Merge pull request #40 from storopoli/move-Graphs

Move From LightGraphs.jl to Graphs.jl

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: 0 * * * *
+
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,12 @@
+name: TagBot
+on:
+  schedule:
+    - cron: 30 * * * *
+  workflow_dispatch:
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml

@@ -0,0 +1,44 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.gitignore

@@ -1,3 +1,10 @@
+.DS_Store
 *.jl.cov
-*.jl.*.cov
 *.jl.mem
+.vscode
+docs/build/
+docs/site/
+benchmark/.results/*
+benchmark/.tune.jld
+*.cov
+Manifest.toml

Project.toml

@@ -1,27 +1,27 @@
 name = "GraphIO"
 uuid = "aa1b3936-2fda-51b9-ab35-c553d3a640a2"
-version = "0.5.0"
+version = "0.6.0"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
 
 [compat]
 EzXML = "1"
-LightGraphs = "1"
-ParserCombinator = "2"
-julia = "1"
+Graphs = "1.4"
+ParserCombinator = "2.1"
 Requires = "1"
 SimpleTraits = "0.9"
+julia = "1"
 
 [extras]
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 ParserCombinator = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CodecZlib", "LightGraphs", "EzXML", "ParserCombinator", "Test"]
+test = ["CodecZlib", "Graphs", "EzXML", "ParserCombinator", "Test"]

README.md

@@ -1,11 +1,9 @@
 # GraphIO
 
-[![Build Status](https://travis-ci.org/JuliaGraphs/GraphIO.jl.svg?branch=master)](https://travis-ci.org/JuliaGraphs/GraphIO.jl)
+[![Build Status](https://github.com/JuliaGraphs/GraphIO.jl/workflows/CI/badge.svg)](https://github.com/JuliaGraphs/GraphIO.jl/actions?query=workflow%3ACI+branch%3Amaster)
 [![codecov.io](http://codecov.io/github/JuliaGraphs/GraphIO.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaGraphs/GraphIO.jl?branch=master)
 
-GraphIO provides support to [LightGraphs.jl](https://github.com/JuliaGraphs/LightGraphs.jl) for reading/writing graphs in various formats.
-
-The current version of GraphIO works with Julia version >= 0.7.
+GraphIO provides support to [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) for reading/writing graphs in various formats.
 
 Currently, the following functionality is provided:
 
@@ -29,11 +27,11 @@ Format        | Read | Write | Multiple Graphs| Format Name  |
 [DOT]: https://en.wikipedia.org/wiki/DOT_(graph_description_language)
 
 Graphs are read using either the `loadgraph` function or, for formats that support multiple graphs in a single file,
-the `loadgraphs` functions. `loadgraph` returns a LightGraph object, while `loadgraphs` returns a dictionary of LightGraph objects.  
+the `loadgraphs` functions. `loadgraph` returns a Graph object, while `loadgraphs` returns a dictionary of Graph objects.
 
 For example, an edgelist file could be loaded as:
 
