add shortest path

haskell-igraph.cabal

 name:                haskell-igraph
-version:             0.6.0
+version:             0.7.0-dev
 synopsis:            Haskell interface of the igraph library.
 description:         igraph<"http://igraph.org/c/"> is a library for creating
                      and manipulating large graphs. This package provides the Haskell
@@ -29,17 +29,18 @@ library
     IGraph.Internal.Constants
     IGraph.Internal
     IGraph
-    IGraph.Types
     IGraph.Mutable
-    IGraph.Clique
-    IGraph.Structure
-    IGraph.Isomorphism
-    IGraph.Community
+    IGraph.Types
     IGraph.Read
-    IGraph.Motif
-    IGraph.Layout
-    IGraph.Generators
     IGraph.Exporter.GEXF
+    IGraph.Algorithms
+    IGraph.Algorithms.Structure
+    IGraph.Algorithms.Community
+    IGraph.Algorithms.Clique
+    IGraph.Algorithms.Layout
+    IGraph.Algorithms.Motif
+    IGraph.Algorithms.Generators
+    IGraph.Algorithms.Isomorphism
 
   other-modules:
     IGraph.Internal.C2HS
@@ -79,14 +80,12 @@ library
 test-suite tests
   type: exitcode-stdio-1.0
   hs-source-dirs: tests
+  ghc-options:         -Wall
   main-is: test.hs
   other-modules:
     Test.Basic
     Test.Attributes
-    Test.Structure
-    Test.Isomorphism
-    Test.Motif
-    Test.Clique
+    Test.Algorithms
     Test.Utils
 
   default-language:    Haskell2010

src/IGraph.hs

@@ -6,6 +6,10 @@
 module IGraph
     ( Graph(..)
     , EdgeType(..)
+    , Node
+    , LNode
+    , Edge
+    , LEdge
     , isDirected
     , nNodes
     , nodeLab
@@ -115,7 +119,7 @@ nEdges :: Graph d v e -> Int
 nEdges = unsafePerformIO . igraphEcount . _graph
 {-# INLINE nEdges #-}
 
-    -- | Return all edges.
+-- | Return all edges.
 edges :: Graph d v e -> [Edge]
 edges gr = map (getEdgeByEid gr) [0 .. nEdges gr - 1]
 {-# INLINE edges #-}

src/IGraph/Algorithms.hs

+module IGraph.Algorithms
+    ( module IGraph.Algorithms.Structure
+    , module IGraph.Algorithms.Community
+    , module IGraph.Algorithms.Clique
+    , module IGraph.Algorithms.Layout
+    , module IGraph.Algorithms.Motif
+    , module IGraph.Algorithms.Generators
+    , module IGraph.Algorithms.Isomorphism
+    ) where
+
+import IGraph.Algorithms.Structure
+import IGraph.Algorithms.Community
+import IGraph.Algorithms.Clique
+import IGraph.Algorithms.Layout
+import IGraph.Algorithms.Motif
+import IGraph.Algorithms.Generators
+import IGraph.Algorithms.Isomorphism

src/IGraph/Clique.chs → src/IGraph/Algorithms/Clique.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
-module IGraph.Clique
+module IGraph.Algorithms.Clique
     ( cliques
     , largestCliques
     , maximalCliques

src/IGraph/Community.chs → src/IGraph/Algorithms/Community.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
 {-# LANGUAGE RecordWildCards #-}
 {-# LANGUAGE DataKinds #-}
-module IGraph.Community
+module IGraph.Algorithms.Community
     ( modularity
     , findCommunity
     , CommunityMethod(..)

src/IGraph/Generators.chs → src/IGraph/Algorithms/Generators.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
 {-# LANGUAGE DataKinds #-}
 {-# LANGUAGE ScopedTypeVariables #-}
-module IGraph.Generators
+module IGraph.Algorithms.Generators
     ( full
     , star
     , ErdosRenyiModel(..)

