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haskell-gargantext
haskell-gargantext
Commit 35e3d393 authored by Grégoire Locqueville's avatar Grégoire Locqueville
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A bit of cleanup. Also make all imports explicit or qualified

parent 06ca7c6f
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          test/Test/Core/LinearAlgebra.hs
          View file @ 35e3d393
          ...@@ -12,16 +12,17 @@ import Data.Array.Accelerate.Interpreter qualified as Naive ...@@ -12,16 +12,17 @@ import Data.Array.Accelerate.Interpreter qualified as Naive
          import Data.Array.Accelerate qualified as A import Data.Array.Accelerate qualified as A
          import Data.Functor ((<&>)) import Data.Functor ((<&>))
          import Data.Massiv.Array qualified as Massiv import Data.Massiv.Array qualified as Massiv
          import Data.Proxy import Data.Proxy (Proxy(Proxy))
          import Data.Scientific import Data.Scientific (Scientific, fromFloatDigits)
          import Gargantext.Core.LinearAlgebra qualified as LA 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 A
          import Gargantext.Core.Methods.Matrix.Accelerate.Utils qualified as Legacy import Gargantext.Core.Methods.Matrix.Accelerate.Utils qualified as Legacy
          import Gargantext.Core.Methods.Similarities.Accelerate.Distributional qualified as Legacy import Gargantext.Core.Methods.Similarities.Accelerate.Distributional qualified as Legacy
          import Gargantext.Orphans.Accelerate (sliceArray) import Gargantext.Orphans.Accelerate (sliceArray)
          import Prelude hiding ((^)) import Prelude hiding ((^))
          import Test.Tasty import Test.Tasty (TestTree, testGroup)
          import Test.Tasty.QuickCheck import qualified Test.Tasty.QuickCheck as QC
          import Test.Tasty.QuickCheck ((===), (.&&.))
          -- --
          ...@@ -31,11 +32,12 @@ import Test.Tasty.QuickCheck ...@@ -31,11 +32,12 @@ import Test.Tasty.QuickCheck
          newtype SquareMatrix a = SquareMatrix { _SquareMatrix :: Matrix a } newtype SquareMatrix a = SquareMatrix { _SquareMatrix :: Matrix a }
          deriving newtype (Show, Eq) deriving newtype (Show, Eq)
          instance (Elt a, Show a, Prelude.Num a, Ord a, Arbitrary a) => Arbitrary (SquareMatrix a) where instance (Elt a, Show a, Prelude.Num a, Ord a, QC.Arbitrary a) =>
          QC.Arbitrary (SquareMatrix a) where
          arbitrary = do arbitrary = do
          x <- choose (1,30) x <- QC.choose (1,30)
          let sh = Z :. x :. x let sh = Z :. x :. x
          SquareMatrix . A.fromList sh <$> vectorOf (x*x) arbitrary SquareMatrix . A.fromList sh <$> QC.vectorOf (x*x) QC.arbitrary
          shrink = map SquareMatrix . sliceArray . _SquareMatrix shrink = map SquareMatrix . sliceArray . _SquareMatrix
          ...@@ -45,16 +47,16 @@ instance (Elt a, Show a, Prelude.Num a, Ord a, Arbitrary a) => Arbitrary (Square ...@@ -45,16 +47,16 @@ instance (Elt a, Show a, Prelude.Num a, Ord a, Arbitrary a) => Arbitrary (Square
          newtype CoocMatrix = CoocMatrix { _CoocMatrix :: Matrix Int } newtype CoocMatrix = CoocMatrix { _CoocMatrix :: Matrix Int }
          deriving newtype (Show, Eq) deriving newtype (Show, Eq)
          instance Arbitrary CoocMatrix where instance QC.Arbitrary CoocMatrix where
          -- | We simulate the creation of a cooccurence matrix: there are `numContexts` -- | We simulate the creation of a cooccurence matrix: there are `numContexts`
          -- "virtual contexts" and `numTerms` "virtual terms"; for each context and -- "virtual contexts" and `numTerms` "virtual terms"; for each context and
