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gargantext
haskell-gargantext
Commits
bb9f1374
Commit
bb9f1374
authored
Apr 06, 2021
by
Alexandre Delanoë
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[FIX] removing cLouvain c++ lib
parent
704dc05e
Pipeline
#1438
canceled with stage
Changes
5
Pipelines
1
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5 changed files
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15 additions
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17 deletions
+15
-17
package.yaml
package.yaml
+0
-1
Bridgeness.hs
src/Gargantext/Core/Viz/Graph/Bridgeness.hs
+0
-4
Tools.hs
src/Gargantext/Core/Viz/Graph/Tools.hs
+10
-4
Cluster.hs
src/Gargantext/Core/Viz/Phylo/Cluster.hs
+5
-5
stack.yaml
stack.yaml
+0
-3
No files found.
package.yaml
View file @
bb9f1374
...
@@ -130,7 +130,6 @@ library:
...
@@ -130,7 +130,6 @@ library:
-
cassava
-
cassava
-
cereal
# (IGraph)
-
cereal
# (IGraph)
-
clock
-
clock
-
clustering-louvain
-
conduit
-
conduit
-
conduit-extra
-
conduit-extra
-
containers
-
containers
...
...
src/Gargantext/Core/Viz/Graph/Bridgeness.hs
View file @
bb9f1374
...
@@ -18,7 +18,6 @@ TODO use Map LouvainNodeId (Map LouvainNodeId)
...
@@ -18,7 +18,6 @@ TODO use Map LouvainNodeId (Map LouvainNodeId)
module
Gargantext.Core.Viz.Graph.Bridgeness
-- (bridgeness)
module
Gargantext.Core.Viz.Graph.Bridgeness
-- (bridgeness)
where
where
import
Data.Graph.Clustering.Louvain.Utils
(
LouvainNode
(
..
))
import
Data.List
(
concat
,
sortOn
)
import
Data.List
(
concat
,
sortOn
)
import
Data.Map
(
Map
,
fromListWith
,
lookup
,
toList
,
mapWithKey
,
elems
)
import
Data.Map
(
Map
,
fromListWith
,
lookup
,
toList
,
mapWithKey
,
elems
)
import
Data.Maybe
(
catMaybes
)
import
Data.Maybe
(
catMaybes
)
...
@@ -37,9 +36,6 @@ type NodeId = Int
...
@@ -37,9 +36,6 @@ type NodeId = Int
type
CommunityId
=
Int
type
CommunityId
=
Int
----------------------------------------------------------------------
----------------------------------------------------------------------
instance
ToComId
LouvainNode
where
nodeId2comId
(
LouvainNode
i1
i2
)
=
(
i1
,
i2
)
instance
ToComId
ClusterNode
where
instance
ToComId
ClusterNode
where
nodeId2comId
(
ClusterNode
i1
i2
)
=
(
i1
,
i2
)
nodeId2comId
(
ClusterNode
i1
i2
)
=
(
i1
,
i2
)
...
...
src/Gargantext/Core/Viz/Graph/Tools.hs
View file @
bb9f1374
...
@@ -15,7 +15,6 @@ module Gargantext.Core.Viz.Graph.Tools
...
@@ -15,7 +15,6 @@ module Gargantext.Core.Viz.Graph.Tools
where
where
-- import Data.Graph.Clustering.Louvain (hLouvain, {-iLouvainMap-})
-- import Data.Graph.Clustering.Louvain (hLouvain, {-iLouvainMap-})
import
Data.Graph.Clustering.Louvain.CplusPlus
(
cLouvain
)
import
Data.HashMap.Strict
(
HashMap
)
import
Data.HashMap.Strict
(
HashMap
)
import
Data.Map
(
Map
)
import
Data.Map
(
Map
)
import
Data.Text
(
Text
)
import
Data.Text
(
Text
)
...
@@ -28,7 +27,7 @@ import Gargantext.Core.Statistics
...
@@ -28,7 +27,7 @@ import Gargantext.Core.Statistics
import
Gargantext.Core.Viz.Graph
import
Gargantext.Core.Viz.Graph
import
Gargantext.Core.Viz.Graph.Bridgeness
(
bridgeness
,
Partitions
,
ToComId
(
..
))
import
Gargantext.Core.Viz.Graph.Bridgeness
(
bridgeness
,
Partitions
,
ToComId
(
..
))
import
Gargantext.Core.Viz.Graph.Index
(
createIndices
,
toIndex
,
map2mat
,
mat2map
,
Index
,
MatrixShape
(
..
))
import
Gargantext.Core.Viz.Graph.Index
(
createIndices
,
toIndex
,
map2mat
,
mat2map
,
Index
,
MatrixShape
(
..
))
import
Gargantext.Core.Viz.Graph.Tools.IGraph
(
mkGraphUfromEdges
,
spinglass
)
import
Gargantext.Core.Viz.Graph.Tools.IGraph
(
mkGraphUfromEdges
,
spinglass
,
ClusterNode
)
import
Gargantext.Prelude
import
Gargantext.Prelude
import
IGraph.Random
-- (Gen(..))
import
IGraph.Random
-- (Gen(..))
import
qualified
Data.HashMap.Strict
as
HashMap
import
qualified
Data.HashMap.Strict
as
HashMap
...
@@ -39,8 +38,15 @@ import qualified Data.Vector.Storable as Vec
...
