[Ord] G.C.Methods.Distances

src/Gargantext/API/Node/Update.hs

@@ -30,7 +30,7 @@ import Gargantext.API.Admin.Orchestrator.Types (JobLog(..), AsyncJobs)
 import Gargantext.API.Admin.Types (HasSettings)
 import Gargantext.API.Prelude (GargServer, simuLogs)
 import Gargantext.Core.Viz.Graph.API (recomputeGraph)
-import Gargantext.Core.Viz.Graph.Distances (GraphMetric(..), Distance(..))
+import Gargantext.Core.Methods.Distances (GraphMetric(..), Distance(..))
 import Gargantext.Database.Action.Flow.Pairing (pairing)
 import Gargantext.Database.Action.Flow.Types (FlowCmdM)
 import Gargantext.Database.Admin.Types.Node

src/Gargantext/Core/Viz/Graph/Distances.hs → src/Gargantext/Core/Methods/Distances.hs

@@ -11,7 +11,7 @@ Portability : POSIX
 
 {-# LANGUAGE Strict            #-}
 
-module Gargantext.Core.Viz.Graph.Distances
+module Gargantext.Core.Methods.Distances
   where
 
 import Data.Aeson
@@ -20,7 +20,7 @@ import Data.Swagger
 import GHC.Generics (Generic)
 import Gargantext.Prelude (Ord, Eq, Int, Double)
 import Gargantext.Prelude (Show)
-import Gargantext.Core.Viz.Graph.Distances.Matrice (measureConditional, distributional)
+import Gargantext.Core.Methods.Distances.Matrice (measureConditional, distributional)
 import Prelude (Enum, Bounded, minBound, maxBound)
 import Test.QuickCheck (elements)
 import Test.QuickCheck.Arbitrary

src/Gargantext/Core/Viz/Graph/Distances/Conditional.hs → src/Gargantext/Core/Methods/Distances/Conditional.hs

 {-|
-Module      : Gargantext.Graph.Distances.Conditional
+Module      : Gargantext.Core.Methods.Distances
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -12,7 +12,7 @@ Motivation and definition of the @Conditional@ distance.
 
 {-# LANGUAGE BangPatterns      #-}
 {-# LANGUAGE Strict            #-}
-module Gargantext.Core.Viz.Graph.Distances.Conditional
+module Gargantext.Core.Methods.Distances.Conditional
   where
 
 import Data.Matrix hiding (identity)

src/Gargantext/Core/Viz/Graph/Distances/Distributional.hs → src/Gargantext/Core/Methods/Distances/Distributional.hs

 {-|
-Module      : Gargantext.Graph.Distances.Distributional
+Module      : Gargantext.Core.Methods.Distances
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -14,7 +14,7 @@ Motivation and definition of the @Distributional@ distance.
 {-# LANGUAGE Strict            #-}
 
 
-module Gargantext.Core.Viz.Graph.Distances.Distributional
+module Gargantext.Core.Methods.Distances.Distributional
   where
 
 import Data.Matrix hiding (identity)

src/Gargantext/Core/Viz/Graph/Distances/Matrice.hs → src/Gargantext/Core/Methods/Distances/Matrice.hs

 {-|
-Module      : Gargantext.Graph.Distances.Matrix
+Module      : Gargantext.Core.Methods.Distances.Matrice
 Description : 
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
@@ -27,7 +27,7 @@ Implementation use Accelerate library which enables GPU and CPU computation:
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE ViewPatterns        #-}
 
-module Gargantext.Core.Viz.Graph.Distances.Matrice
+module Gargantext.Core.Methods.Distances.Matrice
   where
 
 import qualified Data.Foldable as P (foldl1)

src/Gargantext/Core/Viz/Graph/MaxClique.hs → src/Gargantext/Core/Methods/Graph/MaxClique.hs

@@ -6,7 +6,7 @@ Maintainer  : team@gargantext.org
 Stability   : experimental
 Portability : POSIX
 