          -- each term, the term has probability `probAppearance` to appear in the -- each term, the term has probability `probAppearance` to appear in the
          -- context. The generated matrix is the cooccurence matrix of the resulting -- context. The generated matrix is the cooccurence matrix of the resulting
          -- "virtual corpus" -- "virtual corpus"
          arbitrary = do arbitrary = do
          numContexts <- choose (1, 30) numContexts <- QC.choose (1, 30)
          numTerms <- choose (1, 30) numTerms <- QC.choose (1, 30)
          probAppearance <- (choose (0, 1) :: Gen Double) probAppearance <- (QC.choose (0, 1) :: QC.Gen Double)
          -- `appearances` is a list of lists of integers encoding which virtual terms -- `appearances` is a list of lists of integers encoding which virtual terms
          -- appear in which virtual contexts. More specifically, the integer j -- appear in which virtual contexts. More specifically, the integer j
          -- appears in the i-th list iff the virtual term j appears in the i-th -- appears in the i-th list iff the virtual term j appears in the i-th
          ...@@ -63,7 +65,7 @@ instance Arbitrary CoocMatrix where ...@@ -63,7 +65,7 @@ instance Arbitrary CoocMatrix where
          -- In a given virtual context, iterate over all terms and pick whether -- In a given virtual context, iterate over all terms and pick whether
          -- they appear in the context with probability `probAppearance` -- they appear in the context with probability `probAppearance`
          foldM (\termsSoFar candidateTerm -> do foldM (\termsSoFar candidateTerm -> do
          randomVar <- choose (0, 1) randomVar <- QC.choose (0, 1)
          return $ if randomVar < probAppearance then candidateTerm : termsSoFar return $ if randomVar < probAppearance then candidateTerm : termsSoFar
          else termsSoFar else termsSoFar
          ) [] [1..numTerms] ) [] [1..numTerms]
          ...@@ -71,7 +73,7 @@ instance Arbitrary CoocMatrix where ...@@ -71,7 +73,7 @@ instance Arbitrary CoocMatrix where
          [1..numTerms] <&> (\j -> [1..numTerms] <&> (\j ->
          (i, j) )) (i, j) ))
          -- For each pair of virtual terms, iterate over all virtual contexts and add -- For each pair of virtual terms, iterate over all virtual contexts and add
          -- 1 each time both term appear in the context: -- 1 each time both terms appear in the context:
          let coocMatrix = (fmap . fmap) (\(i, j) -> let coocMatrix = (fmap . fmap) (\(i, j) ->
          foldr (\contextTerms currentCoocCount -> foldr (\contextTerms currentCoocCount ->
          if i `elem` contextTerms && j `elem` contextTerms if i `elem` contextTerms && j `elem` contextTerms
          ...@@ -90,7 +92,7 @@ twoByTwo :: SquareMatrix Int ...@@ -90,7 +92,7 @@ twoByTwo :: SquareMatrix Int
          twoByTwo = SquareMatrix $ fromList (Z :. 2 :. 2) (Prelude.replicate 4 5) twoByTwo = SquareMatrix $ fromList (Z :. 2 :. 2) (Prelude.replicate 4 5)
          testMatrix_01 :: SquareMatrix Int testMatrix_01 :: SquareMatrix Int
          testMatrix_01 = SquareMatrix $ fromList (Z :. 14 :. 14) $ testMatrix_01 = SquareMatrix $ fromList (Z :. 14 :. 14)
          [ 30, 36, -36, -16, 0, 7, 34, -7, 5, -4, 0, 21, 6, -35, [ 30, 36, -36, -16, 0, 7, 34, -7, 5, -4, 0, 21, 6, -35,
          0, -31, 20, -15, -22, -7, -22, -37, -29, -29, 23, -31, -29, -23, 0, -31, 20, -15, -22, -7, -22, -37, -29, -29, 23, -31, -29, -23,
          -24, -29, 19, -6, 16, 7, 15, -27, -27, -30, -9, -33, 18, -23, -24, -29, 19, -6, 16, 7, 15, -27, -27, -30, -9, -33, 18, -23,
