Merge pull request #1 from JuliaGraphs/migrate-to-graphs.jl

Author: jpfairbanks

LICENSE.md

@@ -1,4 +1,4 @@
-The LightGraphsFlows.jl package is licensed under the Simplified "2-clause" BSD License:
+The GraphsFlows.jl package is licensed under the Simplified "2-clause" BSD License:
 
 > Copyright (c) 2018: mbesancon.
 > All rights reserved.

Project.toml

@@ -1,19 +1,19 @@
-name = "LightGraphsFlows"
-uuid = "2f5eb75a-258c-59e0-affc-f41c55f75335"
+name = "GraphsFlows"
+uuid = "06909019-6f44-4949-96fc-b9d9aaa02889"
 authors = ["Mathieu Besançon <mathieu.besancon@gmail.com>"]
-version = "0.4.2"
+version = "0.1.0"
 
 [deps]
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
 JuMP = "0.21"
-LightGraphs = "1.3"
+Graphs = "1.4"
 SimpleTraits = "0.9"
 julia = "1.3"
 

README.md

@@ -1,24 +1,23 @@
-# LightGraphsFlows
+# GraphsFlows
 
-[![CI](https://github.com/JuliaGraphs/LightGraphsFlows.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/JuliaGraphs/LightGraphsFlows.jl/actions/workflows/ci.yml)
-[![codecov.io](http://codecov.io/github/JuliaGraphs/LightGraphsFlows.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaGraphs/LightGraphsFlows.jl?branch=master)
-[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliagraphs.github.io/LightGraphsFlows.jl/stable/)
+[![CI](https://github.com/JuliaGraphs/GraphsFlows.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/JuliaGraphs/GraphsFlows.jl/actions/workflows/ci.yml)
+[![codecov.io](http://codecov.io/github/JuliaGraphs/GraphsFlows.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaGraphs/GraphsFlows.jl?branch=master)
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliagraphs.github.io/GraphsFlows.jl/stable/)
 
-Flow algorithms on top of [LightGraphs.jl](https://github.com/JuliaGraphs/LightGraphs.jl),
+Flow algorithms on top of [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl),
 including `maximum_flow`, `multiroute_flow` and `mincost_flow`. 
 See [Maximum flow problem](https://en.wikipedia.org/wiki/Maximum_flow_problem)
 for a detailed description of the problem.
 
-Documentation for this package is available [here](https://juliagraphs.github.io/LightGraphsFlows.jl/latest/). For an overview of JuliaGraphs, see [this page](https://juliagraphs.github.io/).
+Documentation for this package is available [here](https://juliagraphs.github.io/GraphsFlows.jl/latest/). For an overview of JuliaGraphs, see [this page](https://juliagraphs.github.io/).
 
 ## Usage
 
 ### Maxflow 
 
 ```julia
-julia> using LightGraphs, LightGraphsFlows
-julia> const LG = LightGraphs
-julia> flow_graph = LG.DiGraph(8) # Create a flow graph
+julia> using Graphs, GraphsFlows
+julia> flow_graph = Graphs.DiGraph(8) # Create a flow graph
 julia> flow_edges = [
     (1,2,10),(1,3,5),(1,4,15),(2,3,4),(2,5,9),
     (2,6,15),(3,4,4),(3,6,8),(4,7,16),(5,6,15),
@@ -29,7 +28,7 @@ julia> capacity_matrix = zeros(Int, 8, 8)  # Create a capacity matrix
 
 julia> for e in flow_edges
     u, v, f = e
-    LG.add_edge!(flow_graph, u, v)
+    Graphs.add_edge!(flow_graph, u, v)
     capacity_matrix[u,v] = f
 end
 
@@ -47,10 +46,9 @@ julia> f, F, labels = maximum_flow(flow_graph, 1, 8, capacity_matrix, algorithm=
 ### Multi-route flow
 
 ```julia
-julia> using LightGraphs, LightGraphsFlows
-julia> const LG =  LightGraphs
+julia> using Graphs, GraphsFlows
 
-julia> flow_graph = LG.DiGraph(8) # Create a flow graph
+julia> flow_graph = Graphs.DiGraph(8) # Create a flow graph
 
 julia> flow_edges = [
 (1, 2, 10), (1, 3, 5),  (1, 4, 15), (2, 3, 4),  (2, 5, 9),
@@ -62,7 +60,7 @@ julia> capacity_matrix = zeros(Int, 8, 8) # Create a capacity matrix
 
 julia> for e in flow_edges
     u, v, f = e
-    LG.add_edge!(flow_graph, u, v)
+    Graphs.add_edge!(flow_graph, u, v)
     capacity_matrix[u, v] = f
 end
 
