Merge branch 'dev' into dev-doc-table-optimization

package.yaml

@@ -6,15 +6,15 @@ category: Data
 author: Gargantext Team
 maintainer: team@gargantext.org
 copyright:
-    - ! 'Copyright: (c) 2017-2018: see git logs and README'
-license: BSD3
+    - ! 'Copyright: (c) 2017-Present: see git logs and README'
+license: AGPL-3
 homepage: https://gargantext.org
 ghc-options: -Wall
 extra-libraries:
-- gfortran
+  - gfortran
 dependencies:
-- extra
-- text
+  - extra
+  - text
 default-extensions:
   - DataKinds
   - DeriveGeneric
@@ -59,6 +59,7 @@ library:
   - Gargantext.Text
   - Gargantext.Text.Context
   - Gargantext.Text.Corpus.Parsers
+  - Gargantext.Text.Corpus.Parsers.Date.Parsec
   - Gargantext.Text.Corpus.API
   - Gargantext.Text.Corpus.Parsers.CSV
   - Gargantext.Text.Examples
@@ -364,36 +365,58 @@ executables:
 
 
 tests:
-#   garg-test:
-#     main: Main.hs
-#     source-dirs: src-test
-#     ghc-options:
-#     - -threaded
-#     - -rtsopts
-#     - -with-rtsopts=-N
-#     dependencies:
-#     - base
-#     - gargantext
-#     - hspec
-#     - QuickCheck
-#     - quickcheck-instances 
-#     - time
-#     - parsec
-#     - duckling
-#     - text
-  garg-doctest:
-    main: Main.hs
-    source-dirs: src-doctest
-    ghc-options:
-    - -O2
-    - -Wcompat
-    - -Wmissing-signatures
-    - -rtsopts
-    - -threaded
-    - -with-rtsopts=-N
-    dependencies:
-    - doctest
-    - Glob
-    - QuickCheck
-    - base
-    - gargantext
+   garg-test:
+     main: Main.hs
+     source-dirs: src-test
+     default-extensions:
+     - DataKinds
+     - DeriveGeneric
+     - FlexibleContexts
+     - FlexibleInstances
+     - GeneralizedNewtypeDeriving
+     - MultiParamTypeClasses
+     - NoImplicitPrelude
+     - OverloadedStrings
+     - RankNTypes
+     ghc-options:
+     - -threaded
+     - -rtsopts
+     - -with-rtsopts=-N
+     dependencies:
+     - base
+     - gargantext
+     - hspec
+     - QuickCheck
+     - quickcheck-instances
+     - time
+     - parsec
+     - duckling
+     - text
+#  garg-doctest:
+#    main: Main.hs
+#    source-dirs: src-doctest
+#    ghc-options:
+#    - -O2
+#    - -Wcompat
+#    - -Wmissing-signatures
+#    - -rtsopts
+#    - -threaded
+#    - -with-rtsopts=-N
+#    dependencies:
+#    - doctest
+#    - Glob
+#    - QuickCheck
+#    - base
+#    - gargantext
+#    default-extensions:
+#    - DataKinds
+#    - DeriveGeneric
+#    - FlexibleContexts
+#    - FlexibleInstances
+#    - GeneralizedNewtypeDeriving
+#    - MultiParamTypeClasses
+#    - NoImplicitPrelude
+#    - OverloadedStrings
+#    - RankNTypes
+#
+

src-doctest/Main.hs

 import System.FilePath.Glob
 import Test.DocTest
+import Gargantext.Prelude
 
 main :: IO ()
 main = glob "src/Gargantext/" >>= doctest

src-test/Main.hs

@@ -12,15 +12,17 @@ Portability : POSIX
 import Gargantext.Prelude
 import Gargantext.Core (Lang(..))
 --import qualified Ngrams.Lang.Fr as Fr
-import qualified Ngrams.Lang as Lang
+--import qualified Ngrams.Lang as Lang
 import qualified Ngrams.Lang.Occurrences as Occ
 import qualified Ngrams.Metrics as Metrics
 import qualified Parsers.Date as PD
+import qualified Graph.Distance as GD
 
 main :: IO ()
 main = do
-    Occ.parsersTest
-    Lang.ngramsExtractionTest FR
-    Lang.ngramsExtractionTest EN
-    Metrics.main
+--    Occ.parsersTest
+--    Lang.ngramsExtractionTest FR
+--    Lang.ngramsExtractionTest EN
+--    Metrics.main
     PD.testFromRFC3339
+    GD.test

src-test/Ngrams/Lang.hs

@@ -15,6 +15,7 @@ commentary with @some markup@.
 