          ...@@ -107,7 +109,7 @@ testMatrix_01 = SquareMatrix $ fromList (Z :. 14 :. 14) $ ...@@ -107,7 +109,7 @@ testMatrix_01 = SquareMatrix $ fromList (Z :. 14 :. 14) $
          13, -37, -16, 2, 7, -13, 21, -10, -33, -33, -26, -19, -1, 29] 13, -37, -16, 2, 7, -13, 21, -10, -33, -33, -26, -19, -1, 29]
          testMatrix_02 :: SquareMatrix Int testMatrix_02 :: SquareMatrix Int
          testMatrix_02 = SquareMatrix $ fromList (Z :. 7 :. 7) $ testMatrix_02 = SquareMatrix $ fromList (Z :. 7 :. 7)
          [ 30, 36, -36, -16, 0, 7, 34, [ 30, 36, -36, -16, 0, 7, 34,
          0, -31, 20, -15, -22, -7, -22, 0, -31, 20, -15, -22, -7, -22,
          -24, -29, 19, -6, 16, 7, 15, -24, -29, 19, -6, 16, 7, 15,
          ...@@ -117,7 +119,7 @@ testMatrix_02 = SquareMatrix $ fromList (Z :. 7 :. 7) $ ...@@ -117,7 +119,7 @@ testMatrix_02 = SquareMatrix $ fromList (Z :. 7 :. 7) $
          13, -37, -16, 2, 7, -13, 21] 13, -37, -16, 2, 7, -13, 21]
          testMatrix_03 :: SquareMatrix Int testMatrix_03 :: SquareMatrix Int
          testMatrix_03 = SquareMatrix $ fromList (Z :. 11 :. 11) $ testMatrix_03 = SquareMatrix $ fromList (Z :. 11 :. 11)
          [ 1, -1, 1, 0, 1, -1, 0, 1, 1, 0, 0, [ 1, -1, 1, 0, 1, -1, 0, 1, 1, 0, 0,
          1, 1, 1, 1, 1, 0, 1, -1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 1, -1, 1, 0, 0,
          -1, 1, 0, -1, 0, -1, 0, 1, 0, -1, 0, -1, 1, 0, -1, 0, -1, 0, 1, 0, -1, 0,
          ...@@ -131,7 +133,7 @@ testMatrix_03 = SquareMatrix $ fromList (Z :. 11 :. 11) $ ...@@ -131,7 +133,7 @@ testMatrix_03 = SquareMatrix $ fromList (Z :. 11 :. 11) $
          1, 1, -1, 0, -1, -1, 1, 0, 1, 0, -1] 1, 1, -1, 0, -1, -1, 1, 0, 1, 0, -1]
          testMatrix_04 :: SquareMatrix Int testMatrix_04 :: SquareMatrix Int
          testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8) $ testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8)
          [ 3, -1, 0, 1, -1, 1, 1, -3, [ 3, -1, 0, 1, -1, 1, 1, -3,
          -2, -2, 2, 1, 1, -2, 1, -1, -2, -2, 2, 1, 1, -2, 1, -1,
          -2, -3, -1, 1, 1, -3, -2, -1, -2, -3, -1, 1, 1, -3, -2, -1,
          ...@@ -146,28 +148,28 @@ testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8) $ ...@@ -146,28 +148,28 @@ testMatrix_04 = SquareMatrix $ fromList (Z :. 8 :. 8) $
          tests :: TestTree tests :: TestTree
          tests = testGroup "LinearAlgebra" [ tests = testGroup "LinearAlgebra" [
          testProperty "termDivNan" compareTermDivNan QC.testProperty "termDivNan" compareTermDivNan
          , testProperty "diag" compareDiag , QC.testProperty "diag" compareDiag
          , testProperty "sumRows" compareSumRows , QC.testProperty "sumRows" compareSumRows
          , testProperty "matMaxMini" compareMatMaxMini , QC.testProperty "matMaxMini" compareMatMaxMini
          , testProperty "sumM_go" compareSumM_go , QC.testProperty "sumM_go" compareSumM_go
          , testProperty "sumMin_go" compareSumMin_go , QC.testProperty "sumMin_go" compareSumMin_go
          , testProperty "matrixEye" compareMatrixEye , QC.testProperty "matrixEye" compareMatrixEye
          , testProperty "diagNull" compareDiagNull , QC.testProperty "diagNull" compareDiagNull
          , testGroup "distributional" [ , testGroup "distributional" [
          testProperty "reference implementation roundtrips" compareDistributionalImplementations QC.testProperty "reference implementation roundtrips" compareDistributionalImplementations
          , testProperty "2x2" (compareDistributional (Proxy @Double) twoByTwo) , QC.testProperty "2x2" (compareDistributional (Proxy @Double) twoByTwo)
          , testProperty "7x7" (compareDistributional (Proxy @Double) testMatrix_02) , QC.testProperty "7x7" (compareDistributional (Proxy @Double) testMatrix_02)
