merge master (#2)

* removed flow algorithms (sbromberger#815) * fixes sbromberger#820, plus tests (sbromberger#821) * change show() for empty graphs (ref JuliaGraphs/MetaGraphs.jl#20 (comment)) (sbromberger#822) * Pull request clique_percolation.jl (sbromberger#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * in_ / out_ -> in / out (sbromberger#830) * (in,out)_neighbors -> (in,out)neighbors * all_neighbors -> allneighbors * Pull request clique_percolation.jl (sbromberger#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * revert allneighbors * expected_degree_graph (Chung-Lu model) (sbromberger#832) * Expected degree random graph generator implemented, including tests * algorithm corrected * Missing seed corrected in expected_degree_graph * expected_degree_graph! implemented * Added return in function, comment with references removed, references in docs added (expected_degree_graph) * Update randgraphs.jl minor doc update * Update randgraphs.jl * Fixing problems with MST Kruskal's on SimpleWeightedGraphs (sbromberger#835) * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * reverting changes * Revert "reverting changes" This reverts commit ac1760b. * Revert "Update prim.jl" This reverts commit 677f6fa. * Revert "Update kruskal.jl" This reverts commit a0e9c47. * Revert "Update prim.jl" This reverts commit 793bac4. * Revert "Update kruskal.jl" This reverts commit 6114e16. * Revert "Update prim.jl" This reverts commit 551f1e6. * Revert "Update kruskal.jl" This reverts commit 941005e. * Revert "Update kruskal.jl" This reverts commit a404514. * Revert "Update prim.jl" This reverts commit 2d43a60. * Revert "Update kruskal.jl" This reverts commit 4577920. * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * bipartite_map on 2-order graphs fixed. Added proper tests. Fixed test connected to bipartite_map (sbromberger#836) * Correct pre-allocation of memory in Prim's MST (sbromberger#839) * Improve Kruskal's MST by optimizing Union-Find (sbromberger#843) * add missing backtick (sbromberger#846) * Add greedy_color for Graph Coloring (sbromberger#844) * Add greedy_color for Graph Coloring * Improve Kruskal's MST by optimizing Union-Find (sbromberger#843) * Update README.md * Update README.md * first cut at 0.7 compatibility (sbromberger#848) * using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test * first cut * Use mauro/SimpleTraits.jl/m3/where-fns in tests * Fix SimpleTraits checkout (sbromberger#851) * Move up SimpleTraits checkout (sbromberger#852) * Update runtests.jl * Update REQUIRE * Update REQUIRE * femtocleaner with additional depwarn fixes (sbromberger#856) fix deprecation warnings based on local femtocleaner run * use equalto in degeneracy.jl (sbromberger#858) * fix depwarns in linalg submodule (sbromberger#860) * update linalg/spectral to fix deprecations * fix depwarns in graphmatrices * fixes doc deprecation warnings (sbromberger#861) * fixes doc deprecation warnings * adding Base64 to runtests * Update README.md * remove add/remove vertex/edge from core, minor bug fix (sbromberger#862) * remove add/remove vertex/edge from core, minor bug fix * fix tests * export add/rem vertex * remove long-term deprecation warnings (sbromberger#863) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of d… (sbromberger#865) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of deprecated functions from LG to LinAlg * test coverage for digraph eltype * removes equalto (sbromberger#867) * optional sorting algorithm for gdistances (sbromberger#868) add the ability to pass RadixSort to gdistances! * update url and mention directed graphs explicilty (sbromberger#837) * update url and mention directed graphs explicilty * Update graphtypes.md * Update graphtypes.md fixed references. * Speed improvements for function transitiveclosure! (sbromberger#870) * Speed improvements for function transitiveclosure! Instead of checking for all paths i -> k and k -> j for a given vertex k we only iterate over the in- and outneighbours of k. * Merged some conditionals into a single statement * Cache efficient Floyd Warshall (sbromberger#873) * Update floyd-warshall.jl * Cache efficient Floyd Warshall * fixed an error where smallgraph(:frucht) had 20 vertices instead of 12 (sbromberger#878) * Delete .Rhistory * Added function transitivereduction (sbromberger#877) * added function transitivereduction * Update transitivity.jl docstring formatting * Fixed some tests && added testdigraphs for all tests * Johnson Shortest Path for Sparse Graphs (sbromberger#884) * Johnson Shortest Path for Sparse Graphs Johnson Shortest Path for Sparse Graphs * Improved memory efficiency if distmx is mutable * Improved memory efficiency for parallel implementation * Update index.md * Added constructors to create graphs from a vector or an iterator of edges (sbromberger#880) * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Slyles1001/892 (sbromberger#894) * comments are your friend * Most of LightGraphs warnings are fixed * Delete HITS.jl * Slyles1001/872 (sbromberger#891) * DataStructures fixed * missed heappop!, now it tests clean * spaces * Update LightGraphs.jl * Update runtests.jl * fixes most depwarns as of 20180529 (sbromberger#895) * fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again * Update CONTRIBUTING.md (sbromberger#897) * Improve Kruskal and use in-built disjoint set data structure (sbromberger#896) * Improve Kruskal and use in-built disjoint set data structure * Update kruskal.jl Changes requested by @somil55
matbesancon · Jun 5, 2018 · 643c2a0 · 643c2a0
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diff --git a/.Rhistory b/.Rhistory
diff --git a/.travis.yml b/.travis.yml
@@ -5,13 +5,9 @@ os:
 #  - osx
 
 julia:
- - 0.6
+#  - 0.6
  - nightly
 
-matrix:
-  allow_failures:
-    - julia: nightly
-
 notifications:
   email: false
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -14,9 +14,9 @@ Please include version numbers of all relevant libraries and Julia itself.
 - Open an issue to discuss a feature before you start coding (this maximizes the likelihood of patch acceptance).
 - Minimize dependencies on external packages, and avoid introducing new dependencies. In general,
 
-    - PRs introducing dependencies on core Julia packages are ok.
-    - PRs introducing dependencies on non-core "leaf" packages (no subdependencies except for core Julia packages) are less ok.
-    - PRs introducing dependencies on non-core non-leaf packages require strict scrutiny and will likely not be accepted without some compelling reason (urgent bugfix or much-needed functionality).
+    - PRs introducing dependencies on Julia Base or the packages in the Julia Standard Library are ok.
+    - PRs introducing dependencies on third-party non-core "leaf" packages (no subdependencies except for Julia Base / Standard Library packages) are less ok.
+    - PRs introducing dependencies on third-party non-core non-leaf packages (that is, third-party packages that have dependencies on one or more other third-party packages) require strict scrutiny and will likely not be accepted without some compelling reason (urgent bugfix or much-needed functionality).
 
 - Put type assertions on all function arguments where conflict may arise (use abstract types, Union, or Any if necessary).
 - If the algorithm was presented in a paper, include a reference to the paper (i.e. a proper academic citation along with an eprint link).
@@ -27,7 +27,7 @@ Please include version numbers of all relevant libraries and Julia itself.
 - When possible write code to reuse memory. For example:
 ```julia
 function f(g, v)
-    storage = Vector{Int}(nv(g))
+    storage = Vector{Int}(undef, nv(g))
     # some code operating on storage, g, and v.
     for i in 1:nv(g)
         storage[i] = v-i
@@ -38,7 +38,7 @@ end
 should be rewritten as two functions
 ```julia
 function f(g::AbstractGraph, v::Integer)
-    storage = Vector{Int}(nv(g))
+    storage = Vector{Int}(undef, nv(g))
     return f!(g, v, storage)
 end
 
@@ -60,17 +60,17 @@ Locate the section for your github remote in the `.git/config` file. It looks li
 
 ```
 [remote "origin"]
-	fetch = +refs/heads/*:refs/remotes/origin/*
-	url = git@github.com:JuliaGraphs/LightGraphs.jl.git
+    fetch = +refs/heads/*:refs/remotes/origin/*
+    url = git@github.com:JuliaGraphs/LightGraphs.jl.git
 ```
 
 Now add the line `fetch = +refs/pull/*/head:refs/remotes/origin/pr/*` to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:
 
 ```
 [remote "origin"]
-	fetch = +refs/heads/*:refs/remotes/origin/*
-	url = git@github.com:JuliaGraphs/LightGraphs.jl.git
-	fetch = +refs/pull/*/head:refs/remotes/origin/pr/*
+    fetch = +refs/heads/*:refs/remotes/origin/*
+    url = git@github.com:JuliaGraphs/LightGraphs.jl.git
+    fetch = +refs/pull/*/head:refs/remotes/origin/pr/*
 ```
 
 Now fetch all the pull requests:

diff --git a/README.md b/README.md
@@ -48,11 +48,12 @@ julia> Pkg.add("LightGraphs")
 ```
 
 ## Supported Versions
-* LightGraphs master is designed to work with the latest stable version of Julia.