-```
+```julia
 graph = loadgraph("path_to_graph/my_edgelist.txt", "graph_key", EdgeListFormat())
 ``` 
 

src/CDF/Cdf.jl

@@ -4,10 +4,10 @@ module CDF
 # http://www2.ee.washington.edu/research/pstca/formats/cdf.txt
 # http://www2.ee.washington.edu/research/pstca/pf30/ieee30cdf.txt
 
-using LightGraphs
-using LightGraphs: AbstractGraphFormat
+using Graphs
+using Graphs: AbstractGraphFormat
 
-import LightGraphs: loadgraph, loadgraphs, savegraph
+import Graphs: loadgraph, loadgraphs, savegraph
 
 export CDFFormat
 
@@ -45,7 +45,7 @@ function _loadcdf(io::IO)
         end
     end
     n_v = length(vertices)
-    g = LightGraphs.Graph(n_v)
+    g = Graphs.Graph(n_v)
     for p in zip(srcs, dsts)
         add_edge!(g, p)
     end

src/DOT/Dot.jl

@@ -1,31 +1,31 @@
 module DOT
 
 using GraphIO.ParserCombinator.Parsers
-using LightGraphs
-using LightGraphs: AbstractGraphFormat
+using Graphs
+using Graphs: AbstractGraphFormat
 
-import LightGraphs: loadgraph, loadgraphs, savegraph
+import Graphs: loadgraph, loadgraphs, savegraph
 
 export DOTFormat
 
 struct DOTFormat <: AbstractGraphFormat end
 
-function savedot(io::IO, g::LightGraphs.AbstractGraph, gname::String = "")
-    isdir = LightGraphs.is_directed(g)
+function savedot(io::IO, g::Graphs.AbstractGraph, gname::String = "")
+    isdir = Graphs.is_directed(g)
     println(io,(isdir ? "digraph " : "graph ") * gname * " {")
-    for i in LightGraphs.vertices(g)
+    for i in Graphs.vertices(g)
          println(io,"\t" * string(i))
     end
     if isdir
-        for u in LightGraphs.vertices(g)
-            out_nbrs = LightGraphs.outneighbors(g, u)
+        for u in Graphs.vertices(g)
+            out_nbrs = Graphs.outneighbors(g, u)
             length(out_nbrs) == 0 && continue
             println(io, "\t" * string(u) * " -> {" * join(out_nbrs,',') * "}")
         end
     else
-        for e in LightGraphs.edges(g)
-            source = string(LightGraphs.src(e))
-            dest = string(LightGraphs.dst(e))
+        for e in Graphs.edges(g)
+            source = string(Graphs.src(e))
+            dest = string(Graphs.dst(e))
             println(io, "\t" * source * " -- " * dest)
         end
     end
@@ -46,9 +46,9 @@ function _dot_read_one_graph(pg::Parsers.DOT.Graph)
     nvg = length(Parsers.DOT.nodes(pg))
     nodedict = Dict(zip(collect(Parsers.DOT.nodes(pg)), 1:nvg))
     if isdir
-        g = LightGraphs.DiGraph(nvg)
+        g = Graphs.DiGraph(nvg)
     else
-        g = LightGraphs.Graph(nvg)
+        g = Graphs.Graph(nvg)
     end
     for es in Parsers.DOT.edges(pg)
         s = nodedict[es[1]]
@@ -58,27 +58,24 @@ function _dot_read_one_graph(pg::Parsers.DOT.Graph)
     return g
 end
 
+_name(pg::Parsers.DOT.Graph) =
+    pg.id !== nothing ? pg.id.id :
+    Parsers.DOT.StringID(pg.directed ? "digraph" : "graph")
+
 function loaddot(io::IO, gname::String)
     p = Parsers.DOT.parse_dot(read(io, String))
     for pg in p
-        isdir = pg.directed
-        possname = isdir ? Parsers.DOT.StringID("digraph") : Parsers.DOT.StringID("graph")
-        name = get(pg.id, possname).id
-        name == gname && return _dot_read_one_graph(pg)
+        _name(pg) == gname && return _dot_read_one_graph(pg)
     end
     error("Graph $gname not found")
 end
 
 function loaddot_mult(io::IO)
     p = Parsers.DOT.parse_dot(read(io, String))
-
     graphs = Dict{String,AbstractGraph}()
 
     for pg in p
-        isdir = pg.directed
-        possname = isdir ? Parsers.DOT.StringID("digraph") : Parsers.DOT.StringID("graph")
-        name = get(pg.id, possname).id
-        graphs[name] = _dot_read_one_graph(pg)
+        graphs[_name(pg)] = _dot_read_one_graph(pg)
     end
     return graphs
 end

src/Edgelist/Edgelist.jl

@@ -5,10 +5,10 @@ module EdgeList
 # each line. Will return a directed graph.
 
 using DelimitedFiles: writedlm
-using LightGraphs
-using LightGraphs: AbstractGraphFormat
+using Graphs
+using Graphs: AbstractGraphFormat
 