          , testProperty "14x14" (compareDistributional (Proxy @Double) testMatrix_01) , QC.testProperty "14x14" (compareDistributional (Proxy @Double) testMatrix_01)
          , testProperty "roundtrips" (compareDistributional (Proxy @Double)) , QC.testProperty "roundtrips" (compareDistributional (Proxy @Double))
          ] ]
          , testGroup "logDistributional2" [ , testGroup "logDistributional2" [
          testProperty "2x2" (compareLogDistributional2 (Proxy @Double) twoByTwo) QC.testProperty "2x2" (compareLogDistributional2 (Proxy @Double) twoByTwo)
          , testProperty "7x7" (compareLogDistributional2 (Proxy @Double) testMatrix_02) , QC.testProperty "7x7" (compareLogDistributional2 (Proxy @Double) testMatrix_02)
          , testProperty "8x8" (compareLogDistributional2 (Proxy @Double) testMatrix_04) , QC.testProperty "8x8" (compareLogDistributional2 (Proxy @Double) testMatrix_04)
          , testProperty "11x11" (compareLogDistributional2 (Proxy @Double) testMatrix_03) , QC.testProperty "11x11" (compareLogDistributional2 (Proxy @Double) testMatrix_03)
          , testProperty "14x14" (compareLogDistributional2 (Proxy @Double) testMatrix_01) , QC.testProperty "14x14" (compareLogDistributional2 (Proxy @Double) testMatrix_01)
          ,testProperty "roundtrips" (compareLogDistributional2 (Proxy @Double)) ,QC.testProperty "roundtrips" (compareLogDistributional2 (Proxy @Double))
          ] ]
          ] ]
          ...@@ -177,27 +179,27 @@ tests = testGroup "LinearAlgebra" [ ...@@ -177,27 +179,27 @@ tests = testGroup "LinearAlgebra" [
          compareTermDivNan :: (Array TermDivNanShape Double) compareTermDivNan :: (Array TermDivNanShape Double)
          -> (Array TermDivNanShape Double) -> (Array TermDivNanShape Double)
          -> Property -> QC.Property
          compareTermDivNan i1 i2 compareTermDivNan i1 i2
          = let massiv = LA.termDivNan @Massiv.U (LA.accelerate2MassivMatrix i1) (LA.accelerate2MassivMatrix i2) = let massiv = LA.termDivNan @Massiv.U (LA.accelerate2MassivMatrix i1) (LA.accelerate2MassivMatrix i2)
          accelerate = Naive.run (Legacy.termDivNan (use i1) (use i2)) accelerate = Naive.run (Legacy.termDivNan (use i1) (use i2))
          in accelerate === LA.massiv2AccelerateMatrix massiv in accelerate === LA.massiv2AccelerateMatrix massiv
          compareDiag :: SquareMatrix Int -> Property compareDiag :: SquareMatrix Int -> QC.Property
          compareDiag (SquareMatrix i1) compareDiag (SquareMatrix i1)
          = let massiv = LA.diag (LA.accelerate2MassivMatrix i1) = let massiv = LA.diag (LA.accelerate2MassivMatrix i1)
          accelerate = Naive.run (Legacy.diag (use i1)) accelerate = Naive.run (Legacy.diag (use i1))
          in accelerate === LA.massiv2AccelerateVector massiv in accelerate === LA.massiv2AccelerateVector massiv
          compareSumRows :: Array (Z :. Int :. Int :. Int) Int -> Property compareSumRows :: Array (Z :. Int :. Int :. Int) Int -> QC.Property
          compareSumRows i1 compareSumRows i1
          = let massiv = LA.sumRows @_ @Massiv.U (LA.accelerate2Massiv3DMatrix i1) = let massiv = LA.sumRows @_ @Massiv.U (LA.accelerate2Massiv3DMatrix i1)
          massiv' = LA.sumRowsReferenceImplementation @Massiv.U (LA.accelerate2Massiv3DMatrix i1) massiv' = LA.sumRowsReferenceImplementation @Massiv.U (LA.accelerate2Massiv3DMatrix i1)
          accelerate = Naive.run (A.sum (use i1)) accelerate = Naive.run (A.sum (use i1))
          in counterexample "sumRows and reference implementation do not agree" (massiv === massiv') .&&. in QC.counterexample "sumRows and reference implementation do not agree" (massiv === massiv') .&&.