src/IGraph/Isomorphism.chs → src/IGraph/Algorithms/Isomorphism.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
 {-# LANGUAGE ScopedTypeVariables #-}
-module IGraph.Isomorphism
+module IGraph.Algorithms.Isomorphism
     ( getSubisomorphisms
     , isomorphic
     , isoclassCreate

src/IGraph/Layout.chs → src/IGraph/Algorithms/Layout.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
-module IGraph.Layout
+module IGraph.Algorithms.Layout
     ( getLayout
     , LayoutMethod(..)
     , defaultKamadaKawai

src/IGraph/Motif.chs → src/IGraph/Algorithms/Motif.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
 {-# LANGUAGE DataKinds #-}
-module IGraph.Motif
+module IGraph.Algorithms.Motif
     ( triad
     , triadCensus
     ) where

src/IGraph/Structure.chs → src/IGraph/Algorithms/Structure.chs

 {-# LANGUAGE ForeignFunctionInterface #-}
-module IGraph.Structure
-    ( inducedSubgraph
+module IGraph.Algorithms.Structure
+    ( -- * Shortest Path Related Functions
+      getShortestPath
+    , inducedSubgraph
     , closeness
     , betweenness
     , eigenvectorCentrality
@@ -24,7 +26,34 @@ import           IGraph.Mutable (MGraph(..))
 {#import IGraph.Internal #}
 {#import IGraph.Internal.Constants #}
 
-#include "igraph/igraph.h"
+#include "haskell_igraph.h"
+
+{#fun igraph_shortest_paths as ^
+    { `IGraph'
+    , castPtr `Ptr Matrix'
+    , castPtr %`Ptr VertexSelector'
+    , castPtr %`Ptr VertexSelector'
+    , `Neimode'
+    } -> `CInt' void- #}
+
+-- Calculates and returns a single unweighted shortest path from a given vertex
+-- to another one. If there are more than one shortest paths between the two
+-- vertices, then an arbitrary one is returned.
+getShortestPath :: Graph d v e
+                -> Node     -- ^ The id of the source vertex.
+                -> Node     -- ^ The id of the target vertex.
+                -> [Node]
+getShortestPath gr s t = unsafePerformIO $ allocaVector $ \path -> do
+    igraphGetShortestPath (_graph gr) path nullPtr s t IgraphOut
+    map truncate <$> toList path
+{#fun igraph_get_shortest_path as ^
+    { `IGraph'
+    , castPtr `Ptr Vector'
+    , castPtr `Ptr Vector'
+    , `Int'
+    , `Int'
+    , `Neimode'
+    } -> `CInt' void- #}
 
 inducedSubgraph :: (Hashable v, Eq v, Serialize v)
                 => Graph d v e

src/IGraph/Internal.chs

@@ -172,7 +172,7 @@ toList vec = do
     n <- igraphVectorSize vec
     allocaArray n $ \ptr -> do
         igraphVectorCopyTo vec ptr
-        liftM (map realToFrac) $ peekArray n ptr
+        map realToFrac <$> peekArray n ptr
 {-# INLINE toList #-}
 
 {#fun igraph_vector_copy_to as ^ { castPtr `Ptr Vector', id `Ptr CDouble' } -> `()' #}

src/IGraph/Types.hs

@@ -24,7 +24,7 @@ import           GHC.Generics            (Generic)
 $(singletons [d|
     data EdgeType = D
                   | U
-        deriving (Show, Read, Eq, Generic)
+        deriving (Eq, Generic)
     |])
 
 instance Serialize EdgeType

tests/Test/Clique.hs → tests/Test/Algorithms.hs

 {-# LANGUAGE DataKinds #-}
-module Test.Clique
+module Test.Algorithms
     ( tests
     ) where
 
