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new staticgraphs
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‎.gitignore‎

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*.jl.cov
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*.jl.*.cov
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*.jl.mem
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.DS_Store

‎.travis.yml‎

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language: julia
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os:
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- linux
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- osx
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# - osx
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julia:
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- 0.6
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- nightly
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# - nightly
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notifications:
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email: false
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git:
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#script:
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# - julia -e 'Pkg.clone(pwd()); Pkg.build("StaticGraphs"); Pkg.test("StaticGraphs"; coverage=true)'
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after_success:
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# push coverage results to Coveralls
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- julia -e 'cd(Pkg.dir("StaticGraphs")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
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# push coverage results to Codecov
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- julia -e 'cd(Pkg.dir("StaticGraphs")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

‎LICENSE.md‎

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@@ -2,21 +2,49 @@ The StaticGraphs.jl package is licensed under the MIT "Expat" License:
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> Copyright (c) 2017: Seth Bromberger.
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>
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> Permission is hereby granted, free of charge, to any person obtaining a copy
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> of this software and associated documentation files (the "Software"), to deal
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> in the Software without restriction, including without limitation the rights
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> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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> copies of the Software, and to permit persons to whom the Software is
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> furnished to do so, subject to the following conditions:
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>
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> The above copyright notice and this permission notice shall be included in all
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> copies or substantial portions of the Software.
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>
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> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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> Permission is hereby granted, free of charge, to any person obtaining
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> a copy of this software and associated documentation files (the
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> "Software"), to deal in the Software without restriction, including
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> without limitation the rights to use, copy, modify, merge, publish,
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> distribute, sublicense, and/or sell copies of the Software, and to
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> permit persons to whom the Software is furnished to do so, subject to
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> the following conditions:
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> The above copyright notice and this permission notice shall be
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> included in all copies or substantial portions of the Software.
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> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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> NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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> BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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> ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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> CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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> SOFTWARE.
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This package uses code derived from RigidBodyDynamics.jl:
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The RigidBodyDynamics.jl package is licensed under the MIT "Expat" License:
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> Copyright (c) 2016: Twan Koolen.
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>
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> Permission is hereby granted, free of charge, to any person obtaining
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> a copy of this software and associated documentation files (the
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> "Software"), to deal in the Software without restriction, including
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> without limitation the rights to use, copy, modify, merge, publish,
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> distribute, sublicense, and/or sell copies of the Software, and to
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> permit persons to whom the Software is furnished to do so, subject to
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> the following conditions:
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> The above copyright notice and this permission notice shall be
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> included in all copies or substantial portions of the Software.
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> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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> NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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> BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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> ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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> CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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> SOFTWARE.

‎README.md‎

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[![Build Status](https://travis-ci.org/sbromberger/StaticGraphs.jl.svg?branch=master)](https://travis-ci.org/sbromberger/StaticGraphs.jl)
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[![Coverage Status](https://coveralls.io/repos/sbromberger/StaticGraphs.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/sbromberger/StaticGraphs.jl?branch=master)
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[![codecov.io](http://codecov.io/github/sbromberger/StaticGraphs.jl/coverage.svg?branch=master)](http://codecov.io/github/sbromberger/StaticGraphs.jl?branch=master)

‎REQUIRE‎

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julia 0.6
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LightGraphs 0.10.5