          accelerate === LA.massiv2AccelerateMatrix massiv accelerate === LA.massiv2AccelerateMatrix massiv
          compareDistributionalImplementations :: SquareMatrix Int -> Property compareDistributionalImplementations :: SquareMatrix Int -> QC.Property
          compareDistributionalImplementations (SquareMatrix i1) = compareDistributionalImplementations (SquareMatrix i1) =
          let ma = LA.accelerate2MassivMatrix i1 let ma = LA.accelerate2MassivMatrix i1
          in LA.distributional @Massiv.U @Double ma === LA.distributionalReferenceImplementation ma in LA.distributional @Massiv.U @Double ma === LA.distributionalReferenceImplementation ma
          ...@@ -215,13 +217,13 @@ compareDistributional :: forall e. ...@@ -215,13 +217,13 @@ compareDistributional :: forall e.
          , Monoid e , Monoid e
          ) => Proxy e ) => Proxy e
          -> SquareMatrix Int -> SquareMatrix Int
          -> Property -> QC.Property
          compareDistributional Proxy (SquareMatrix i1) compareDistributional Proxy (SquareMatrix i1)
          = let massiv = Massiv.computeAs Massiv.B $ LA.distributional @_ @e (LA.accelerate2MassivMatrix i1) = let massiv = Massiv.computeAs Massiv.B $ LA.distributional @_ @e (LA.accelerate2MassivMatrix i1)
          accelerate = Legacy.distributionalWith Naive.run i1 accelerate = Legacy.distributionalWith Naive.run i1
          expected = map conv (A.toList accelerate) expected = map conv (A.toList accelerate)
          actual = map conv (mconcat (Massiv.toLists2 massiv)) actual = map conv (mconcat (Massiv.toLists2 massiv))
          in counterexample "size not equal" (Prelude.length expected === Prelude.length actual) .&&. expected === actual in QC.counterexample "size not equal" (Prelude.length expected === Prelude.length actual) .&&. expected === actual
          where where
          conv :: e -> Scientific conv :: e -> Scientific
          conv = fromFloatDigits conv = fromFloatDigits
          ...@@ -241,42 +243,42 @@ compareLogDistributional2 :: forall e. ...@@ -241,42 +243,42 @@ compareLogDistributional2 :: forall e.