+import           Control.Arrow
 import           Control.Monad.ST
 import           Data.List
-import           System.IO.Unsafe
+import qualified Data.Matrix.Unboxed as M
 import           Test.Tasty
 import           Test.Tasty.HUnit
-import           Test.Utils
 
 import           IGraph
-import           IGraph.Clique
-import           IGraph.Generators
+import           IGraph.Algorithms
 import           IGraph.Mutable
 
 tests :: TestTree
-tests = testGroup "Clique"
+tests = testGroup "Algorithms"
+    [ graphIsomorphism
+    , motifTest
+    , cliqueTest
+    , subGraphs
+    , pagerankTest
+    ]
+
+graphIsomorphism :: TestTree
+graphIsomorphism = testCase "Graph isomorphism" $ assertBool "" $
+    and (zipWith isomorphic triad triad) &&
+    (not . or) (zipWith isomorphic triad $ reverse triad)
+
+motifTest :: TestTree
+motifTest = testGroup "Network motif"
+    [ testCase "triad Census" $ M.toLists (M.ident 16 :: M.Matrix Int) @=?
+        map triadCensus triad ]
+
+cliqueTest :: TestTree
+cliqueTest = testGroup "Clique"
     [ testCase "case 1" $ sort (map sort $ cliques gr (4,-1)) @=? c4
     , testCase "case 2" $ sort (map sort $ cliques gr (2,2)) @=? c2
     , testCase "case 3" $ sort (map sort $ largestCliques gr) @=? c4
@@ -34,3 +52,25 @@ tests = testGroup "Clique"
     c3 = [ [0,3,4], [0,4,5], [1,2,3], [1,2,4], [1,2,5], [1,3,4], [1,4,5],
         [2,3,4], [2,4,5] ]
     c4 = [[1, 2, 3, 4], [1, 2, 4, 5]]
+
+subGraphs :: TestTree
+subGraphs = testGroup "generate induced subgraphs"
+    [ testCase "" $ test case1 ]
+  where
+    case1 = ( [("a","b"), ("b","c"), ("c","a"), ("a","c")]
+            , ["a","c"], [("a","c"), ("c","a")] )
+    test (ori,ns,expect) = sort expect @=? sort result
+      where
+        gr = fromLabeledEdges $ zip ori $ repeat () :: Graph 'D String ()
+        ns' = map (head . getNodes gr) ns
+        gr' = inducedSubgraph gr ns'
+        result = map (nodeLab gr' *** nodeLab gr') $ edges gr'
+
+pagerankTest :: TestTree
+pagerankTest = testGroup "PageRank"
+    [ testCase "case 1" $ ranks @=? ranks' ]
+  where
+    gr = star 11
+    ranks = [0.47,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05]
+    ranks' = map ((/100) . fromIntegral . round. (*100)) $
+        pagerank gr Nothing Nothing 0.85

tests/Test/Attributes.hs

@@ -3,14 +3,8 @@ module Test.Attributes
     ( tests
     ) where
 
-import           Conduit
-import           Control.Monad
-import           Control.Monad.ST
 import           Data.List
-import           Data.List.Ordered         (nubSort)
-import           Data.Maybe
 import           Data.Serialize
-import           Foreign
 import           System.IO.Unsafe
 import           Test.Tasty
 import           Test.Tasty.HUnit
@@ -20,7 +14,6 @@ import           IGraph
 import           IGraph.Exporter.GEXF
 import           IGraph.Internal
 import           IGraph.Mutable
-import           IGraph.Structure
 
 tests :: TestTree
 tests = testGroup "Attribute tests"

tests/Test/Basic.hs

@@ -3,19 +3,17 @@ module Test.Basic
     ( tests
     ) where
 
+import           Conduit
 import           Control.Monad.ST
 import           Data.List
 import           Data.List.Ordered (nubSort)
-import           Data.Maybe
 import           System.IO.Unsafe
 import           Test.Tasty
 import           Test.Tasty.HUnit
 import           Test.Utils
-import Conduit
 