 module Ngrams.Lang where
 
+{-
 import Gargantext.Prelude (IO())
 
 import Gargantext.Core (Lang(..))
@@ -24,4 +25,4 @@ import qualified Ngrams.Lang.En as En
 ngramsExtractionTest :: Lang -> IO ()
 ngramsExtractionTest FR = Fr.ngramsExtractionTest
 ngramsExtractionTest EN = En.ngramsExtractionTest
-
+-}

src-test/Ngrams/Lang/En.hs

@@ -15,6 +15,7 @@ commentary with @some markup@.
 
 module Ngrams.Lang.En where
 
+{-
 import Data.List ((!!))
 import Data.Text (Text)
 
@@ -22,8 +23,11 @@ import Test.Hspec
 
 import Gargantext.Prelude
 import Gargantext.Core (Lang(..))
-import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
 
+-- TODO this import is not used anymore
+import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
+-- use instead
+-- import Gargantext.Text.Terms (extractNgramsT)
 
 ngramsExtractionTest :: IO ()
 ngramsExtractionTest = hspec $ do
@@ -43,4 +47,4 @@ ngramsExtractionTest = hspec $ do
             t2 <- map (selectNgrams EN) <$> extractNgrams EN t
             t2 `shouldBe` [[("Donald Trump","NNP","PERSON"),("president of the United-States of America","NN","LOCATION")]]
 
-
+-}

src-test/Ngrams/Lang/Fr.hs

@@ -15,12 +15,15 @@ commentary with @some markup@.
 
 module Ngrams.Lang.Fr where
 
+{-
 import Test.Hspec
 
 import Gargantext.Prelude
 import Gargantext.Core (Lang(..))
+-- TODO this import is not used anymore
 import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
-
+-- use instead
+-
 ngramsExtractionTest :: IO ()
 ngramsExtractionTest = hspec $ do
     describe "Behavioral tests: ngrams extraction in French Language" $ do
@@ -61,4 +64,4 @@ ngramsExtractionTest = hspec $ do
             let textFr1 = "L'heure d'arrivée des coureurs dépend de la météo du jour."
             testFr1 <- map (selectNgrams FR) <$> (extractNgrams FR) textFr1
             testFr1 `shouldBe` [[("heure d' arrivée des coureurs","NC","O"),("météo du jour","NC","O")]]
-
+-}

src-test/Ngrams/Lang/Occurrences.hs

@@ -15,6 +15,7 @@ commentary with @some markup@.
 
 module Ngrams.Lang.Occurrences where
 
+{-
 import Test.Hspec
 
 import Data.Either (Either(Right))
@@ -59,4 +60,4 @@ parsersTest = hspec $ do
 --  describe "Parser for nodes" $ do
 --    it "returns the result of one parsing after space" $ do
 --      occOfCorpus 249509 "sciences" `shouldReturn` 7
-
+-}

src-test/Ngrams/Metrics.hs

@@ -15,8 +15,10 @@ commentary with @some markup@.
 
 {-# LANGUAGE CPP                  #-}
 
-module Ngrams.Metrics (main) where
+--module Ngrams.Metrics (main) where
+module Ngrams.Metrics  where
 
+{-
 import           Data.Text (Text)
 import qualified Data.Text as T
 import           Data.Ratio
@@ -139,3 +141,5 @@ testPair :: (Eq a, Show a)
   -> SpecWith ()
 testPair f a b r = it ("‘" <> T.unpack a <> "’ and ‘" <> T.unpack b <> "’") $
   f a b `shouldBe` r
+
+-}

src-test/Parsers/Date.hs

@@ -28,7 +28,7 @@ import Duckling.Time.Types (toRFC3339)
 