+* LightGraphs master is generally designed to work with the latest stable version of Julia (except during Julia version increments as we transition to the new version).
 * Julia 0.3: LightGraphs v0.3.7 is the last version guaranteed to work with Julia 0.3.
 * Julia 0.4: LightGraphs versions in the 0.6 series are designed to work with Julia 0.4.
 * Julia 0.5: LightGraphs versions in the 0.7 series are designed to work with Julia 0.5.
-* Julia 0.6: LightGraphs versions in the 0.8 through 0.11 series are designed to work with Julia 0.6.
+* Julia 0.6: LightGraphs versions in the 0.8 through 0.12 series are designed to work with Julia 0.6.
+* Julia 0.7: LightGraphs versions in the 0.13 series are designed to work with Julia 0.7.
 * Later versions: Some functionality might not work with prerelease / unstable / nightly versions of Julia. If you run into a problem, please file an issue.
 
 # Contributing and Reporting Bugs

diff --git a/REQUIRE b/REQUIRE
@@ -1,4 +1,4 @@
-julia 0.6
+julia 0.7-
 CodecZlib 0.4
 DataStructures 0.7
-SimpleTraits 0.4.0
+SimpleTraits 0.7.1
diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl
@@ -32,6 +32,5 @@ GRAPHS = Dict{String,Graph}(
   include("edges.jl")
   include("centrality.jl")
   include("connectivity.jl")
-  include("max-flow.jl")
   include("traversals.jl")
 end
diff --git a/benchmark/core.jl b/benchmark/core.jl
@@ -7,7 +7,7 @@ function bench_iteredges(g::AbstractGraph)
 end
 
 function bench_has_edge(g::AbstractGraph)
-    srand(1)
+    Random.srand(1)
     nvg = nv(g)
     srcs = rand([1:nvg;], cld(nvg, 4))
     dsts = rand([1:nvg;], cld(nvg, 4))

diff --git a/benchmark/max-flow.jl b/benchmark/max-flow.jl
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,5 +1,5 @@
 using Documenter
-include("../src/LightGraphs.jl")
+#include("../src/LightGraphs.jl")
 using LightGraphs
 
 # same for contributing and license
@@ -28,7 +28,6 @@ makedocs(
         "Matching"                          => "matching.md",
         "Community Structures"              => "community.md",
         "Degeneracy"                        => "degeneracy.md",
-        "Flow and Cut"                      => "flowcut.md",
         "Integration with other packages"   => "integration.md",
         "Contributing"                      => "contributing.md",
         "Developer Notes"                   => "developing.md",

diff --git a/docs/src/basicproperties.md b/docs/src/basicproperties.md
@@ -15,10 +15,10 @@ The following is an overview of functions for accessing graph properties. For fu
 
 ## Vertex Properties
 
-- `neighbors`: Return array of neighbors of a vertex. If graph is directed, output is equivalent of `out_neighbors`.
-- `all_neighbors`:  Returns array of all neighbors (both `in_neighbors` and `out_neighbors`). For undirected graphs, equivalent to `neighbors`.
-- `in_neighbors`: Return array of in-neighbors. Equivalent to `neighbors` for undirected graphs.
-- `out_neighbors`: Return array of out-neighbors. Equivalent to `neighbors` for undirected graphs.