-- Result of Pyremiel 2019
+- Result of the workshop, Pyremiel 2019
   - First written by Bruno Gaume in Python        (see below for details)
   - Then  written by Alexandre Delanoë in Haskell (see below for details)
 
@@ -49,7 +49,7 @@ def fast_maximal_cliques(g):
 
 
 
-module Gargantext.Core.Viz.Graph.MaxClique
+module Gargantext.Core.Methods.Graph.MaxClique
   where
 
 import Data.Maybe (catMaybes)
@@ -62,12 +62,12 @@ import Data.Set (fromList, toList, isSubsetOf)
 import Data.Graph.Inductive hiding (Graph, neighbors, subgraph, (&))
 import Gargantext.Core.Viz.Graph.FGL (Graph_Undirected, degree, neighbors, mkGraphUfromEdges)
 import Gargantext.Core.Viz.Graph.Tools (cooc2graph', Threshold)
-import Gargantext.Core.Viz.Graph.Distances (Distance)
+import Gargantext.Core.Methods.Distances (Distance)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex)
+
 type Graph = Graph_Undirected
 type Neighbor = Node
 
-
 -- | getMaxCliques
 -- TODO chose distance order
 getMaxCliques :: Ord a => Distance -> Threshold -> Map (a, a) Int -> [[a]]

src/Gargantext/Core/Text/Examples.hs

@@ -26,29 +26,24 @@ This document defines basic of Text definitions according to Gargantext..
 module Gargantext.Core.Text.Examples
   where
 
-import Data.Ord (Down(..))
-import qualified Data.List as L
-
+import Data.Array.Accelerate (toList, Matrix)
 import Data.Map (Map)
-import qualified Data.Map  as M
-
+import Data.Ord (Down(..))
 import Data.Text (Text)
-import qualified Data.Text as T
-
 import Data.Tuple.Extra (both)
-import Data.Array.Accelerate (toList, Matrix)
-
-import Gargantext.Prelude
-import Gargantext.Core.Text.Metrics.Count (occurrences, cooc)
-import Gargantext.Core.Text.Terms (TermType(MonoMulti), terms)
 import Gargantext.Core (Lang(EN))
-import Gargantext.Core.Types (Terms(..), Label)
+import Gargantext.Core.Methods.Distances.Matrice
 import Gargantext.Core.Text.Context (splitBy, SplitContext(Sentences))
 import Gargantext.Core.Text.Metrics.Count (Grouped)
-import Gargantext.Core.Viz.Graph.Distances.Matrice
+import Gargantext.Core.Text.Metrics.Count (occurrences, cooc)
+import Gargantext.Core.Text.Terms (TermType(MonoMulti), terms)
+import Gargantext.Core.Types (Terms(..), Label)
 import Gargantext.Core.Viz.Graph.Index
-
+import Gargantext.Prelude
 import qualified Data.Array.Accelerate as DAA
+import qualified Data.List as List
+import qualified Data.Map  as Map
+import qualified Data.Text as Text
 
 -- | Sentences
 -- Let be a list of Texts: ['Data.Text.Text']. Each text in this example is a sentence.
@@ -70,7 +65,7 @@ ex_sentences = [ "There is a table with a glass of wine and a spoon."
 -- >>> T.intercalate (T.pack " ") ex_sentences
 -- "There is a table with a glass of wine and a spoon. I can see the glass on the table. There was only a spoon on that table. The glass just fall from the table, pouring wine everywhere. I wish the glass did not contain wine."
 ex_paragraph :: Text
-ex_paragraph = T.intercalate " " ex_sentences
+ex_paragraph = Text.intercalate " " ex_sentences
 
 -- | Let split sentences by Contexts of text.
 -- More about 'Gargantext.Core.Text.Context'
@@ -88,10 +83,10 @@ ex_terms = mapM (terms (MonoMulti EN)) $ splitBy (Sentences 0) ex_paragraph
 