 -----------------------------------------------------------
 import Gargantext.Prelude
-import Gargantext.Text.Parsers.Date (fromRFC3339)
+import Gargantext.Text.Corpus.Parsers.Date.Parsec (fromRFC3339)
 import Parsers.Types
 -----------------------------------------------------------
 

src/Gargantext/API/Admin/Orchestrator/Types.hs

@@ -27,12 +27,12 @@ instance Arbitrary a => Arbitrary (JobOutput a) where
   arbitrary = JobOutput <$> arbitrary
 
 -- | Main Types
+-- TODO IsidoreAuth
 data ExternalAPIs = All
                   | PubMed
                   | HAL
                   | IsTex
                   | Isidore
-                  -- | IsidoreAuth
   deriving (Show, Eq, Enum, Bounded, Generic)
 
 

src/Gargantext/API/Node/Update.hs

@@ -81,7 +81,7 @@ updateNode uId nId (UpdateNodeParamsGraph metric) logStatus = do
 
   logStatus JobLog { _scst_succeeded = Just 1
                    , _scst_failed    = Just 0
-                   , _scst_remaining = Just 2
+                   , _scst_remaining = Just 1
                    , _scst_events    = Just []
                    }
 

src/Gargantext/Text/Terms.hs

@@ -175,6 +175,6 @@ newTries n t = buildTries n (fmap toToken $ uniText t)
 uniText :: Text -> [[Text]]
 uniText = map (List.filter (not . isPunctuation))
         . map tokenize
-        . sentences       -- | TODO get sentences according to lang
+        . sentences       -- TODO get sentences according to lang
         . Text.toLower
 

src/Gargantext/Text/Terms/Eleve.hs

@@ -73,12 +73,12 @@ subst (src, dst) x | sim src x = dst
                    | otherwise = x
 ------------------------------------------------------------------------
 
+-- | TODO: Show Instance only used for debugging
 type Entropy e =
   ( Fractional e
   , Floating e
   , P.RealFloat e
   , Show e
-  -- ^ TODO: only used for debugging
   )
 ------------------------------------------------------------------------
 -- | Example and tests for development

src/Gargantext/Viz/AdaptativePhylo.hs

@@ -65,11 +65,13 @@ data SeaElevation =
 
 data Proximity = 
       WeightedLogJaccard 
-      { _wlj_sensibility   :: Double 
+      { _wlj_sensibility   :: Double
+{-
       -- , _wlj_thresholdInit :: Double
       -- , _wlj_thresholdStep :: Double
       -- | max height for sea level in temporal matching
       -- , _wlj_elevation     :: Double
+-}
       }
     | Hamming 
     deriving (Show,Generic,Eq) 

src/Gargantext/Viz/Graph/API.hs

@@ -147,8 +147,9 @@ computeGraph cId d nt repo = do
   lIds <- selectNodesWithUsername NodeList userMaster
   let ngs = filterListWithRoot MapTerm $ mapTermListRoot [lId] nt repo
 
+  -- TODO split diagonal
   myCooc <- Map.filter (>1)
-         <$> getCoocByNgrams (Diagonal True)
+         <$> getCoocByNgrams (Diagonal False)
          <$> groupNodesByNgrams ngs
          <$> getNodesByNgramsOnlyUser cId (lIds <> [lId]) nt (Map.keys ngs)
 

src/Gargantext/Viz/Graph/Distances.hs

@@ -27,6 +27,7 @@ import Test.QuickCheck.Arbitrary
 
 ------------------------------------------------------------------------
 data Distance = Conditional | Distributional
+  deriving (Show)
 
 measure :: Distance -> Matrix Int -> Matrix Double
 measure Conditional    = measureConditional

src/Gargantext/Viz/Graph/Distances/Distributional.hs

@@ -18,18 +18,15 @@ module Gargantext.Viz.Graph.Distances.Distributional
   where
 
 import Data.Matrix hiding (identity)
-
 import qualified Data.Map as M
-
 import Data.Vector (Vector)
 import qualified Data.Vector as V
-
 import Gargantext.Prelude
 import Gargantext.Viz.Graph.Utils
 