+- `neighbors`: Return array of neighbors of a vertex. If graph is directed, output is equivalent of `outneighbors`.
+- `all_neighbors`:  Returns array of all neighbors (both `inneighbors` and `outneighbors`). For undirected graphs, equivalent to `neighbors`.
+- `inneighbors`: Return array of in-neighbors. Equivalent to `neighbors` for undirected graphs.
+- `outneighbors`: Return array of out-neighbors. Equivalent to `neighbors` for undirected graphs.
 
 ## Edge Properties
 

diff --git a/docs/src/developing.md b/docs/src/developing.md
@@ -10,14 +10,14 @@ within the LightGraphs package should just work:
 - [`eltype`](@ref)
 - [`has_edge`](@ref)
 - [`has_vertex`](@ref)
-- [`in_neighbors`](@ref)
+- [`inneighbors`](@ref)
 - [`is_directed`](@ref): Note that since we use traits to determine directedness, `is_directed` for a `CustomGraph` type should have the following signatures:
   - `is_directed(::Type{CustomGraph})::Bool`
   - `is_directed(g::CustomGraph)::Bool`
 
 - [`ne`](@ref)
 - [`nv`](@ref)
-- [`out_neighbors`](@ref)
+- [`outneighbors`](@ref)
 - [`vertices`](@ref)
 
 If the graph structure is designed to represent weights on edges, the [`weights`](@ref) function should also be defined. Note that the output does not necessarily have to be a dense matrix, but it must be indexable via `[u, v]`.

diff --git a/docs/src/distance.md b/docs/src/distance.md
@@ -11,8 +11,8 @@ Pages   = ["distance.md"]
 ```@autodocs
 Modules = [LightGraphs]
 Pages   = [
-	"distance.jl",
-	"transitivity.jl"
+    "distance.jl",
+    "transitivity.jl"
 ]
 Private = false
 ```
diff --git a/docs/src/flowcut.md b/docs/src/flowcut.md
diff --git a/docs/src/graphtypes.md b/docs/src/graphtypes.md
@@ -2,16 +2,16 @@
 
 In addition to providing `SimpleGraph` and `SimpleDiGraph` implementations, LightGraphs also serves as a framework for other graph types. Currently, there are several alternative graph types, each with its own package:
 
-- [SimpleWeightedGraphs](https://github.com/JuliaGraphs/SimpleGraphs.jl) provides a graph structure with the ability to specify weights on edges.
-- [MetaGraphs](https://github.com/JuliaGraphs/MetaGraphs.jl) provides a graph structure that supports user-defined properties on the graph, vertices, and edges.
+- [SimpleWeightedGraphs](https://github.com/JuliaGraphs/SimpleWeightedGraphs.jl) provides a structure for (un)directed graphs with the ability to specify weights on edges.
+- [MetaGraphs](https://github.com/JuliaGraphs/MetaGraphs.jl) provides a structure (un)directed graphs that supports user-defined properties on the graph, vertices, and edges.
 - [StaticGraphs](https://github.com/JuliaGraphs/StaticGraphs.jl) supports very large graph structures in a space- and time-efficient manner, but as the name implies, does not allow modification of the graph once
 created.
 
 ### Which Graph Type Should I Use?
 
 These are general guidelines to help you select the proper graph type.
 
-- In general, prefer `SimpleGraphs`.
-- If you need edge weights and don't require large numbers of graph modifications, use `SimpleWeightedGraphs`.
-- If you need labeling of vertices or edges, use `MetaGraphs`.
-- If you work with very large graphs (billons to tens of billions of edges) and don't need mutability, use `StaticGraphs`.
+- In general, prefer the native `SimpleGraphs`/`SimpleDiGraphs` structures in [LightGraphs.jl](https://github.com/JuliaGraphs/LightGraphs.jl).
+- If you need edge weights and don't require large numbers of graph modifications, use [SimpleWeightedGraphs](https://github.com/JuliaGraphss/SimpleWeightedGraphs.jl).
+- If you need labeling of vertices or edges, use [MetaGraphs](https://github.com/JuliaGraphs/MetaGraphs.jl).
