
+stop	approches	
+candidate	article	
+candidate	articulation	
+candidate	association	
+map	atmosphère familiale	
+candidate	attentes	
+stop	attention	
+candidate	auteurs	
+map	autonome	autonomie
+map	autonomie	
+map	autorité	
+stop	autre part	
+candidate	base	
+candidate	bases	
+map	belle émotion	
+candidate	besoin	
+candidate	biais	
+stop	but	
+map	bébé	
+candidate	cadre	
+map	cahier	
+candidate	caractéristiques	
+stop	carte	
+candidate	cas	
+map	cas cliniques	
+candidate	centaine	
+candidate	centre	
+map	changement	
+candidate	charge	
+map	charge familiale	
+map	charge individuelle	
+candidate	chercheurs	
+candidate	choix	
+candidate	cliniciens	
+map	clinique	
+map	communication	
+candidate	complexité	
+candidate	complément	
+candidate	comportement	
+candidate	compréhension	
+candidate	compte	
+candidate	concept	
+stop	conclusion	
+stop	conditions	
+map	conduites addictives	addiction|&|transaction addictive
+map	conférence	
+candidate	considération	
+map	constellations familiales	
+stop	construction	
+map	consultation	
+candidate	contexte	
+candidate	contextes	
+candidate	continuité	
+map	coopération	
+map	couple	couples
+map	couples	
+candidate	cours	
+map	crise existentielle	
+candidate	croyances	
+candidate	culture	
+map	cycle	
+map	demande	
+stop	demi	
+candidate	dernières années	
+map	dialogue	
+candidate	difficultés	
+candidate	différences	
+candidate	différentes modalités	
+stop	discours	
+stop	discussion	discussions
+stop	discussions	discours
+candidate	dispositif	
+candidate	diversité	
+map	données	
+map	dynamique familiale	
+map	découvrir ensemble	
+map	déficience intellectuelle	
+map	dépressif	
+map	dépression	dépressif
+map	détresse	
+candidate	développement	
+candidate	effet	
+stop	effets	
+map	efficacité	
+map	emdr	
+map	emplois	
+map	enfants porteurs	
+candidate	engagement	
+candidate	ensemble	
+map	entreprise	
+map	entreprises	entreprise
+map	entretiens	
+candidate	entrée	
+candidate	espace	
+map	estime de soi	
+stop	evaluation	
+stop	exemple	
+stop	existence	
+candidate	expert	
+stop	expression	
+map	expérience	
+candidate	extraits	
+candidate	facteur	
+candidate	fait	
+map	familiale	
+map	familiarité	
+map	famille	atmosphère familiale|&|familiale|&|familles|&|familles recomposées
+map	familles	
+map	familles recomposées	
+candidate	family	
+map	fille	
+map	fièvre	
+candidate	fonction	
+map	fonctionnement	
+candidate	forme	
+map	fossé	
+map	fratries	
+map	frustration	
+map	frère	frères
+map	frères	
+map	groupe	groupes
+map	groupe familial	
+map	groupes	
+candidate	guerres	
+map	histoire	
+map	hypothèse	
+candidate	hypothèses	
+map	identification	
+map	illustration clinique	
+stop	impact	
+stop	implication	
+candidate	importance	
+candidate	incidence	
+candidate	individu	
+candidate	information	
+candidate	institutionnalisation	
+candidate	interaction	
+candidate	interactionnelles	
+map	interactions familiales	
+map	interactions négatives	
+map	interactions précoces	
+map	intervention	interventions
+map	interventions	
+candidate	introduction	
+candidate	intérêt	
+candidate	issue	
+map	jalouse	
+map	jalousie	jalouse|&|jaloux
+map	jaloux	
+map	jeu	jeux|&|jouer
+map	jeune enfant	
+candidate	jeunes	
+map	jeunes adultes	
+map	jeux	
+map	jouer	
+map	journal	
+candidate	langage	
+map	langue	
+candidate	lettre	
+stop	lettres	
+map	lettré	lettrée
+map	lettrée	
+candidate	lien	
+stop	liens	
+candidate	lieu	
+candidate	lieux	
+map	littéraire	
+map	littérature	cahier|&|littéraire|&|roman|&|romancier|&|romans|&|écriture
+candidate	l’émouvait	
+map	malade	
+map	maladie	fièvre|&|malade
+map	maman	
+candidate	maîtresse	
+map	meilleure acceptation	
+map	meilleure coopération	
+map	membres	
+map	mentalisation	
+map	mineurs	
+candidate	ministère	
+candidate	mise	
+candidate	modalités	
+candidate	modèle	
+candidate	modérateurs	
+candidate	mois	
+candidate	moitié	
+candidate	monde	
+candidate	murmure	
+map	mutations psychosociétales	
+map	mère	maman
+map	médiateur	médiateurs|&|médiation
+map	médiateurs	
+map	médiation	
+map	médication	
+map	méthode	méthodes
+map	méthodes	
+map	métiers	ouvriers
+map	nombreux adolescents	
+map	nouvelles stratégies	
+map	nouvelles technologies	
+candidate	nécessité	
+candidate	objectif	
+map	objectifs	
+map	objet	
+candidate	objets	
+candidate	organisation	
+candidate	origine	
+candidate	outils	