 
-distributional :: (Floating a, Ord a) => Matrix a -> [((Int, Int), a)]
-distributional m = filter (\((x,y), d) -> foldl' (&&) True (conditions x y d) ) distriList
+distributional' :: (Floating a, Ord a) => Matrix a -> [((Int, Int), a)]
+distributional' m = filter (\((x,y), d) -> foldl' (&&) True (conditions x y d) ) distriList
   where
     conditions x y d  =  [ (x /= y)
                          , (d > miniMax')
@@ -51,7 +48,6 @@ ri m = matrix c r doRi
                            $ V.zip (ax Col x y mi') (ax Row x y mi')
     (c,r) = (nOf Col m, nOf Row m)
 
-
 mi :: (Ord a, Floating a) => Matrix a -> Matrix a
 mi m = matrix c r createMat
   where

src/Gargantext/Viz/Graph/Tools.hs

@@ -56,6 +56,7 @@ cooc2graph :: Distance
            -> (Map (Text, Text) Int)
            -> IO Graph
 cooc2graph distance threshold myCooc = do
+  printDebug "cooc2graph" distance
   let
     (ti, _) = createIndices myCooc
     myCooc' = toIndex ti myCooc

src/Gargantext/Viz/Phylo/LevelMaker.hs

@@ -207,7 +207,7 @@ toNthLevel lvlMax prox clus p
   | otherwise     = toNthLevel lvlMax prox clus
                   $ traceBranches (lvl + 1)
                   $ setPhyloBranches (lvl + 1)
-                  -- $ transposePeriodLinks (lvl + 1)
+                  -- \$ transposePeriodLinks (lvl + 1)
                   $ traceTranspose (lvl + 1) Descendant
                   $ transposeLinks (lvl + 1) Descendant
                   $ traceTranspose (lvl + 1) Ascendant
@@ -230,15 +230,15 @@ toNthLevel lvlMax prox clus p
 toPhylo1 :: Cluster -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
 toPhylo1 clus prox d p = case clus of
   Fis (FisParams k s t) -> traceBranches 1 
-                       -- $ reLinkPhyloBranches 1 
-                       -- $ traceBranches 1 
+                       -- \$ reLinkPhyloBranches 1 
+                       -- \$ traceBranches 1 
                        $ setPhyloBranches 1
                        $ traceTempoMatching Descendant 1
                        $ interTempoMatching Descendant 1 prox
                        $ traceTempoMatching Ascendant 1
                        $ interTempoMatching Ascendant 1 prox
                        $ tracePhyloN 1
-                       -- $ setLevelLinks (0,1)
+                       -- \$ setLevelLinks (0,1)
                        $ addPhyloLevel 1 (getPhyloFis phyloFis)
                        $ trace (show (size $ getPhyloFis phyloFis) <> " Fis created") $ phyloFis
     where

src/Gargantext/Viz/Phylo/LinkMaker.hs

@@ -126,15 +126,15 @@ phyloGroupMatching :: [PhyloPeriodId] -> PhyloGroup -> Phylo -> [Pointer]
 phyloGroupMatching periods g p = case pointers of
   Nothing  -> []
   Just pts -> head' "phyloGroupMatching"  
-            -- | Keep only the best set of pointers grouped by proximity
+            -- Keep only the best set of pointers grouped by proximity
             $ groupBy (\pt pt' -> snd pt == snd pt') 
             $ reverse $ sortOn snd pts
-            -- | Find the first time frame where at leats one pointer satisfies the proximity threshold
+            -- Find the first time frame where at leats one pointer satisfies the proximity threshold
   where
     --------------------------------------
     pointers :: Maybe [Pointer]
     pointers = find (not . null)
-             -- | For each time frame, process the Proximity on relevant pairs of targeted groups
+             -- For each time frame, process the Proximity on relevant pairs of targeted groups
              $ scanl (\acc frame -> 
                  let pairs = makePairs frame g p
                  in  acc ++ ( filter (\(_,proxi) -> filterProximity proxi (getPhyloProximity p))
@@ -145,7 +145,7 @@ phyloGroupMatching periods g p = case pointers of
                                   if (t == t')
                                     then [(getGroupId t,proxi)]
                                     else [(getGroupId t,proxi),(getGroupId t',proxi)] ) pairs ) ) []
-             -- | [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
+             -- [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
              $ inits periods
     --------------------------------------           
 