@@ -86,18 +84,17 @@ defined by [MathOptInterface.jl](https://www.juliaopt.org/MathOptInterface.jl/st
 julia> using SparseArrays: spzeros
 julia> import Clp
 
-julia> using LightGraphs, LightGraphsFlows
-julia> const LG =  LightGraphs
-
-julia> g = LG.DiGraph(6)
-julia> LG.add_edge!(g, 5, 1)
-julia> LG.add_edge!(g, 5, 2)
-julia> LG.add_edge!(g, 3, 6)
-julia> LG.add_edge!(g, 4, 6)
-julia> LG.add_edge!(g, 1, 3)
-julia> LG.add_edge!(g, 1, 4)
-julia> LG.add_edge!(g, 2, 3)
-julia> LG.add_edge!(g, 2, 4)
+julia> using Graphs, GraphsFlows
+
+julia> g = Graphs.DiGraph(6)
+julia> Graphs.add_edge!(g, 5, 1)
+julia> Graphs.add_edge!(g, 5, 2)
+julia> Graphs.add_edge!(g, 3, 6)
+julia> Graphs.add_edge!(g, 4, 6)
+julia> Graphs.add_edge!(g, 1, 3)
+julia> Graphs.add_edge!(g, 1, 4)
+julia> Graphs.add_edge!(g, 2, 3)
+julia> Graphs.add_edge!(g, 2, 4)
 julia> cost = zeros(6,6)
 julia> cost[1,3] = 10.
 julia> cost[1,4] = 5.

docs/Project.toml

@@ -1,4 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
-LightGraphsFlows = "2f5eb75a-258c-59e0-affc-f41c55f75335"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+GraphsFlows = "06909019-6f44-4949-96fc-b9d9aaa02889"
+

docs/make.jl

@@ -1,12 +1,11 @@
 using Documenter
-using LightGraphsFlows
-using LightGraphs
-const lg = LightGraphs
+using GraphsFlows
+using Graphs
 
 makedocs(
-    modules = [LightGraphsFlows],
+    modules = [GraphsFlows],
     format = Documenter.HTML(),
-    sitename = "LightGraphsFlows",
+    sitename = "GraphsFlows",
 	pages = Any[
 		"Getting started"    => "index.md",
         "Maxflow algorithms" => "maxflow.md",
@@ -19,6 +18,6 @@ makedocs(
 deploydocs(
     deps        = nothing,
     make        = nothing,
-    repo        = "github.com/JuliaGraphs/LightGraphsFlows.jl.git",
+    repo        = "github.com/JuliaGraphs/GraphsFlows.jl.git",
     versions = ["stable" => "v^", "v#.#", "dev" => "master"],
 )

docs/mkdocs.yml

@@ -1,6 +1,6 @@
-site_name:        LightGraphsFlows.jl
-repo_url:         https://github.com/JuliaGraphs/LightGraphsFlows.jl
-site_description: Documentation for LightGraphsFlows, the JuliaGraphs package for flow and cut problems
+site_name:        GraphsFlows.jl
+repo_url:         https://github.com/JuliaGraphs/GraphsFlows.jl
+site_description: Documentation for GraphsFlows, the JuliaGraphs package for flow and cut problems
 site_author:      JuliaGraphs
 
 theme: material

docs/src/index.md

@@ -1,26 +1,23 @@
- # LightGraphsFlows.jl: flow algorithms for LightGraphs
+ # GraphsFlows.jl: flow algorithms for Graphs.jl
 
 ```@meta
-CurrentModule = LightGraphsFlows
+CurrentModule = GraphsFlows
 DocTestSetup = quote
-    using LightGraphsFlows
-    import LightGraphs
-    const lg = LightGraphs
+    using GraphsFlows
+    import Graphs
 end
 ```
 
 ```@autodocs
-Modules = [LightGraphsFlows]
-Pages = ["LightGraphsFlows.jl"]
+Modules = [GraphsFlows]
+Pages = ["GraphsFlows.jl"]
 Order = [:function, :type]
 ```
 