-import LightGraphs: loadgraph, loadgraphs, savegraph
+import Graphs: loadgraph, loadgraphs, savegraph
 
 export EdgeListFormat
 
@@ -36,15 +36,15 @@ function loadedgelist(io::IO, gname::String)
     end
 
     n_v = length(vxset)
-    g = LightGraphs.DiGraph(n_v)
+    g = Graphs.DiGraph(n_v)
     for (u, v) in zip(srcs, dsts)
         add_edge!(g, vxdict[u], vxdict[v])
     end
     return g
 end
 
-function saveedgelist(io::IO, g::LightGraphs.AbstractGraph, gname::String)
-    writedlm(io, ([src(e), dst(e)] for e in LightGraphs.edges(g)), ',')
+function saveedgelist(io::IO, g::Graphs.AbstractGraph, gname::String)
+    writedlm(io, ([src(e), dst(e)] for e in Graphs.edges(g)), ',')
     return 1
 end
 

src/Edgelist/IntEdgeList.jl

@@ -40,7 +40,7 @@ function loadintedgelist(io::IO, gname::String, offset::Int64)
     		push!(badjlist[v], u)
     	end
     end
-    return LightGraphs.DiGraph(neg, fadjlist, badjlist)
+    return Graphs.DiGraph(neg, fadjlist, badjlist)
 end
 
 loadgraph(io::IO, gname::String, fmt::IntEdgeListFormat) = loadintedgelist(io, gname, fmt.offset)

src/GEXF/Gexf.jl

@@ -1,10 +1,10 @@
 module GEXF
 
 using GraphIO.EzXML
-using LightGraphs
-using LightGraphs: AbstractGraph, AbstractGraphFormat
+using Graphs
+using Graphs: AbstractGraph, AbstractGraphFormat
 
-import LightGraphs: savegraph
+import Graphs: savegraph
 
 export GEXFFormat 
 
@@ -16,7 +16,7 @@ struct GEXFFormat <: AbstractGraphFormat end
 Write a graph `g` with name `gname` to an IO stream `io` in the
 [Gexf](http://gexf.net/format/) format. Return 1 (number of graphs written).
 """
-function savegexf(io::IO, g::LightGraphs.AbstractGraph, gname::String)
+function savegexf(io::IO, g::Graphs.AbstractGraph, gname::String)
     xdoc = XMLDocument()
     xroot = setroot!(xdoc, ElementNode("gexf"))
     xroot["xmlns"] = "http://www.gexf.net/1.2draft"
@@ -38,7 +38,7 @@ function savegexf(io::IO, g::LightGraphs.AbstractGraph, gname::String)
 
     xedges = addelement!(xg, "edges")
     m = 0
-    for e in LightGraphs.edges(g)
+    for e in Graphs.edges(g)
         xe = addelement!(xedges, "edge")
         xe["id"] = "$m"
         xe["source"] = "$(src(e)-1)"

src/GML/Gml.jl

@@ -1,10 +1,10 @@
 module GML
 
 using GraphIO.ParserCombinator.Parsers
-using LightGraphs
-using LightGraphs: AbstractGraphFormat
+using Graphs
+using Graphs: AbstractGraphFormat
 
-import LightGraphs: loadgraph, loadgraphs, savegraph
+import Graphs: loadgraph, loadgraphs, savegraph
 
 export GMLFormat
 
@@ -14,9 +14,9 @@ struct GMLFormat <: AbstractGraphFormat end
 function _gml_read_one_graph(gs, dir)
     nodes = [x[:id] for x in gs[:node]]
     if dir
-        g = LightGraphs.DiGraph(length(nodes))
+        g = Graphs.DiGraph(length(nodes))
     else
-        g = LightGraphs.Graph(length(nodes))
+        g = Graphs.Graph(length(nodes))
     end
     mapping = Dict{Int,Int}()
     for (i, n) in enumerate(nodes)
@@ -42,7 +42,7 @@ end
 
 function loadgml_mult(io::IO)
     p = Parsers.GML.parse_dict(read(io, String))
-    graphs = Dict{String,LightGraphs.AbstractGraph}()
+    graphs = Dict{String,Graphs.AbstractGraph}()
     for gs in p[:graph]
         dir = Bool(get(gs, :directed, 0))
         graphname = get(gs, :label, dir ? "digraph" : "graph")
@@ -57,7 +57,7 @@ end
 Write a graph `g` with name `gname` to an IO stream `io` in the
 [GML](https://en.wikipedia.org/wiki/Graph_Modelling_Language) format. Return 1.
 """
-function savegml(io::IO, g::LightGraphs.AbstractGraph, gname::String = "")
+function savegml(io::IO, g::Graphs.AbstractGraph, gname::String = "")
     println(io, "graph")
     println(io, "[")
     length(gname) > 0 && println(io, "label \"$gname\"")
@@ -68,7 +68,7 @@ function savegml(io::IO, g::LightGraphs.AbstractGraph, gname::String = "")
         println(io, "\t\tid $i")
         println(io, "\t]")
     end
-    for e in LightGraphs.edges(g)
+    for e in Graphs.edges(g)
         s, t = Tuple(e)
         println(io, "\tedge")
         println(io, "\t[")