@@ -218,8 +218,6 @@ interTempoMatching fil lvl _ p = updateGroups fil lvl (Map.fromList pointers) p
 
 ------------------------------------------------------------------------
 -- | Make links from Period to Period after level 1
-
-
 listToTuple :: (a -> b) -> [a] -> [(b,a)]
 listToTuple f l = map (\x -> (f x, x)) l
 

src/Gargantext/Viz/Phylo/Metrics.hs

@@ -90,13 +90,13 @@ findDynamics n pv pn m =
         bid = fromJust $ (pn ^. pn_bid)
         end = last' "dynamics" (sort $ map snd $ elems m)
     in  if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
-            -- | emergence
+            -- emergence
             then 2
         else if ((fst prd) == (fst $ m ! n))
-            -- | recombination
+            -- recombination
             then 0
         else if (not $ sharedWithParents (fst prd) bid n pv)
-            -- | decrease
+            -- decrease
             then 1
         else 3
 
@@ -175,9 +175,3 @@ hamming f1 f2 = fromIntegral $ max ((size inter) - (size f1)) ((size inter) - (s
     inter :: Map (Int, Int) Double
     inter = intersection f1 f2 
     --------------------------------------
-
-
-
-
-
-

src/Gargantext/Viz/Phylo/PhyloExport.hs

@@ -171,12 +171,12 @@ exportToDot phylo export =
          <> "##########################") $
     digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do 
 
-        -- | 1) init the dot graph
+        {- 1) init the dot graph -}
         graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))]
                   <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps
                      , Ratio FillRatio
                      , Style [SItem Filled []],Color [toWColor White]]
-                  -- | home made attributes
+                  {-- home made attributes -}
                   <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo))
                      ,(toAttr (fromStrict "phyloTerms") $ pack $ show (length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups))
                      ,(toAttr (fromStrict "phyloDocs") $ pack $ show (sum $ elems $ phylo ^. phylo_timeDocs))
@@ -185,36 +185,36 @@ exportToDot phylo export =
                      ,(toAttr (fromStrict "phyloGroups") $ pack $ show (length $ export ^. export_groups))
                      ])
 
-
+{-
  -- toAttr (fromStrict k) $ (pack . unwords) $ map show v
 
-        -- | 2) create a layer for the branches labels
+        --  2) create a layer for the branches labels -}
         subgraph (Str "Branches peaks") $ do 
 
             graphAttrs [Rank SameRank]
-
-            -- | 3) group the branches by hierarchy
+{-
+            --  3) group the branches by hierarchy
             -- mapM (\branches -> 
             --         subgraph (Str "Branches clade") $ do
             --             graphAttrs [Rank SameRank]
 
-            --             -- | 4) create a node for each branch
+            --             --  4) create a node for each branch
             --             mapM branchToDotNode branches
             --     ) $ elems $ fromListWith (++) $ map (\b -> ((init . snd) $ b ^. branch_id,[b])) $ export ^. export_branches
-
+-}
             mapM (\b -> branchToDotNode b (fromJust $ elemIndex b (export ^. export_branches))) $ export ^. export_branches
 
-        -- | 5) create a layer for each period
+        {--  5) create a layer for each period -}
         _ <- mapM (\period ->
                 subgraph ((Str . fromStrict . Text.pack) $ ("Period" <> show (fst period) <> show (snd period))) $ do 
                     graphAttrs [Rank SameRank]
                     periodToDotNode period
 
-                    -- | 6) create a node for each group 
+                    {--  6) create a node for each group -}
                     mapM (\g -> groupToDotNode (getRoots phylo) g (toBid g (export ^. export_branches))) (filter (\g -> g ^. phylo_groupPeriod == period) $ export ^. export_groups)
             ) $ getPeriodIds phylo
 