‎src/StaticGraphs.jl‎

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module StaticGraphs
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# package code goes here
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using LightGraphs
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import Base:
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convert, eltype, show, ==, Pair, Tuple, in, copy, length, start, next, done, issubset, zero, one,
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size, getindex, setindex!, length, IndexStyle
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import LightGraphs:
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_NI, _insert_and_dedup!, AbstractEdge, AbstractEdgeIter,
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src, dst, edgetype, nv, ne, vertices, edges, is_directed,
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has_vertex, has_edge, in_neighbors, out_neighbors,
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indegree, outdegree, degree, insorted,
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AbstractGraphFormat, loadgraph, savegraph
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import LightGraphs.SimpleGraphs:
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AbstractSimpleGraph,
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fadj,
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badj,
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SimpleEdge,
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AbstractSimpleEdge
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export
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AbstractStaticGraph,
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StaticEdge,
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StaticGraph,
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StaticDiGraph,
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StaticDiGraphEdge,
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# weight,
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# weighttype,
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# get_weight,
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out_edges,
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in_edges,
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SGraph,
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SDiGraph,
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SGFormat,
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SDGFormat
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include("utils.jl")
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const StaticEdgeIter{G} = LightGraphs.SimpleGraphs.SimpleEdgeIter{G}
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const AbstractStaticEdge = AbstractSimpleEdge
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const StaticEdge = SimpleEdge
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"""
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AbstractStaticGraph
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An abstract type representing a simple graph structure.
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AbstractStaticGraphs must have the following elements:
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- weightmx::AbstractSparseMatrix{Real}
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"""
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abstract type AbstractStaticGraph <: AbstractSimpleGraph end
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function show(io::IO, g::AbstractStaticGraph)
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if is_directed(g)
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dir = "directed"
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else
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dir = "undirected"
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end
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if nv(g) == 0
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print(io, "empty $dir simple static $(eltype(g)) graph")
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else
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print(io, "{$(nv(g)), $(ne(g))} $dir simple static $(eltype(g)) graph")
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end
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end
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@inline function _fvrange(g::AbstractStaticGraph, s::Integer)
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@inbounds r_start = g.f_ind[s]
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@inbounds r_end = g.f_ind[s + 1] - 1
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return r_start:r_end
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end
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@inline function fadj(g::AbstractStaticGraph, s::Integer)
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r = _fvrange(g, s)
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return fastview(g.f_vec, r)
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end
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nv(g::AbstractStaticGraph) = length(g.f_ind) - 1
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vertices(g::AbstractStaticGraph) = one(eltype(g)):nv(g)
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eltype(x::AbstractStaticGraph) = eltype(x.f_vec)
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has_edge(g::AbstractStaticGraph, e::AbstractStaticEdge) =
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insorted(dst(e), neighbors(g, src(e)))
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edgetype(g::AbstractStaticGraph) = StaticEdge
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edges(g::AbstractStaticGraph) = StaticEdgeIter(g)
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has_vertex(g::AbstractStaticGraph, v::Integer) = v in vertices(g)
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out_neighbors(g::AbstractStaticGraph, v::Integer) = fadj(g, v)
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in_neighbors(g::AbstractStaticGraph, v::Integer) = badj(g, v)
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zero(g::T) where T<:AbstractStaticGraph = T()
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copy(g::T) where T <: AbstractStaticGraph = T(copy(g.f_vec), copy(g.f_ind))
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const StaticGraphEdge = StaticEdge
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const StaticDiGraphEdge = StaticEdge
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include("staticgraph.jl")
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include("staticdigraph.jl")
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include("persistence.jl")
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const SGraph = StaticGraph
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const SDiGraph = StaticDiGraph
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end # module

‎src/overrides.jl‎

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‎src/persistence.jl‎

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# StaticGraphs are binary files with the following format:
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# f_vec, 0, f_ind
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# StaticDiGraphs have the following format:
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# f_vec, 0, f_ind, 0, b_vec, 0, b_ind
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abstract type StaticGraphFormat <: AbstractGraphFormat end
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struct SGFormat{T<:Integer} <: StaticGraphFormat end
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struct SDGFormat{T<:Integer} <: StaticGraphFormat end
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SGFormat() = SGFormat{Int64}()
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SGFormat(T::DataType) = SGFormat{T}()
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SDGFormat() = SDGFormat{Int64}()
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SDGFormat(T::DataType) = SDGFormat{T}()
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function savesg(fn::AbstractString, g::StaticGraph, T::DataType)
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open(fn, "w+") do io
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arr = vcat(g.f_vec, [0], g.f_ind)
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v = Mmap.mmap(io, Vector{T}, length(arr))
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for i = 1:length(arr)
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@inbounds v[i] = arr[i]
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end
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Mmap.sync!(v)
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end
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return 1
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end
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function savesg(fn::AbstractString, g::StaticDiGraph, T::DataType)
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open(fn, "w+") do io
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farr = vcat(g.f_vec, [0], g.f_ind)
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barr = vcat(g.b_vec, [0], g.b_ind)
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arr = vcat(farr, [0], barr)
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v = Mmap.mmap(io, Vector{T}, length(arr))
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for i = 1:length(arr)
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@inbounds v[i] = arr[i]
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end
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Mmap.sync!(v)
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end
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return 1
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end
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function loadsg(fn::AbstractString, ::SGFormat{T}) where T <: Integer
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open(fn, "r") do io
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arr = Mmap.mmap(io, Vector{T})
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zeroind = findfirst(arr, 0)
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StaticGraph{T}(arr[1:zeroind-1], arr[zeroind+1:end])
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end
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end
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function loadsg(fn::AbstractString, ::SDGFormat{T}) where T <: Integer
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open(fn, "r") do io
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arr = Mmap.mmap(io, Vector{T})
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(z1, z2, z3) = findin(arr, 0)
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f_arr = fastview(arr, 1:(z1 - 1))
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f_ind = fastview(arr, (z1 + 1):(z2 - 1))
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b_arr = fastview(arr, (z2 + 1):(z3 - 1))
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b_ind = fastview(arr, (z3 + 1):length(arr))
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StaticDiGraph{T}(f_arr, f_ind, b_arr, b_ind)
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end
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end
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loadgraph(fn::AbstractString, gname::String, s::T) where T <: StaticGraphFormat = loadsg(fn, s)
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savegraph(fn::AbstractString, g::AbstractStaticGraph, gname::String) = savegraph(fn, g)
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savegraph(fn::AbstractString, g::AbstractStaticGraph) = savesg(fn, g, eltype(g))