+map	ouvriers	
+map	paradigme	
+candidate	parallèle	
+map	parentalité	
+map	parents	père
+candidate	parole	
+candidate	part	
+candidate	participants	
+candidate	partie	
+candidate	passage	
+map	pathologie	pathologies
+map	pathologies	
+map	patient	
+stop	patients	
+candidate	perception	
+stop	personne	
+stop	perspective	
+map	petite enfance	
+map	phénomène	
+candidate	pistes	
+candidate	place	
+map	population	
+map	population française	
+candidate	possibilité	
+map	pratique	pratiques
+map	pratiques	
+map	pratiques cliniques	
+candidate	première partie	
+stop	prise	
+candidate	problème	
+candidate	problèmes	
+candidate	processus	
+map	processus thérapeutiques	
+map	processus émotionnels	
+candidate	proches	
+candidate	professionnel	
+map	professionnels	
+candidate	programme	
+stop	propos	
+map	propres stratégies	
+map	protection judiciaire	
+candidate	présence	
+stop	présentation	
+map	prévention	
+map	psychanalyste	
+map	psychiatre	psychiatrie
+map	psychiatrie	
+map	psychologues	
+map	psychométriques	
+map	psychose	
+map	psychosociale	
+map	psychothérapie	
+map	psychothérapie familiale	
+map	père	
+map	pédopsychiatrie	
+stop	période	
+map	qualité	
+map	qualité de vie	
+map	question	
+candidate	questionnaire	
+map	questions	question
+map	quête de sens	
+stop	rapport	
+map	recherche	
+candidate	recherches	
+candidate	reconnaissance	
+map	recrutement	recruter
+map	recruter	
+map	relation fraternelle	
+map	relation thérapeutique	
+candidate	rencontre	
+map	rendre compte	
+candidate	renforcement	
+map	revue	
+candidate	risque	
+map	roman	
+map	romancier	
+map	romans	
+candidate	réflexions	
+candidate	régulation	
+map	régulation émotionnelle	
+candidate	répercussions	
+candidate	réponse	
+candidate	réponses	
+candidate	réseau	
+map	résultats	
+map	rétroaction	
+map	santé	
+map	santé mentale	
+map	santé publique	
+map	schizophrenia	
+map	schizophrenie	
+map	schizophrénie	schizophrenia|&|schizophrenie
+candidate	scène	
+map	sein	
+map	sens	
+candidate	service	
+candidate	situation	
+candidate	situations	
+map	situations cliniques	
+map	sociologie	
+map	soins	
+candidate	solution	
+map	soutien	
+candidate	spécificités	
+map	stratégie	stratégies
+map	stratégies	
+map	stress	
+map	subjectivation	
+candidate	sujet	
+candidate	sujets	
+map	symptôme	
+candidate	système	
+map	système familial	
+candidate	systèmes	
+map	séance	
+map	séances	séance
+map	sœur	sœurs
+map	sœurs	
+map	teenagers	
+stop	terme	
+stop	termes	terme
+map	thérapeute	
+candidate	thérapeutes	
+map	thérapeutes familiaux	
+map	thérapie	thérapies
+map	thérapie familiale	thérapies familiales
+map	thérapie familiale psychanalytique	
+map	thérapie familiale systémique	thérapie systémique|&|thérapies systémiques
+map	thérapie individuelle	
+map	thérapie systémique	
+map	thérapies	
+map	thérapies familiales	
+map	thérapies systémiques	
+candidate	traduction	
+candidate	traitement	
+map	traitement pharmacologique	
+candidate	traitements	
+map	transaction addictive	
+map	transgénérationnel	
+candidate	transmission	
+map	transmission intergénérationnelle	
+map	trauma	trauma history|&|trauma studies|&|traumatisme
+map	trauma history	
+map	trauma studies	
+map	traumatisme	
+candidate	travail	
+map	travaux	
+candidate	travers	
+map	trouble	troubles
+map	trouble développemental	
+map	troubles	
+candidate	type	
+candidate	uns	
+stop	utilisation	
+map	victime	
+map	vie	
+map	vie familiale	
+candidate	voix	murmure
+candidate	vue	
+map	vécu	
+map	young adolescents	
+candidate	zone	
+map	échanges	
+candidate	école	maîtresse|&|éducation|&|élèves
+map	écriture	journal|&|lettre|&|lettres|&|lettré|&|lettrée|&|écrivaine
+map	écrivaine	
+candidate	éducation	
+map	éducation thérapeutique	
+candidate	élaboration	
+map	élaboration mentale	
+candidate	élèves	
+candidate	émergence	
+map	émotion	l’émouvait
+map	émotions	belle émotion|&|émotion
+candidate	épreuve	
+candidate	étapes	
+candidate	état	
+candidate	étude	
+map	évaluation	
+candidate	évidence	
+stop	évolution	
+candidate	œuvre	

test/Test/Utils/Jobs.hs

@@ -20,7 +20,6 @@ import Control.Concurrent
 import Control.Concurrent.Async
 import Control.Concurrent.Async qualified as Async
 import Control.Concurrent.STM
-import Data.List (isInfixOf)
 import Data.Sequence ((|>), fromList)
 import Data.Time
 import Debug.RecoverRTTI (anythingToString)