-        -- | 7) create the edges between a branch and its first groups
+        {--  7) create the edges between a branch and its first groups -}
         _ <- mapM (\(bId,groups) ->
                 mapM (\g -> toDotEdge (branchIdToDotId bId) (groupIdToDotId $ getGroupId g) "" BranchToGroup) groups 
              )
@@ -224,31 +224,29 @@ exportToDot phylo export =
                            $ sortOn (fst . _phylo_groupPeriod) groups) 
            $ fromListWith (++) $ map (\g -> (g ^. phylo_groupBranchId,[g])) $ export ^. export_groups
 
-        -- | 8) create the edges between the groups
+        {-  8) create the edges between the groups -}
         _ <- mapM (\((k,k'),_) -> 
                 toDotEdge (groupIdToDotId k) (groupIdToDotId k') "" GroupToGroup
             ) $ (toList . mergePointers) $ export ^. export_groups
 
-        -- | 7) create the edges between the periods 
+        {-  7) create the edges between the periods -}
         _ <- mapM (\(prd,prd') ->
                 toDotEdge (periodIdToDotId prd) (periodIdToDotId prd') "" PeriodToPeriod
             ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ getPeriodIds phylo
 
-        -- | 8) create the edges between the branches 
+        {-  8) create the edges between the branches 
         -- _ <- mapM (\(bId,bId') ->
         --         toDotEdge (branchIdToDotId bId) (branchIdToDotId bId') 
         --         (Text.pack $ show(branchIdsToProximity bId bId' 
         --                             (getThresholdInit $ phyloProximity $ getConfig phylo)
         --                             (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch
         --     ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches
+        -}
 
 
         graphAttrs [Rank SameRank]
 
 
-        
-
-
 ----------------
 -- | Filter | --
 ----------------
@@ -439,13 +437,13 @@ toDynamics n parents g m =
     let prd = g ^. phylo_groupPeriod
         end = last' "dynamics" (sort $ map snd $ elems m)
     in  if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
-            -- | decrease
+            {- decrease -}
             then 2
         else if ((fst prd) == (fst $ m ! n))
-            -- | recombination
+            {- recombination -}
             then 0
         else if isNew
-            -- | emergence
+            {- emergence -}
             then 1
         else 3
     where

src/Gargantext/Viz/Phylo/PhyloMaker.hs

@@ -115,7 +115,7 @@ cliqueToGroup fis pId lvl idx fdt coocs =
                    (fis ^. phyloClique_support)
                    ngrams
                    (ngramsToCooc ngrams coocs)
-                   (1,[0]) -- | branchid (lvl,[path in the branching tree])
+                   (1,[0]) --  branchid (lvl,[path in the branching tree])
                    (fromList [("breaks",[0]),("seaLevels",[0])])
                    [] [] [] []
 
@@ -142,24 +142,24 @@ toPhylo1 docs phyloBase = case (getSeaElevation phyloBase) of
 ---------------------------
 
 
--- | To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
+--  To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
 filterClique :: Bool -> Int -> (Int -> [PhyloClique] -> [PhyloClique]) -> Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
 filterClique keep thr f m = case keep of
   False -> map (\l -> f thr l) m
   True  -> map (\l -> keepFilled (f) thr l) m
 
 
--- | To filter Fis with small Support
+--  To filter Fis with small Support
 filterCliqueBySupport :: Int -> [PhyloClique] -> [PhyloClique]
 filterCliqueBySupport thr l = filter (\clq -> (clq ^. phyloClique_support) >= thr) l
 
 
--- | To filter Fis with small Clique size
+--  To filter Fis with small Clique size
 filterCliqueBySize :: Int -> [PhyloClique] -> [PhyloClique]
 filterCliqueBySize thr l = filter (\clq -> (size $ clq ^. phyloClique_nodes) >= thr) l
 
 
--- | To filter nested Fis
+--  To filter nested Fis
 filterCliqueByNested :: Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
 filterCliqueByNested m = 
   let clq  = map (\l -> 
@@ -173,16 +173,16 @@ filterCliqueByNested m =
   in  fromList $ zip (keys m) clq' 
 
