Fix circular dependencies (#65)

* Fix circular dependencies

* Remove old extension files

---------

Co-authored-by: Guillaume Dalle <22795598+gdalle@users.noreply.github.com>

Project.toml

@@ -13,10 +13,8 @@ EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 ParserCombinator = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
 
 [extensions]
-GraphIODOTExt = "ParserCombinator"
-GraphIOGEXFExt = "EzXML"
-GraphIOGMLExt = "ParserCombinator"
-GraphIOGraphMLExt = "EzXML"
+GraphIOParserCombinator = "ParserCombinator"
+GraphIOXML = "EzXML"
 GraphIOLGCompressedExt = "CodecZlib"
 
 [compat]

ext/GraphIOLGCompressedExt.jl

@@ -3,15 +3,9 @@ module GraphIOLGCompressedExt
 using Graphs
 import Graphs: loadgraph, loadgraphs, savegraph, LGFormat
 
-@static if isdefined(Base, :get_extension)
-    using GraphIO
-    using CodecZlib
-    import GraphIO.LGCompressed.LGCompressedFormat
-else # not required for julia >= v1.9
-    using ..GraphIO
-    using ..CodecZlib
-    import ..GraphIO.LGCompressed.LGCompressedFormat
-end
+using GraphIO
+using CodecZlib
+import GraphIO.LGCompressed.LGCompressedFormat
 
 function savegraph(
     fn::AbstractString, g::AbstractGraph, gname::AbstractString, format::LGCompressedFormat

ext/GraphIOGMLExt.jl → ext/GraphIOParserCombinator.jl

@@ -1,18 +1,92 @@
-module GraphIOGMLExt
+module GraphIOParserCombinator
 
 using Graphs
 import Graphs: loadgraph, loadgraphs, savegraph
 
-@static if isdefined(Base, :get_extension)
-    using GraphIO
-    using ParserCombinator
-    import GraphIO.GML.GMLFormat
-else # not required for julia >= v1.9
-    using ..GraphIO
-    using ..ParserCombinator
-    import ..GraphIO.GML.GMLFormat
+using GraphIO
+using ParserCombinator
+import GraphIO.DOT.DOTFormat
+import GraphIO.GML.GMLFormat
+
+function savedot(io::IO, g::AbstractGraph, gname::String="")
+    isdir = is_directed(g)
+    println(io, (isdir ? "digraph " : "graph ") * gname * " {")
+    for i in vertices(g)
+        println(io, "\t" * string(i))
+    end
+    if isdir
+        for u in vertices(g)
+            out_nbrs = outneighbors(g, u)
+            length(out_nbrs) == 0 && continue
+            println(io, "\t" * string(u) * " -> {" * join(out_nbrs, ',') * "}")
+        end
+    else
+        for e in edges(g)
+            source = string(src(e))
+            dest = string(dst(e))
+            println(io, "\t" * source * " -- " * dest)
+        end
+    end
+    println(io, "}")
+    return 1
+end
+
+function savedot_mult(io::IO, graphs::Dict)
+    ng = 0
+    for (gname, g) in graphs
+        ng += savedot(io, g, gname)
+    end
+    return ng
+end
+
+function _dot_read_one_graph(pg::Parsers.DOT.Graph)
+    isdir = pg.directed
+    nvg = length(Parsers.DOT.nodes(pg))
+    nodedict = Dict(zip(collect(Parsers.DOT.nodes(pg)), 1:nvg))
+    if isdir
+        g = DiGraph(nvg)
+    else
+        g = Graph(nvg)
+    end
+    for es in Parsers.DOT.edges(pg)
+        s = nodedict[es[1]]
+        d = nodedict[es[2]]
+        add_edge!(g, s, d)
+    end
+    return g
+end
+
+function _name(pg::Parsers.DOT.Graph)
+    return if pg.id !== nothing
+        pg.id.id
+    else
+        Parsers.DOT.StringID(pg.directed ? "digraph" : "graph")
+    end
+end
+
+function loaddot(io::IO, gname::String)
+    p = Parsers.DOT.parse_dot(read(io, String))
+    for pg in p
+        _name(pg) == gname && return _dot_read_one_graph(pg)
+    end
+    return 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
+        graphs[_name(pg)] = _dot_read_one_graph(pg)
+    end
+    return graphs
 end
 