 import           IGraph
 import qualified IGraph.Mutable    as GM
-import           IGraph.Structure
 
 tests :: TestTree
 tests = testGroup "Basic tests"

tests/Test/Isomorphism.hs

-module Test.Isomorphism
-    ( tests
-    ) where
-
-import           Control.Arrow
-import           Control.Monad.ST
-import           Data.List
-import qualified Data.Matrix.Unboxed as M
-import           System.IO.Unsafe
-import           Test.Tasty
-import           Test.Tasty.HUnit
-import           Test.Utils
-
-import           IGraph
-import           IGraph
-import           IGraph.Motif
-import IGraph.Isomorphism
-
-tests :: TestTree
-tests = testGroup "Isomorphism"
-    [ graphIsomorphism ]
-
-graphIsomorphism :: TestTree
-graphIsomorphism = testCase "Graph isomorphism" $ assertBool "" $
-    and (zipWith isomorphic triad triad) &&
-    (not . or) (zipWith isomorphic triad $ reverse triad)

tests/Test/Motif.hs

-module Test.Motif
-    ( tests
-    ) where
-
-import           Control.Arrow
-import           Control.Monad.ST
-import           Data.List
-import qualified Data.Matrix.Unboxed as M
-import           System.IO.Unsafe
-import           Test.Tasty
-import           Test.Tasty.HUnit
-import           Test.Utils
-
-import           IGraph
-import           IGraph
-import           IGraph.Motif
-
-tests :: TestTree
-tests = testGroup "Network motif"
-    [ testCase "triad Census" $ M.toLists (M.ident 16 :: M.Matrix Int) @=?
-        map triadCensus triad ]

tests/Test/Structure.hs

-{-# LANGUAGE DataKinds #-}
-module Test.Structure
-    ( tests
-    ) where
-
-import Control.Arrow
-import Control.Monad.ST
-import Test.Tasty
-import Test.Tasty.HUnit
-import Test.Utils
-import System.IO.Unsafe
-import Data.List
-
-import IGraph
-import IGraph.Mutable
-import IGraph.Structure
-import IGraph.Generators
-
-tests :: TestTree
-tests = testGroup "Structure property tests"
-    [ subGraphs
-    , pagerankTest
-    ]
-
-subGraphs :: TestTree
-subGraphs = testGroup "generate induced subgraphs"
-    [ testCase "" $ test case1 ]
-  where
-    case1 = ( [("a","b"), ("b","c"), ("c","a"), ("a","c")]
-            , ["a","c"], [("a","c"), ("c","a")] )
-    test (ori,ns,expect) = sort expect @=? sort result
-      where
-        gr = fromLabeledEdges $ zip ori $ repeat () :: Graph 'D String ()
-        ns' = map (head . getNodes gr) ns
-        gr' = inducedSubgraph gr ns'
-        result = map (nodeLab gr' *** nodeLab gr') $ edges gr'
-
-pagerankTest :: TestTree
-pagerankTest = testGroup "PageRank"
-    [ testCase "case 1" $ ranks @=? ranks' ]
-  where
-    gr = star 11
-    ranks = [0.47,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05,0.05]
-    ranks' = map ((/100) . fromIntegral . round. (*100)) $
-        pagerank gr Nothing Nothing 0.85

tests/test.hs

+import qualified Test.Algorithms as Algorithms
 import qualified Test.Attributes as Attributes
 import qualified Test.Basic      as Basic
-import qualified Test.Clique      as Clique
-import qualified Test.Isomorphism as Isomorphism
-import qualified Test.Motif       as Motif
-import qualified Test.Structure   as Structure
 import           Test.Tasty
 
 main :: IO ()
 main = defaultMain $ testGroup "Haskell-igraph Tests"
     [ Basic.tests
-    , Structure.tests
-    , Motif.tests
-    , Isomorphism.tests
+    , Algorithms.tests
     , Attributes.tests
-    , Clique.tests
     ]