 
--- | To transform a time map of docs innto a time map of Fis with some filters
+--  To transform a time map of docs innto a time map of Fis with some filters
 toPhyloClique :: Phylo -> Map (Date, Date) [Document] -> Map (Date,Date) [PhyloClique]
 toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of 
     Fis s s' -> -- traceFis "Filtered Fis"
                 filterCliqueByNested 
-                -- $ traceFis "Filtered by clique size"
+                {- \$ traceFis "Filtered by clique size" -}
                 $ filterClique True s' (filterCliqueBySize)
-                -- $ traceFis "Filtered by support"
+                {- \$ traceFis "Filtered by support" -}
                 $ filterClique True s (filterCliqueBySupport)
-                -- $ traceFis "Unfiltered Fis" 
+                {- \$ traceFis "Unfiltered Fis" -}
                 phyloClique
     MaxClique _ -> undefined
     where
@@ -204,7 +204,7 @@ toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of
 --------------------
 
 
--- | To transform the docs into a time map of coocurency matrix 
+--  To transform the docs into a time map of coocurency matrix 
 docsToTimeScaleCooc :: [Document] -> Vector Ngrams -> Map Date Cooc
 docsToTimeScaleCooc docs fdt = 
     let mCooc  = fromListWith sumCooc
@@ -221,7 +221,7 @@ docsToTimeScaleCooc docs fdt =
 -- | to Phylo Base | --
 -----------------------
 
--- | To group a list of Documents by fixed periods
+--  To group a list of Documents by fixed periods
 groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
 groupDocsByPeriod' f pds docs = 
   let docs'    = groupBy (\d d' -> f d == f d') $ sortOn f docs
@@ -237,7 +237,7 @@ groupDocsByPeriod' f pds docs =
 
 
 
--- | To group a list of Documents by fixed periods
+--  To group a list of Documents by fixed periods
 groupDocsByPeriod :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
 groupDocsByPeriod _ _   [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents] can not have any periods"
 groupDocsByPeriod f pds es = 
@@ -265,7 +265,7 @@ docsToTermFreq docs fdt =
    in map (/sumFreqs) freqs
 
 
--- | To count the number of docs by unit of time
+--  To count the number of docs by unit of time
 docsToTimeScaleNb :: [Document] -> Map Date Double
 docsToTimeScaleNb docs = 
     let docs' = fromListWith (+) $ map (\d -> (date d,1)) docs
@@ -279,7 +279,7 @@ initPhyloLevels lvlMax pId =
     fromList $ map (\lvl -> ((pId,lvl),PhyloLevel pId lvl empty)) [1..lvlMax]
 
 
--- | To init the basic elements of a Phylo
+--  To init the basic elements of a Phylo
 toPhyloBase :: [Document] -> TermList -> Config -> Phylo
 toPhyloBase docs lst conf = 
     let foundations  = PhyloFoundations (Vector.fromList $ nub $ concat $ map text docs) lst

src/Gargantext/Viz/Phylo/SynchronicClustering.hs

@@ -36,13 +36,13 @@ import qualified Data.Set as Set
 mergeBranchIds :: [[Int]] -> [Int]
 mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq') ids
   where
-    -- | 2) find the most Up Left ids in the hierarchy of similarity
+    --  2) find the most Up Left ids in the hierarchy of similarity
     -- mostUpLeft :: [[Int]] -> [[Int]]
     -- mostUpLeft ids' = 
     --      let groupIds = (map (\gIds -> (length $ head' "gIds" gIds, head' "gIds" gIds)) . groupBy (\id id' -> length id == length id') . sortOn length) ids'
     --          inf = (fst . minimum) groupIds
     --      in map snd $ filter (\gIds -> fst gIds == inf) groupIds
-    -- | 1) find the most frequent ids
+    --  1) find the most frequent ids
     mostFreq' :: [[Int]] -> [[Int]]
     mostFreq' ids' = 
        let groupIds = (map (\gIds -> (length gIds, head' "gIds" gIds)) . group . sort) ids'
@@ -58,12 +58,12 @@ mergeMeta bId groups =
 
 groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
 groupsToBranches' groups =
-    -- | run the related component algorithm
+    --  run the related component algorithm
     let egos  = map (\g -> [getGroupId g] 
                         ++ (map fst $ g ^. phylo_groupPeriodParents)
                         ++ (map fst $ g ^. phylo_groupPeriodChilds) ) $ elems groups
         graph = relatedComponents egos
-    -- | update each group's branch id
+    --  update each group's branch id
     in map (\ids ->
         let groups' = elems $ restrictKeys groups (Set.fromList ids)
             bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) groups'
@@ -103,26 +103,26 @@ toNextLevel' phylo groups =
         newGroups = concat $ groupsToBranches'
                   $ fromList $ map (\g -> (getGroupId g, g))
                   $ foldlWithKey (\acc id groups' ->
-                        -- | 4) create the parent group
+                        --  4) create the parent group
                         let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
                         in  acc ++ [parent]) []
-                  -- | 3) group the current groups by parentId
+                  --  3) group the current groups by parentId
                   $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
 
         newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
     in  traceSynchronyEnd 
       $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
-             -- | 6) update each period at curLvl + 1
+             --  6) update each period at curLvl + 1
              . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
-             -- | 7) by adding the parents
+             --  7) by adding the parents
              (\phyloLvl -> 
                 if member (phyloLvl ^. phylo_levelPeriod) newPeriods
                     then phyloLvl & phylo_levelGroups
                             .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
                     else phyloLvl)
-      -- | 2) add the curLvl + 1 phyloLevel to the phylo
+      --  2) add the curLvl + 1 phyloLevel to the phylo
       $ addPhyloLevel (curLvl + 1)
-      -- | 1) update the current groups (with level parent pointers) in the phylo
+      --  1) update the current groups (with level parent pointers) in the phylo
       $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo 
 
 --------------------
@@ -187,19 +187,19 @@ toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1),
 
 reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 reduceGroups prox sync docs diagos branch =
-    -- | 1) reduce a branch as a set of periods & groups
+    --  1) reduce a branch as a set of periods & groups
     let periods = fromListWith (++)
                  $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
     in  (concat . concat . elems)
       $ mapWithKey (\prd groups -> 
-            -- | 2) for each period, transform the groups as a proximity graph filtered by a threshold
+            --  2) for each period, transform the groups as a proximity graph filtered by a threshold
             let diago = reduceDiagos $ filterDiago diagos [prd]
                 edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
              in map (\comp -> 
-                    -- | 4) add to each groups their futur level parent group
+                    --  4) add to each groups their futur level parent group
                     let parentId = toParentId (head' "parentId" comp)
                     in  map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
-                -- |3) reduce the graph a a set of related components
+                -- 3) reduce the graph a a set of related components
               $ toRelatedComponents groups edges) periods 
 
 
@@ -251,4 +251,4 @@ synchronicClustering phylo =
 --                                               <> "\n"
 --                                         ) "" edges 
 --                      ) ""  $ elems $ groupByField _phylo_groupPeriod branch)
---     ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo
\ No newline at end of file
+--     ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo

stack.yaml

@@ -58,7 +58,6 @@ extra-deps:
   commit: 308c74b71a1abb0a91546fa57d353131248e3a7f
 - Unique-0.4.7.6@sha256:a1ff411f4d68c756e01e8d532fbe8e57f1ac77f2cc0ee8a999770be2bca185c5,2723
 - KMP-0.1.0.2
-- accelerate-1.2.0.1
 - aeson-lens-0.5.0.0
 - deepseq-th-0.1.0.4
 - duckling-0.1.3.0
@@ -84,3 +83,7 @@ extra-deps:
 - password-2.0.1.1
 - base64-0.4.2@sha256:e9523e18bdadc3cab9dc32dfe3ac09c718fe792076326d6d353437b8b255cb5b,2888
 - ghc-byteorder-4.11.0.0.10@sha256:5ee4a907279bfec27b0f9de7b8fba4cecfd34395a0235a7784494de70ad4e98f,1535
+  # Matrix Computation
+- accelerate-1.2.0.1
+
+