+loadgraph(io::IO, gname::String, ::DOTFormat) = loaddot(io, gname)
+loadgraphs(io::IO, ::DOTFormat) = loaddot_mult(io)
+savegraph(io::IO, g::AbstractGraph, gname::String, ::DOTFormat) = savedot(io, g, gname)
+savegraph(io::IO, d::Dict, ::DOTFormat) = savedot_mult(io, d)
+
 function _gml_read_one_graph(gs, dir)
     nodes = [x[:id] for x in gs[:node]]
     if dir
@@ -54,7 +128,7 @@ function loadgml_mult(io::IO)
 end
 
 """
-    savegml(f, g, gname="graph")
+  savegml(f, g, gname="graph")
 
 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.
@@ -83,7 +157,7 @@ function savegml(io::IO, g::AbstractGraph, gname::String="")
 end
 
 """
-    savegml_mult(io, graphs)
+  savegml_mult(io, graphs)
 Write a dictionary of (name=>graph) to an IO stream `io` Return number of graphs written.
 """
 function savegml_mult(io::IO, graphs::Dict)

ext/GraphIOGraphMLExt.jl → ext/GraphIOXML.jl

@@ -1,18 +1,55 @@
-module GraphIOGraphMLExt
+module GraphIOXML
 
 using Graphs
-import Graphs: loadgraph, loadgraphs, savegraph
-
-@static if isdefined(Base, :get_extension)
-    using GraphIO
-    using EzXML
-    import GraphIO.GraphML.GraphMLFormat
-else # not required for julia >= v1.9
-    using ..GraphIO
-    using ..EzXML
-    import ..GraphIO.GraphML.GraphMLFormat
+import Graphs: loadgraph, loadgraphs, savegraph, AbstractGraph
+
+using GraphIO
+using EzXML
+import GraphIO.GEXF.GEXFFormat
+import GraphIO.GraphML.GraphMLFormat
+
+"""
+    savegexf(f, g, gname)
+
+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::AbstractGraph, gname::String)
+    xdoc = XMLDocument()
+    xroot = setroot!(xdoc, ElementNode("gexf"))
+    xroot["xmlns"] = "http://www.gexf.net/1.2draft"
+    xroot["version"] = "1.2"
+    xroot["xmlns:xsi"] = "http://www.w3.org/2001/XMLSchema-instance"
+    xroot["xsi:schemaLocation"] = "http://www.gexf.net/1.2draft/gexf.xsd"
+
+    xmeta = addelement!(xroot, "meta")
+    addelement!(xmeta, "description", gname)
+    xg = addelement!(xroot, "graph")
+    strdir = is_directed(g) ? "directed" : "undirected"
+    xg["defaultedgetype"] = strdir
+
+    xnodes = addelement!(xg, "nodes")
+    for i in 1:nv(g)
+        xv = addelement!(xnodes, "node")
+        xv["id"] = "$(i-1)"
+    end
+
+    xedges = addelement!(xg, "edges")
+    m = 0
+    for e in edges(g)
+        xe = addelement!(xedges, "edge")
+        xe["id"] = "$m"
+        xe["source"] = "$(src(e)-1)"
+        xe["target"] = "$(dst(e)-1)"
+        m += 1
+    end
+
+    prettyprint(io, xdoc)
+    return 1
 end
 
+savegraph(io::IO, g::AbstractGraph, gname::String, ::GEXFFormat) = savegexf(io, g, gname)
+
 function _graphml_read_one_graph(reader::EzXML.StreamReader, isdirected::Bool)
     nodes = Dict{String,Int}()
     xedges = Vector{Edge}()

test/runtests.jl

@@ -18,7 +18,7 @@ include("graphio.jl")
         Aqua.test_all(GraphIO)
     end
     @testset "Code formatting" begin
-        @test JuliaFormatter.format(GraphIO; verbose=false, overwrite=false)
+        @test JuliaFormatter.format(GraphIO; verbose=true, overwrite=false)
     end
     for name in modules
         path = joinpath(testdir, name, "runtests.jl")