          , Monoid e , Monoid e
          ) => Proxy e ) => Proxy e
          -> SquareMatrix Int -> SquareMatrix Int
          -> Property -> QC.Property
          compareLogDistributional2 Proxy (SquareMatrix i1) compareLogDistributional2 Proxy (SquareMatrix i1)
          = let massiv = Massiv.computeAs Massiv.B $ LA.logDistributional2 @_ @e (LA.accelerate2MassivMatrix i1) = let massiv = Massiv.computeAs Massiv.B $ LA.logDistributional2 @_ @e (LA.accelerate2MassivMatrix i1)
          accelerate = Legacy.logDistributional2With Naive.run i1 accelerate = Legacy.logDistributional2With Naive.run i1
          expected = map conv (A.toList accelerate) expected = map conv (A.toList accelerate)
          actual = map conv (mconcat (Massiv.toLists2 massiv)) actual = map conv (mconcat (Massiv.toLists2 massiv))
          in counterexample "size not equal" (Prelude.length expected === Prelude.length actual) .&&. expected === actual in QC.counterexample "size not equal" (Prelude.length expected === Prelude.length actual) .&&. expected === actual
          where where
          conv :: e -> Scientific conv :: e -> Scientific
          conv = fromFloatDigits conv = fromFloatDigits
          compareMatMaxMini :: SquareMatrix Int -> Property compareMatMaxMini :: SquareMatrix Int -> QC.Property
          compareMatMaxMini (SquareMatrix i1) compareMatMaxMini (SquareMatrix i1)
          = let massiv = LA.matMaxMini (LA.accelerate2MassivMatrix i1) = let massiv = LA.matMaxMini (LA.accelerate2MassivMatrix i1)
          accelerate = Naive.run (A.matMaxMini (use i1)) accelerate = Naive.run (A.matMaxMini (use i1))
          in accelerate === LA.massiv2AccelerateMatrix massiv in accelerate === LA.massiv2AccelerateMatrix massiv
          compareSumMin_go :: SquareMatrix Int -> Property compareSumMin_go :: SquareMatrix Int -> QC.Property
          compareSumMin_go (SquareMatrix i1) compareSumMin_go (SquareMatrix i1)
          = let massiv = LA.sumMin_go (A.dim i1) (LA.accelerate2MassivMatrix i1) = let massiv = LA.sumMin_go (A.dim i1) (LA.accelerate2MassivMatrix i1)
          accelerate = Naive.run (Legacy.sumMin_go (A.dim i1) (use i1)) accelerate = Naive.run (Legacy.sumMin_go (A.dim i1) (use i1))
          in accelerate === LA.massiv2AccelerateMatrix massiv in accelerate === LA.massiv2AccelerateMatrix massiv
          compareSumM_go :: SquareMatrix Int -> Property compareSumM_go :: SquareMatrix Int -> QC.Property
          compareSumM_go (SquareMatrix i1) compareSumM_go (SquareMatrix i1)
          = let massiv = LA.sumM_go (A.dim i1) (LA.accelerate2MassivMatrix i1) = let massiv = LA.sumM_go (A.dim i1) (LA.accelerate2MassivMatrix i1)
          accelerate = Naive.run (Legacy.sumM_go (A.dim i1) (use i1)) accelerate = Naive.run (Legacy.sumM_go (A.dim i1) (use i1))
          in accelerate === LA.massiv2AccelerateMatrix massiv in accelerate === LA.massiv2AccelerateMatrix massiv
          compareMatrixEye :: Positive Int -> Property compareMatrixEye :: QC.Positive Int -> QC.Property
          compareMatrixEye (getPositive -> n) compareMatrixEye (QC.getPositive -> n)
          = let massiv = Massiv.compute @Massiv.U $ LA.matrixEye @Int n = let massiv = Massiv.compute @Massiv.U $ LA.matrixEye @Int n
          accelerate = Naive.run (Legacy.matrixEye n) accelerate = Naive.run (Legacy.matrixEye n)
          in accelerate === LA.massiv2AccelerateMatrix massiv in accelerate === LA.massiv2AccelerateMatrix massiv
          compareDiagNull :: SquareMatrix Int -> Property compareDiagNull :: SquareMatrix Int -> QC.Property
          compareDiagNull (SquareMatrix i1) compareDiagNull (SquareMatrix i1)
          = let massiv = Massiv.compute @Massiv.U $ LA.diagNull (A.dim i1) (LA.accelerate2MassivMatrix i1) = let massiv = Massiv.compute @Massiv.U $ LA.diagNull (A.dim i1) (LA.accelerate2MassivMatrix i1)
          accelerate = Naive.run (Legacy.diagNull (A.dim i1) (use i1)) accelerate = Naive.run (Legacy.diagNull (A.dim i1) (use i1))
          ......
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