Introduce the Gargantext.Core.LinearAlgebra module

The main idea is trying to refactor/improve the existing linear algebra
functions one function at the time, using reference implementations and
benchmarks along the way.

gargantext.cabal

@@ -204,6 +204,7 @@ library
       Gargantext.Core.Notifications.Dispatcher.Types
       Gargantext.Core.Notifications.Dispatcher.WebSocket
       Gargantext.Core.Notifications.Nanomsg
+      Gargantext.Core.LinearAlgebra
       Gargantext.Core.Text
       Gargantext.Core.Text.Context
       Gargantext.Core.Text.Corpus.API
@@ -795,6 +796,7 @@ test-suite garg-test-tasty
       Test.API.Setup
       Test.API.Prelude
       Test.API.UpdateList
+      Test.Core.LinearAlgebra
       Test.Core.Notifications
       Test.Core.Orchestrator
       Test.Core.Similarity

src/Gargantext/Core/LinearAlgebra.hs

+{-# LANGUAGE DerivingStrategies #-}
+{-|
+Module      : Gargantext.Core.LinearAlgebra
+Description : Linear Algebra utility functions
+Copyright   : (c) CNRS, 2017-Present
+License     : AGPL + CECILL v3
+Maintainer  : team@gargantext.org
+Stability   : experimental
+Portability : POSIX
+
+Linear algebra utility functions to be used across all the Gargantext modules requiring it.
+-}
+
+module Gargantext.Core.LinearAlgebra (
+  -- * Types
+    Index(..)
+
+  -- * Functions
+  , createIndices
+  ) where
+
+import Prelude
+import Data.Map.Strict qualified as M
+import Data.Set qualified as S
+import Data.Set (Set)
+import Data.Map.Strict (Map)
+import Data.Foldable (foldl')
+
+newtype Index = Index { _Index :: Int }
+  deriving newtype (Eq, Show, Ord, Num, Enum)
+
+createIndices :: Ord t => Map (t, t) b -> (Map t Index, Map Index t)
+createIndices = set2indices . map2set
+  where
+    map2set :: Ord t => Map (t, t) a -> Set t
+    map2set cs' = foldl' (\s ((t1,t2),_) -> insert [t1,t2] s ) S.empty (M.toList cs')
+      where
+        insert as s = foldl' (\s' t -> S.insert t s') s as
+
+    set2indices :: Ord t => Set t -> (Map t Index, Map Index t)
+    set2indices s = (M.fromList toIndex', M.fromList fromIndex')
+      where
+        fromIndex' = zip [0..] xs
+        toIndex'   = zip xs [0..]
+        xs         = S.toList s

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

@@ -20,6 +20,7 @@ TODO:
 {-# LANGUAGE BangPatterns      #-}
 {-# LANGUAGE TypeOperators     #-}
 {-# LANGUAGE MonoLocalBinds    #-}
+{-# OPTIONS_GHC -Wno-unused-top-binds #-}
 
 module Gargantext.Core.Viz.Graph.Index
   where

test/Test/Core/LinearAlgebra.hs

+{-# LANGUAGE TypeApplications #-}
+
+module Test.Core.LinearAlgebra where
+
+import Prelude
+import Test.Tasty.QuickCheck
+import Gargantext.Core.LinearAlgebra qualified as LA
+import Test.Tasty
+import Gargantext.Core.Viz.Graph.Index qualified as Legacy
+import Data.Map.Strict (Map)
+import Data.Map.Strict qualified as M
+
+compareImplementations :: (Arbitrary a, Eq b, Show b)
+                       => (a -> b)
+                       -> (a -> c)
+                       -> (c -> b)
+                       -> a
+                       -> Property
+compareImplementations implementation1 implementation2 mapResults inputData
+  = implementation1 inputData === mapResults (implementation2 inputData)
+
+mapCreateIndices :: (Map t Legacy.Index, Map Legacy.Index t) -> (Map t LA.Index, Map LA.Index t)
+mapCreateIndices (m1, m2) = (M.map LA.Index m1, M.mapKeys LA.Index m2)
+
+tests :: TestTree
+tests = testGroup "LinearAlgebra" [
+    testProperty "createIndices roundtrip" (compareImplementations (LA.createIndices @Int @Int) Legacy.createIndices mapCreateIndices)
+    ]

test/drivers/tasty/Main.hs

@@ -30,6 +30,9 @@ import qualified Test.Offline.Phylo              as Phylo
 import qualified Test.Offline.Stemming.Lancaster as Lancaster
 import qualified Test.Parsers.Date               as PD
 import qualified Test.Utils.Crypto               as Crypto
+import qualified Test.Core.LinearAlgebra         as LinearAlgebra
+import qualified Test.Core.Notifications         as Notifications
+import qualified Test.Core.Similarity            as Similarity
 import qualified Test.Utils.Jobs                 as Jobs
 
 import System.IO (hGetBuffering, hSetBuffering)
@@ -78,4 +81,5 @@ main = do
     , Notifications.qcTests
     , Orchestrator.qcTests
     , NgramsTerms.tests
+    , LinearAlgebra.tests
     ]