Code review amendments

bench/Main.hs

@@ -21,7 +21,6 @@ import qualified Data.Array.Accelerate.LLVM.Native as LLVM
 import qualified Data.Array.Accelerate.Interpreter as Naive
 import qualified Data.List.Split as Split
 import qualified Data.Massiv.Array as Massiv
-import qualified Data.Massiv.Array.Numeric as Massiv
 import qualified Gargantext.Core.LinearAlgebra as LA
 import qualified Gargantext.Core.Methods.Matrix.Accelerate.Utils as Accelerate
 import qualified Gargantext.Core.Methods.Similarities.Accelerate.Distributional as Accelerate
@@ -81,7 +80,6 @@ main = do
   issue290PhyloSmall <- force . setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290-small.json")
   let !accInput       = force testMatrix
   let !accVector      = force testVector
-  let !massivInput    = force testMassivMatrix
   let !massivVector   = force testMassivVector
   let !(accDoubleInput :: Accelerate.Matrix Double) = force $ Naive.run $ Accelerate.map Accelerate.fromIntegral (Accelerate.use testMatrix)
   let !massivInput    = force testMassivMatrix
@@ -124,8 +122,8 @@ main = do
       ,   bench "Massiv " $ nf (LA.matrixEye @Double) 1000
       ]
       , bgroup "matMaxMini" [
-          bench "Accelerate (Naive)" $ nf (\v -> Naive.run . Accelerate.matMaxMini @Double . Accelerate.use) accDoubleInput
-      ,   bench "Accelerate (LLVM)"  $ nf (\v -> LLVM.run  . Accelerate.matMaxMini @Double . Accelerate.use) accDoubleInput
+          bench "Accelerate (Naive)" $ nf (Naive.run . Accelerate.matMaxMini @Double . Accelerate.use) accDoubleInput
+      ,   bench "Accelerate (LLVM)"  $ nf (LLVM.run  . Accelerate.matMaxMini @Double . Accelerate.use) accDoubleInput
       ,   bench "Massiv " $ nf LA.matMaxMini massivDoubleInput
       ]
       , bgroup "(.*)" [

gargantext.cabal

@@ -710,15 +710,17 @@ executable gargantext
     , vector >= 0.12.3.0 && <= 0.13.1.0
   ghc-options: -Wall -Wincomplete-uni-patterns -Wincomplete-record-updates -Wmissing-signatures -Wunused-binds -Wunused-imports -Werror -freduction-depth=300 -fprint-potential-instances
 
-common testDependencies
+-- Dependencies needed by both test stanzas. Dependencies
+-- which are not shared must be placed in the `build-depends`
+-- of each separate stanza to not trigger any warning if `-Wunused-packages`
+-- is enabled.
+common commonTestDependencies
   build-depends:
       base >=4.7 && <5
     , QuickCheck ^>= 2.14.2
-    , accelerate >= 1.3.0.0
     , aeson ^>= 2.1.2.1
     , aeson-qq
     , async ^>= 2.2.4
-    , bimap >= 0.5.0
     , bytestring ^>= 0.11.5.3
     , cache >= 0.1.3.0
     , containers ^>= 0.6.7
@@ -740,8 +742,6 @@ common testDependencies
     , http-client-tls == 0.3.6.1
     , http-types
     , lens >= 5.2.2 && < 5.3
-    , massiv < 1.1
-    , massiv-test < 1.2
     , monad-control >= 1.0.3 && < 1.1
     , mtl ^>= 2.2.2
     , network-uri
@@ -754,7 +754,6 @@ common testDependencies
     , raw-strings-qq
     , resource-pool >= 0.4.0.0 && < 0.5
     , safe-exceptions >= 0.1.7.4 && < 0.2
-    , scientific < 0.4
     , servant-auth-client
     , servant-client >= 0.20 && < 0.21
     , servant-client-core >= 0.20 && < 0.21
@@ -762,7 +761,6 @@ common testDependencies
     , shelly >= 1.9 && < 2
     , stm >= 2.5.1.0 && < 2.6
     , streaming-commons
-    , split
     , tasty-hunit
     , tasty-quickcheck
     , text ^>= 2.0.2
@@ -778,17 +776,20 @@ common testDependencies
 test-suite garg-test-tasty
   import:
       defaults
-    , testDependencies
+    , commonTestDependencies
   type: exitcode-stdio-1.0
   main-is: drivers/tasty/Main.hs
   build-depends:
       aeson-pretty ^>= 0.8.9
+    , accelerate >= 1.3.0.0
     , boolexpr ^>= 0.3
     , conduit ^>= 1.3.4.2
     , crawlerArxiv
     , cryptohash
     , directory ^>= 1.3.7.1
     , graphviz ^>= 2999.20.1.0
+    , massiv < 1.1
+    , scientific < 0.4
     , split
     , tasty >= 1.4.3 && < 1.6
     , tasty-golden
@@ -861,7 +862,7 @@ test-suite garg-test-tasty
 test-suite garg-test-hspec
   import:
       defaults
-    , testDependencies
+    , commonTestDependencies
   type: exitcode-stdio-1.0
   main-is: drivers/hspec/Main.hs
   build-depends: process ^>= 1.6.18.0
@@ -905,7 +906,6 @@ benchmark garg-bench
   other-modules:
       Paths_gargantext
   build-depends: base
-               , bytestring ^>= 0.11.5.3
                , accelerate
                , accelerate-llvm-native
                , hmatrix

src/Gargantext/Core/LinearAlgebra.hs

@@ -15,35 +15,10 @@ Linear algebra utility functions to be used across all the Gargantext modules re
 -}
 
 module Gargantext.Core.LinearAlgebra (
-  -- * Types
-    Index(..)
-
-  -- * Functions
-  , createIndices
-
   -- * Handy re-exports
-  , module Gargantext.Core.LinearAlgebra.Operations
+    module Gargantext.Core.LinearAlgebra.Operations
   , module Gargantext.Core.LinearAlgebra.Distributional
   ) where
 