-This is the documentation page for `LightGraphsFlows`. In all pages, we assume
-LightGraphsFlows has been imported into scope and that LightGraphs is 
-available with the alias `lg`:
+This is the documentation page for `GraphsFlows`. In all pages, we assume
+GraphsFlows has been imported into scope and that Graphs.jl has been imported.
 
 ```julia
-using LightGraphsFlows
-import LightGraphs
-const lg = LightGraphs
+using GraphsFlows
+import Graphs
 ```

docs/src/maxflow.md

@@ -1,7 +1,7 @@
 ## Max flow algorithms
 
 ```@autodocs
-Modules = [LightGraphsFlows]
+Modules = [GraphsFlows]
 Pages = ["maxflow.jl", "boykov_kolmogorov.jl", "push_relabel.jl", "dinic.jl", "edmonds_karp.jl"]
 Order = [:function, :type]
 ```

docs/src/mincost.md

@@ -1,7 +1,7 @@
 ## Min-cost flow
 
 ```@autodocs
-Modules = [LightGraphsFlows]
+Modules = [GraphsFlows]
 Pages = ["mincost.jl"]
 Order = [:function, :type]
 ```

docs/src/mincut.md

@@ -1,7 +1,7 @@
 ## Min-cut
 
 ```@autodocs
-Modules = [LightGraphsFlows]
+Modules = [GraphsFlows]
 Pages = ["mincut.jl"]
 Order = [:function, :type]
 ```

docs/src/multiroute.md

@@ -1,7 +1,7 @@
 ## Multi-route flow
 
 ```@autodocs
-Modules = [LightGraphsFlows]
+Modules = [GraphsFlows]
 Pages = ["multiroute_flow.jl", "ext_multiroute_flow.jl", "kishimoto.jl"]
 Order = [:function, :type]
 ```

src/LightGraphsFlows.jl renamed to src/GraphsFlows.jl

@@ -1,7 +1,6 @@
-module LightGraphsFlows
+module GraphsFlows
 
-using LightGraphs
-const lg = LightGraphs
+using Graphs
 
 using SimpleTraits: @traitfn, @traitimpl
 import SimpleTraits

src/boykov_kolmogorov.jl

@@ -17,12 +17,12 @@ Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision.
 function boykov_kolmogorov_impl end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
 @traitfn function boykov_kolmogorov_impl(
-        residual_graph::AG::lg.IsDirected,    # the input graph
+        residual_graph::AG::Graphs.IsDirected,    # the input graph
         source::Integer,                      # the source vertex
         target::Integer,                      # the target vertex
         capacity_matrix::AbstractMatrix{T}    # edge flow capacities
-    ) where {T, U, AG<:lg.AbstractGraph{U}}
-    n = lg.nv(residual_graph)
+    ) where {T, U, AG<:Graphs.AbstractGraph{U}}
+    n = Graphs.nv(residual_graph)
 
     flow = 0
     flow_matrix = zeros(T, n, n)
@@ -54,20 +54,20 @@ end
 
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
 @traitfn function find_path!(
-        residual_graph::AG::lg.IsDirected, # the input graph
+        residual_graph::AG::Graphs.IsDirected, # the input graph
         source::Integer,                   # the source vertex
         target::Integer,                   # the target vertex
         flow_matrix::AbstractMatrix,       # the current flow matrix
         capacity_matrix::AbstractMatrix,   # edge flow capacities
         PARENT::Vector,                    # parent table
         TREE::Vector,                      # tree table
         A::Vector                          # active set
-    ) where {T, AG<:lg.AbstractGraph{T}}
+    ) where {T, AG<:Graphs.AbstractGraph{T}}
     tree_cap(p, q) = TREE[p] == one(T) ? capacity_matrix[p, q] - flow_matrix[p, q] :
     capacity_matrix[q, p] - flow_matrix[q, p]
     while !isempty(A)
         p = last(A)
-        for q in lg.neighbors(residual_graph, p)
+        for q in Graphs.neighbors(residual_graph, p)
             if tree_cap(p, q) > 0
                 if TREE[q] == zero(T)
                     TREE[q] = TREE[p]
@@ -147,7 +147,7 @@ function augment!(
 end
 