+- If you work with very large graphs (billons to tens of billions of edges) and don't need mutability, use [StaticGraphs](https://github.com/JuliaGraphs/StaticGraphs.jl).
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,4 +1,4 @@
-# Light Graphs
+# LightGraphs
 
 The goal of *LightGraphs.jl* is to offer a performant platform for network and graph analysis in Julia. To this end, LightGraphs offers both (a) a set of simple, concrete graph implementations -- `SimpleGraph` (for undirected graphs) and `SimpleDiGraph` (for directed graphs), and (b) an API for the development of more sophisticated graph implementations under the `AbstractGraph` type.
 

diff --git a/docs/src/plotting.md b/docs/src/plotting.md
@@ -8,7 +8,7 @@ This excellent graph visualization package can be used with *LightGraphs.jl*
 as follows:
 
 ```julia
-julia> g = WheelGraph(10); am = full(adjacency_matrix(g))
+julia> g = WheelGraph(10); am = Matrix(adjacency_matrix(g))
 julia> loc_x, loc_y = layout_spring_adj(am)
 julia> draw_layout_adj(am, loc_x, loc_y, filename="wheel10.svg")
 ```

diff --git a/src/LightGraphs.jl b/src/LightGraphs.jl
@@ -1,28 +1,42 @@
 __precompile__(true)
 module LightGraphs
 
-import CodecZlib
-using DataStructures
 using SimpleTraits
 
+import CodecZlib
+import DataStructures
+import DelimitedFiles
+import Distributed
+import IterativeEigensolvers
+import LinearAlgebra
+import Markdown
+import Random
+import SharedArrays
+import SparseArrays
+
 import Base: write, ==, <, *, ≈, convert, isless, issubset, union, intersect,
-            reverse, reverse!, blkdiag, isassigned, getindex, setindex!, show,
-            print, copy, in, sum, size, sparse, eltype, length, ndims, transpose,
-            ctranspose, join, start, next, done, eltype, get, issymmetric, A_mul_B!,
-            Pair, Tuple, zero
+            reverse, reverse!, isassigned, getindex, setindex!, show,
+            print, copy, in, sum, size, eltype, length, ndims, transpose,
+            ctranspose, join, start, next, done, eltype, get, Pair, Tuple, zero
+
+
 export
 # Interface
 AbstractGraph, AbstractEdge, AbstractEdgeIter,
-Edge, Graph, SimpleGraph, DiGraph, SimpleDiGraph, vertices, edges, edgetype, nv, ne, src, dst,
-is_directed, add_vertex!, add_edge!, rem_vertex!, rem_edge!,
-has_vertex, has_edge, in_neighbors, out_neighbors,
+Edge, Graph, SimpleGraph, SimpleGraphFromIterator, DiGraph, SimpleDiGraphFromIterator,
+SimpleDiGraph, vertices, edges, edgetype, nv, ne, src, dst,
+is_directed,
+has_vertex, has_edge, inneighbors, outneighbors,
 
 # core
 is_ordered, add_vertices!, indegree, outdegree, degree,
 Δout, Δin, δout, δin, Δ, δ, degree_histogram,
 neighbors, all_neighbors, common_neighbors,
 has_self_loops, num_self_loops, density, squash, weights,
 
+# simplegraphs
+add_edge!, add_vertex!, add_vertices!, rem_edge!, rem_vertex!,
+
 # decomposition
 core_number, k_core, k_shell, k_crust, k_corona,
 
@@ -37,7 +51,7 @@ spectral_distance, edit_distance,
 MinkowskiCost, BoundedMinkowskiCost,
 
 # operators
-complement, reverse, reverse!, blkdiag, union, intersect,
+complement, reverse, reverse!, blockdiag, union, intersect,
 difference, symmetric_difference,
 join, tensor_product, cartesian_product, crosspath,
 induced_subgraph, egonet, merge_vertices!, merge_vertices,
@@ -62,6 +76,9 @@ randomwalk, saw, non_backtracking_randomwalk,
 # diffusion
 diffusion, diffusion_rate,
 