 -- | Test the Occurrences
 --
--- >>> occurrences <$> L.concat <$> ex_terms
+-- >>> occurrences <$> List.concat <$> ex_terms
 -- fromList [(fromList ["glass"],fromList [(["glass"],4)]),(fromList ["spoon"],fromList [(["spoon"],2)]),(fromList ["tabl"],fromList [(["table"],4)]),(fromList ["wine"],fromList [(["wine"],3)])]
 ex_occ :: IO (Map Grouped (Map Terms Int))
-ex_occ = occurrences <$> L.concat <$> ex_terms
+ex_occ = occurrences <$> List.concat <$> ex_terms
 
 -- | Test the cooccurrences
 -- Use the 'Gargantext.Core.Text.Metrics.Count.cooc' function.
@@ -132,6 +127,6 @@ incExcSpeGen_sorted m = both ordonne (incExcSpeGen $ cooc2mat ti m)
   where
     (ti,fi) = createIndices m
     ordonne x = sortWith (Down . snd)
-              $ zip (map snd $ M.toList fi) (toList x)
+              $ zip (map snd $ Map.toList fi) (toList x)
 
 

src/Gargantext/Core/Text/Metrics.hs

@@ -20,7 +20,7 @@ module Gargantext.Core.Text.Metrics
 --import Math.KMeans (kmeans, euclidSq, elements)
 import Data.Map (Map)
 import Gargantext.Prelude
-import Gargantext.Core.Viz.Graph.Distances.Matrice
+import Gargantext.Core.Methods.Distances.Matrice
 import Gargantext.Core.Viz.Graph.Index
 import Gargantext.Core.Statistics (pcaReduceTo, Dimension(..))
 import qualified Data.Array.Accelerate as DAA

src/Gargantext/Core/Viz/Graph.hs

@@ -27,7 +27,7 @@ import qualified Text.Read as T
 import Gargantext.Core.Types (ListId)
 import Gargantext.Database.Admin.Types.Hyperdata.Prelude
 import Gargantext.Database.Admin.Types.Node (NodeId)
-import Gargantext.Core.Viz.Graph.Distances (GraphMetric)
+import Gargantext.Core.Methods.Distances (GraphMetric)
 import Gargantext.Prelude
 
 

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

@@ -48,7 +48,7 @@ import Gargantext.Prelude
 import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.GEXF ()
 import Gargantext.Core.Viz.Graph.Tools -- (cooc2graph)
-import Gargantext.Core.Viz.Graph.Distances (Distance(..), GraphMetric(..))
+import Gargantext.Core.Methods.Distances (Distance(..), GraphMetric(..))
 
 ------------------------------------------------------------------------
 -- | There is no Delete specific API for Graph since it can be deleted

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

@@ -24,7 +24,7 @@ import Gargantext.Prelude
 import Gargantext.Core.Statistics
 import Gargantext.Core.Viz.Graph
 import Gargantext.Core.Viz.Graph.Bridgeness (bridgeness)
-import Gargantext.Core.Viz.Graph.Distances (Distance(..), measure)
+import Gargantext.Core.Methods.Distances (Distance(..), measure)
 import Gargantext.Core.Viz.Graph.Index (createIndices, toIndex, map2mat, mat2map, Index)
 import Gargantext.Core.Viz.Graph.IGraph (mkGraphUfromEdges)
 import Gargantext.Core.Methods.Graph.BAC.Proxemy (confluence)

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

@@ -22,8 +22,8 @@ import Gargantext.Core.Viz.Phylo.TemporalMatching (adaptativeTemporalMatching, c
 import Gargantext.Core.Viz.Phylo.SynchronicClustering (synchronicClustering)
 import Gargantext.Core.Text.Context (TermList)
 import Gargantext.Core.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, Size(..))
-import Gargantext.Core.Viz.Graph.MaxClique (getMaxCliques)
-import Gargantext.Core.Viz.Graph.Distances (Distance(Conditional))
+import Gargantext.Core.Methods.Graph.MaxClique (getMaxCliques)
+import Gargantext.Core.Methods.Distances (Distance(Conditional))
 
 import Control.DeepSeq (NFData)
 import Control.Parallel.Strategies (parList, rdeepseq, using)