‎src/staticdigraph.jl‎

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"""
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StaticDiGraph{T}
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A type representing a static directed graph.
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"""
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struct StaticDiGraph{T<:Integer} <: AbstractStaticGraph
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f_vec::Vector{T}
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f_ind::Vector{T}
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b_vec::Vector{T}
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b_ind::Vector{T}
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end
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@inline function _bvrange(g::StaticDiGraph, s)
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@inbounds r_start = g.b_ind[s]
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@inbounds r_end = g.b_ind[s + 1] - 1
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return r_start:r_end
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end
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@inline function badj(g::StaticDiGraph, s)
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r = _bvrange(g, s)
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return fastview(g.b_vec, r)
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end
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ne(g::StaticDiGraph) = length(g.f_vec)
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# sorted src, dst vectors for forward and backward edgelists.
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function StaticDiGraph(n_v, f_ss::Vector{T}, f_ds::Vector{T}, b_ss::Vector{T}, b_ds::Vector{T}) where T <: Integer
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length(f_ss) == length(f_ds) == length(b_ss) == length(b_ds) || error("source and destination vectors must be equal length")
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(n_v == 0 || length(f_ss) == 0) && return StaticDiGraph(T[], T[1], T[], T[1])
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f_ind = [searchsortedfirst(f_ss, x) for x in 1:n_v]
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push!(f_ind, length(f_ss)+1)
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b_ind = [searchsortedfirst(b_ss, x) for x in 1:n_v]
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push!(b_ind, length(b_ss)+1)
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return StaticDiGraph{T}(f_ds, f_ind, b_ds, b_ind)
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end
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# sorted src, dst tuples for forward and backward
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function StaticDiGraph(n_v, f_sd::Vector{Tuple{T, T}}, b_sd::Vector{Tuple{T, T}}) where T <: Integer
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f_ss = [x[1] for x in f_sd]
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f_ds = [x[2] for x in f_sd]
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b_ss = [x[1] for x in b_sd]
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b_ds = [x[2] for x in b_sd]
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StaticDiGraph(n_v, f_ss, f_ds, b_ss, b_ds)
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end
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function StaticDiGraph(g::LightGraphs.SimpleGraphs.SimpleDiGraph)
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f_sd = [Tuple(e) for e in edges(g)]
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b_sd = sort([Tuple(reverse(e)) for e in edges(g)])
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StaticDiGraph(nv(g), f_sd, b_sd)
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end
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#
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==(g::StaticDiGraph, h::StaticDiGraph) = g.f_vec == h.f_vec && g.f_ind == h.f_ind && g.b_vec == h.b_vec && g.b_ind == h.b_ind
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degree(g::StaticDiGraph, v::Integer) = indegree(g, v) + outdegree(g, v)
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degree(g::StaticDiGraph) = [degree(g, v) for v in vertices(g)]
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indegree(g::StaticDiGraph, v::Integer) = length(_bvrange(g, v))
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indegree(g::StaticDiGraph) = [indegree(g, v) for v in vertices(g)]
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outdegree(g::StaticDiGraph, v::Integer) = length(_fvrange(g, v))
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outdegree(g::StaticDiGraph) = [outdegree(g, v) for v in vertices(g)]
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"""
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is_directed(g)
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Return `true` if `g` is a directed graph.
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"""
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is_directed(::Type{StaticDiGraph}) = true
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is_directed(::Type{StaticDiGraph{T}}) where T = true
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is_directed(g::StaticDiGraph) = true

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