+# coloring
+greedy_color,
+
 # connectivity
 connected_components, strongly_connected_components, weakly_connected_components,
 is_connected, is_strongly_connected, is_weakly_connected, period,
@@ -77,9 +94,9 @@ MaximumAdjacency, AbstractMASVisitor, mincut, maximum_adjacency_visit,
 
 # a-star, dijkstra, bellman-ford, floyd-warshall
 a_star, dijkstra_shortest_paths, bellman_ford_shortest_paths,
-has_negative_edge_cycle, enumerate_paths, floyd_warshall_shortest_paths,
-transitiveclosure!, transitiveclosure, yen_k_shortest_paths,
-parallel_multisource_dijkstra_shortest_paths,
+has_negative_edge_cycle, enumerate_paths, johnson_shortest_paths,
+floyd_warshall_shortest_paths, transitiveclosure!, transitiveclosure, transitivereduction, 
+yen_k_shortest_paths, parallel_multisource_dijkstra_shortest_paths,
 
 # centrality
 betweenness_centrality, closeness_centrality, degree_centrality,
@@ -97,20 +114,16 @@ contract,
 # persistence
 loadgraph, loadgraphs, savegraph, LGFormat,
 
-# flow
-maximum_flow, EdmondsKarpAlgorithm, DinicAlgorithm, BoykovKolmogorovAlgorithm, PushRelabelAlgorithm,
-multiroute_flow, KishimotoAlgorithm, ExtendedMultirouteFlowAlgorithm,
-
 # randgraphs
-erdos_renyi, watts_strogatz, random_regular_graph, random_regular_digraph, random_configuration_model,
-random_tournament_digraph, StochasticBlockModel, make_edgestream, nearbipartiteSBM, blockcounts,
-blockfractions, stochastic_block_model, barabasi_albert, barabasi_albert!, static_fitness_model,
-static_scale_free, kronecker,
+erdos_renyi, expected_degree_graph, watts_strogatz, random_regular_graph, random_regular_digraph,
+random_configuration_model, random_tournament_digraph, StochasticBlockModel, make_edgestream,
+nearbipartiteSBM, blockcounts, blockfractions, stochastic_block_model, barabasi_albert,
+barabasi_albert!, static_fitness_model, static_scale_free, kronecker,
 
 #community
 modularity, core_periphery_deg,
 local_clustering,local_clustering_coefficient, global_clustering_coefficient, triangles,
-label_propagation, maximal_cliques,
+label_propagation, maximal_cliques, clique_percolation,
 
 #generators
 CompleteGraph, StarGraph, PathGraph, WheelGraph, CycleGraph,
@@ -189,6 +202,7 @@ include("digraph/cycles/hadwick-james.jl")
 include("digraph/cycles/karp.jl")
 include("traversals/bfs.jl")
 include("traversals/bipartition.jl")
+include("traversals/greedy_color.jl")
 include("traversals/parallel_bfs.jl")
 include("traversals/dfs.jl")
 include("traversals/maxadjvisit.jl")
@@ -200,6 +214,7 @@ include("edit_distance.jl")
 include("shortestpaths/astar.jl")
 include("shortestpaths/bellman-ford.jl")
 include("shortestpaths/dijkstra.jl")
+include("shortestpaths/johnson.jl")
 include("shortestpaths/floyd-warshall.jl")
 include("shortestpaths/yen.jl")
 include("linalg/LinAlg.jl")
@@ -223,14 +238,7 @@ include("community/label_propagation.jl")
 include("community/core-periphery.jl")
 include("community/clustering.jl")
 include("community/cliques.jl")
-include("flow/maximum_flow.jl")
-include("flow/edmonds_karp.jl")
-include("flow/dinic.jl")
-include("flow/boykov_kolmogorov.jl")
-include("flow/push_relabel.jl")
-include("flow/multiroute_flow.jl")
-include("flow/kishimoto.jl")
-include("flow/ext_multiroute_flow.jl")
+include("community/clique_percolation.jl")
 include("spanningtrees/kruskal.jl")
 include("spanningtrees/prim.jl")
 include("biconnectivity/articulation.jl")