-import Data.Bimap (Bimap)
-import Data.Bimap qualified as Bimap
-import Data.Map.Strict (Map)
-import Data.Map.Strict qualified as M
-import Data.Set qualified as S
-import Data.Set (Set)
-import Prelude
 import Gargantext.Core.LinearAlgebra.Operations
 import Gargantext.Core.LinearAlgebra.Distributional
-
-newtype Index = Index { _Index :: Int }
-  deriving newtype (Eq, Show, Ord, Num, Enum)
-
-createIndices :: Ord t => Map (t, t) b -> Bimap Index t
-createIndices = set2indices . map2set
-  where
-    map2set :: Ord t => Map (t, t) a -> Set t
-    map2set cs' = foldr (\(t1, t2) s -> S.insert t1 $! S.insert t2 $! s) mempty $ M.keys cs'
-
-    set2indices :: Ord t => Set t -> Bimap Index t
-    set2indices s = foldr (uncurry Bimap.insert) Bimap.empty (zip [0..] $ S.toList s)

src/Gargantext/Core/LinearAlgebra/Distributional.hs

 {-# LANGUAGE DerivingStrategies #-}
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE TypeApplications #-}
-{-# LANGUAGE TypeOperators #-}
-{-# OPTIONS_GHC -Wall-missed-specialisations #-}
 {-|
 Module      : Gargantext.Core.LinearAlgebra.Distributional
 Description : The "distributional" algorithm, fast and slow implementations
@@ -27,7 +25,7 @@ import Data.Massiv.Array qualified as A
 import Gargantext.Core.LinearAlgebra.Operations
 import Prelude
 
--- | `distributional m` returns the distributional distance between terms each
+-- | `distributional m` returns the distributional distance between each
 -- pair of terms as a matrix.  The argument m is the matrix $[n_{ij}]_{i,j}$
 -- where $n_{ij}$ is the coocccurrence between term $i$ and term $j$.
 --
@@ -228,7 +226,6 @@ logDistributional2 m = A.computeP
                      $ logDistributional' n m
   where
     n = dim m
-{-# SPECIALIZE logDistributional2 :: Matrix A.U Int -> Matrix A.U Double #-}
 
 logDistributional' :: forall r e.
                    ( A.Manifest r e

test/Test/Core/LinearAlgebra.hs

@@ -10,11 +10,6 @@ module Test.Core.LinearAlgebra where
 import Data.Array.Accelerate hiding (Ord, Eq, map, (<=))
 import Data.Array.Accelerate.Interpreter qualified as Naive
 import Data.Array.Accelerate qualified as A
-import Data.Bifunctor (first)
-import Data.Bimap (Bimap)
-import Data.Bimap qualified as Bimap
-import Data.Map.Strict (Map)
-import Data.Map.Strict qualified as M
 import Data.Massiv.Array qualified as Massiv
 import Data.Proxy
 import Data.Scientific
@@ -22,7 +17,6 @@ import Gargantext.Core.LinearAlgebra qualified as LA
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils qualified as A
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils qualified as Legacy
 import Gargantext.Core.Methods.Similarities.Accelerate.Distributional qualified as Legacy
-import Gargantext.Core.Viz.Graph.Index qualified as Legacy
 import Gargantext.Orphans.Accelerate (sliceArray)
 import Prelude hiding ((^))
 import Test.Tasty
@@ -43,27 +37,6 @@ instance (Elt a, Show a, Prelude.Num a, Ord a, Arbitrary a) => Arbitrary (Square
     SquareMatrix . A.fromList sh <$> vectorOf (x*x) arbitrary
   shrink = map (SquareMatrix) . sliceArray . _SquareMatrix
 
-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)
-
-compareImplementations' :: (Arbitrary a, Eq c, Show c)
-                       => (a -> b)
-                       -> (a -> b)
-                       -> (b -> c)
-                       -> a
-                       -> Property
-compareImplementations' implementation1 implementation2 mapResults inputData
-  = mapResults (implementation1 inputData) === mapResults (implementation2 inputData)
-
-mapCreateIndices :: Ord t => (Map t Legacy.Index, Map Legacy.Index t) -> Bimap LA.Index t
-mapCreateIndices (_m1, m2) = Bimap.fromList $ map (first LA.Index) $ M.toList m2
-
 type TermDivNanShape = Z :. Int :. Int
 
 twoByTwo :: SquareMatrix Int
@@ -126,8 +99,7 @@ testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8) $
 
 tests :: TestTree
 tests = testGroup "LinearAlgebra" [
-      testProperty "createIndices roundtrip" (compareImplementations (LA.createIndices @Int @Int) Legacy.createIndices mapCreateIndices)
-    , testProperty "termDivNan"     compareTermDivNan
+      testProperty "termDivNan"     compareTermDivNan
     , testProperty "diag"           compareDiag
     , testProperty "sumRows"        compareSumRows
     , testProperty "matMaxMini"     compareMatMaxMini