@@ -39,8 +38,15 @@ import qualified Data.Vector.Storable as Vec
import
qualified
IGraph
as
Igraph
import
qualified
IGraph
as
Igraph
import
qualified
IGraph.Algorithms.Layout
as
Layout
import
qualified
IGraph.Algorithms.Layout
as
Layout
type
Threshold
=
Double
-------------------------------------------------------------
defaultClustering
::
Map
(
Int
,
Int
)
Double
->
IO
[
ClusterNode
]
defaultClustering
=
spinglass
1
-------------------------------------------------------------
type
Threshold
=
Double
cooc2graph'
::
Ord
t
=>
Distance
cooc2graph'
::
Ord
t
=>
Distance
->
Double
->
Double
...
@@ -68,7 +74,7 @@ cooc2graphWith :: PartitionMethod
...
@@ -68,7 +74,7 @@ cooc2graphWith :: PartitionMethod
->
Threshold
->
Threshold
->
HashMap
(
NgramsTerm
,
NgramsTerm
)
Int
->
HashMap
(
NgramsTerm
,
NgramsTerm
)
Int
->
IO
Graph
->
IO
Graph
cooc2graphWith
Louvain
=
cooc2graphWith'
(
cLouvain
"1"
)
cooc2graphWith
Louvain
=
undefined
-- TODO use IGraph bindings
cooc2graphWith
Spinglass
=
cooc2graphWith'
(
spinglass
1
)
cooc2graphWith
Spinglass
=
cooc2graphWith'
(
spinglass
1
)
...
...
src/Gargantext/Core/Viz/Phylo/Cluster.hs
View file @
bb9f1374
...
@@ -15,11 +15,11 @@ Portability : POSIX
...
@@ -15,11 +15,11 @@ Portability : POSIX
module
Gargantext.Core.Viz.Phylo.Cluster
module
Gargantext.Core.Viz.Phylo.Cluster
where
where
import
Control.Parallel.Strategies
import
Control.Parallel.Strategies
import
Data.Graph.Clustering.Louvain.CplusPlus
import
Data.Graph.Clustering.Louvain.Utils
(
LouvainNode
(
..
))
import
Data.List
(
null
,
concat
,
sort
,
intersect
,(
++
),
elemIndex
,
groupBy
,
nub
,
union
,
(
\\
),
(
!!
))
import
Data.List
(
null
,
concat
,
sort
,
intersect
,(
++
),
elemIndex
,
groupBy
,
nub
,
union
,
(
\\
),
(
!!
))
import
Data.Map
(
Map
,
fromList
,
mapKeys
)
import
Data.Map
(
Map
,
fromList
,
mapKeys
)
import
Gargantext.Prelude
import
Gargantext.Prelude
import
Gargantext.Core.Viz.Graph.Tools
(
defaultClustering
)
import
Gargantext.Core.Viz.Graph.Tools.IGraph
(
ClusterNode
(
..
))
import
Gargantext.Core.Viz.Phylo
import
Gargantext.Core.Viz.Phylo
import
Gargantext.Core.Viz.Phylo.Tools
import
Gargantext.Core.Viz.Phylo.Tools
import
Gargantext.Core.Viz.Phylo.Metrics
import
Gargantext.Core.Viz.Phylo.Metrics
...
@@ -48,9 +48,9 @@ relatedComp graphs = foldl' (\mem groups ->
...
@@ -48,9 +48,9 @@ relatedComp graphs = foldl' (\mem groups ->
louvain
::
([
GroupNode
],[
GroupEdge
])
->
IO
[[
PhyloGroup
]]
louvain
::
([
GroupNode
],[
GroupEdge
])
->
IO
[[
PhyloGroup
]]
louvain
(
nodes
,
edges
)
=
map
(
\
community
->
map
(
\
node
->
nodes
!!
(
l_node_id
node
))
community
)
louvain
(
nodes
,
edges
)
=
map
(
\
community
->
map
(
\
node
->
nodes
!!
(
c
l_node_id
node
))
community
)
<$>
groupBy
(
\
a
b
->
(
l_community_id
a
)
==
(
l_community_id
b
))
<$>
groupBy
(
\
a
b
->
(
cl_community_id
a
)
==
(
c
l_community_id
b
))
<$>
(
cLouvain
"0.0001"
$
mapKeys
(
\
(
x
,
y
)
->
(
idx
x
,
idx
y
))
$
fromList
edges
)
<$>
(
defaultClustering
$
mapKeys
(
\
(
x
,
y
)
->
(
idx
x
,
idx
y
))
$
fromList
edges
)
where
where
--------------------------------------
--------------------------------------
idx
::
PhyloGroup
->
Int
idx
::
PhyloGroup
->
Int
...
...
stack.yaml
View file @
bb9f1374
...
@@ -6,7 +6,6 @@ packages:
...
@@ -6,7 +6,6 @@ packages:
#- 'deps/patches-class'
#- 'deps/patches-class'
#- 'deps/patches-map'
#- 'deps/patches-map'
#- 'deps/servant-job'
#- 'deps/servant-job'
#- 'deps/clustering-louvain'
#- 'deps/accelerate'
#- 'deps/accelerate'
#- 'deps/accelerate-utility'
#- 'deps/accelerate-utility'
...
@@ -71,8 +70,6 @@ extra-deps:
...
@@ -71,8 +70,6 @@ extra-deps:
# Graph libs
# Graph libs
-
git
:
https://github.com/kaizhang/haskell-igraph.git
-
git
:
https://github.com/kaizhang/haskell-igraph.git
commit
:
34553acc4ebdcae7065311dcefb426e0fd58c5a0
commit
:
34553acc4ebdcae7065311dcefb426e0fd58c5a0
-
git
:
https://gitlab.iscpif.fr/gargantext/clustering-louvain.git
commit
:
7d74f96dfea8e51fbab1793cc0429b2fe741f73d
# Accelerate Linear Algebra and specific instances
# Accelerate Linear Algebra and specific instances
# (UndecidableInstances for newer GHC version)
# (UndecidableInstances for newer GHC version)
...
...
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