 @traitfn function adopt!(
-        residual_graph::AG::lg.IsDirected,  # the input graph
+        residual_graph::AG::Graphs.IsDirected,  # the input graph
         source::Integer,                    # the source vertex
         target::Integer,                    # the target vertex
         flow_matrix::AbstractMatrix,        # the current flow matrix
@@ -156,14 +156,14 @@ end
         TREE::Vector,                       # tree table
         A::Vector,                          # active set
         O::Vector                           # orphan set
-    ) where {T, AG<:lg.AbstractGraph{T}}
+    ) where {T, AG<:Graphs.AbstractGraph{T}}
     tree_cap(p, q) = TREE[p] == 1 ? capacity_matrix[p, q] - flow_matrix[p, q] :
     capacity_matrix[q, p] - flow_matrix[q, p]
     while !isempty(O)
         p = pop!(O)
         # try to find parent that is not an orphan
         parent_found = false
-        for q in lg.neighbors(residual_graph, p)
+        for q in Graphs.neighbors(residual_graph, p)
             if TREE[q] == TREE[p] && tree_cap(q, p) > 0
                 # check if "origin" is either source or target
                 o = q
@@ -180,7 +180,7 @@ end
 
         if !parent_found
             # scan all neighbors and make the orphan a free node
-            for q in lg.neighbors(residual_graph, p)
+            for q in Graphs.neighbors(residual_graph, p)
                 if TREE[q] == TREE[p]
                     if tree_cap(q, p) > 0
                         pushfirst!(A, q)

src/dinic.jl

@@ -8,12 +8,12 @@ Return the value of the maximum flow as well as the final flow matrix.
 """
 function dinic_impl end
 @traitfn function dinic_impl(
-        residual_graph::::lg.IsDirected,               # the input graph
+        residual_graph::::Graphs.IsDirected,               # the input graph
         source::Integer,                       # the source vertex
         target::Integer,                       # the target vertex
         capacity_matrix::AbstractMatrix{T}    # edge flow capacities
     ) where {T}
-    n = lg.nv(residual_graph)                     # number of vertexes
+    n = Graphs.nv(residual_graph)                     # number of vertexes
     flow_matrix = zeros(T, n, n)           # initialize flow matrix
     P = zeros(Int, n)                      # Sharable parent vector
 
@@ -37,14 +37,14 @@ Like `blocking_flow`, but requires a preallocated parent vector `P`.
 """
 function blocking_flow! end
 @traitfn function blocking_flow!(
-        residual_graph::::lg.IsDirected,     # the input graph
+        residual_graph::::Graphs.IsDirected,     # the input graph
         source::Integer,                     # the source vertex
         target::Integer,                     # the target vertex
         capacity_matrix::AbstractMatrix{T},  # edge flow capacities
         flow_matrix::AbstractMatrix,         # the current flow matrix
         P::AbstractVector{Int}               # Parent vector to store Level Graph
     ) where {T}
-    n = lg.nv(residual_graph)                # number of vertexes
+    n = Graphs.nv(residual_graph)                # number of vertexes
     fill!(P, -1)
     P[source] = -2
 
@@ -53,7 +53,7 @@ function blocking_flow! end
 
     while length(Q) > 0                   # Construct the Level Graph using BFS
         u = pop!(Q)
-        for v in lg.outneighbors(residual_graph, u)
+        for v in Graphs.outneighbors(residual_graph, u)
             if P[v] == -1 && capacity_matrix[u, v] > flow_matrix[u, v]
                 P[v] = u
                 pushfirst!(Q, v)
@@ -65,7 +65,7 @@ function blocking_flow! end
 
     total_flow = 0
 
-    for bv in lg.inneighbors(residual_graph, target)    # Trace all possible routes to source
+    for bv in Graphs.inneighbors(residual_graph, target)    # Trace all possible routes to source
         flow = typemax(T)
         v = target
         u = bv
@@ -104,7 +104,7 @@ matrix `flow_matrix`and then backtrack from `target` to `source`,
 augmenting flow along all possible paths.
 """
 blocking_flow(
-    residual_graph::lg.AbstractGraph,  # the input graph
+    residual_graph::Graphs.AbstractGraph,  # the input graph
     source::Integer,                   # the source vertex
     target::Integer,                   # the target vertex
     capacity_matrix::AbstractMatrix,   # edge flow capacities
@@ -115,4 +115,4 @@ blocking_flow(
             target,
             capacity_matrix,
             flow_matrix,
-            zeros(Int, lg.nv(residual_graph)))
+            zeros(Int, Graphs.nv(residual_graph)))