Merge pull request #16 from simonschoelly/v1.0_fixes

Working version for Julia v1.0

Author: sbromberger

.travis.yml

@@ -5,7 +5,8 @@ os:
 #  - osx
 
 julia:
- - 0.6
+ - 0.7
+ - 1.0
  - nightly
 
 matrix:
@@ -18,10 +19,9 @@ notifications:
 # uncomment the following lines to override the default test script
 script:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-  - julia -e 'Pkg.add("LightGraphs")'
-  - julia -e 'Pkg.clone(pwd()); Pkg.build("GraphIO"); Pkg.test("GraphIO"; coverage=true)'
+  - julia -e 'using Pkg, InteractiveUtils; versioninfo(); Pkg.clone(pwd()); Pkg.build("GraphIO"); Pkg.test("GraphIO"; coverage=true)'
 
 after_success:
-    - julia -e 'cd(Pkg.dir("GraphIO")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
-    - julia -e 'Pkg.add("Documenter")'
-    - julia -e 'cd(Pkg.dir("GraphIO")); include(joinpath("docs", "make.jl"))'
+    - julia -e 'using Pkg; cd(Pkg.dir("GraphIO")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
+    - julia -e 'using Pkg; Pkg.add("Documenter")'
+    - julia -e 'using Pkg; cd(Pkg.dir("GraphIO")); include(joinpath("docs", "make.jl"))'

README.md

@@ -17,6 +17,8 @@ Note that support for the jld format was removed from this branch.
 
 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.
+
 Currently, the following functionality is provided:
 
 Format        | Read | Write | Multiple Graphs| Format Name  |

REQUIRE

@@ -1,6 +1,6 @@
-julia 0.6
+julia 0.7
 LightGraphs 0.9.5
-EzXML 0.5
-ParserCombinator
-JLD
+EzXML 0.9.0
+ParserCombinator 2.0.0
+#JLD
 SimpleTraits

src/GraphIO.jl

@@ -1,18 +1,18 @@
-__precompile__(true)
 module GraphIO
 
 using LightGraphs
 using SimpleTraits
 
 import LightGraphs: loadgraph, loadgraphs, savegraph, AbstractGraphFormat
 using EzXML
-using ParserCombinator: Parsers.DOT, Parsers.GML
+using ParserCombinator.Parsers.DOT
+using ParserCombinator.Parsers.GML
 
 export DOTFormat, GEXFFormat, GMLFormat, Graph6Format,
 GraphMLFormat, NETFormat, EdgeListFormat, CDFFormat
 # package code goes here
 
-include("jld.jl")
+#include("jld.jl")
 include("dot.jl")
 include("gexf.jl")
 include("gml.jl")

src/cdf.jl

@@ -13,19 +13,19 @@ function _loadcdf(io::IO)
     while !eof(io)
         line = strip(chomp(readline(io)))
         if inbusdata
-            if contains(line, "-999")
+            if occursin("-999", line)
                 inbusdata = false
             else
                 v = parse(Int, split(line)[1])
                 push!(vertices, v)
             end
         elseif inbranchdata
-            if contains(line, "-999")
+            if occursin("-999", line)
                 inbranchdata = false
             else
                 (src_s, dst_s) = split(line)[1:2]
-                src = findfirst(vertices, parse(Int, src_s))
-                dst = findfirst(vertices, parse(Int, dst_s))
+                src = something(findfirst(isequal(parse(Int, src_s)), vertices), 0)
+                dst = something(findfirst(isequal(parse(Int, dst_s)), vertices), 0)
                 push!(srcs, src)
                 push!(dsts, dst)
             end

src/dot.jl

@@ -20,7 +20,7 @@ function _dot_read_one_graph(pg::DOT.Graph)
 end
 
 function loaddot(io::IO, gname::String)
-    p = DOT.parse_dot(readstring(io))
+    p = DOT.parse_dot(read(io, String))
     for pg in p
         isdir = pg.directed
         possname = isdir ? DOT.StringID("digraph") : DOT.StringID("graph")
@@ -31,7 +31,7 @@ function loaddot(io::IO, gname::String)
 end
 
 function loaddot_mult(io::IO)
-    p = DOT.parse_dot(readstring(io))
+    p = DOT.parse_dot(read(io, String))
 
     graphs = Dict{String,LightGraphs.AbstractGraph}()
 

src/edgelist.jl

@@ -2,6 +2,8 @@
 # by commas or whitespace. Will only read the first two elements on
 # each line. Will return a directed graph.
 
+using DelimitedFiles: writedlm
+
 struct EdgeListFormat <: AbstractGraphFormat end
 
 function loadedgelist(io::IO, gname::String)
@@ -33,7 +35,7 @@ function loadedgelist(io::IO, gname::String)
 end
 
 function saveedgelist(io::IO, g::LightGraphs.AbstractGraph, gname::String)
-    writecsv(io, [src(e), dst(e)] for e in collect(LightGraphs.edges(g)))
+    writedlm(io, ([src(e), dst(e)] for e in LightGraphs.edges(g)), ',')
     return 1
 end
 

src/gml.jl

@@ -17,8 +17,9 @@ function _gml_read_one_graph(gs, dir)
     end
     return g
 end
+
 function loadgml(io::IO, gname::String)
-    p = GML.parse_dict(readstring(io))
+    p = GML.parse_dict(read(io, String))
     for gs in p[:graph]
         dir = Bool(get(gs, :directed, 0))
         graphname = get(gs, :label, dir ? "digraph" : "graph")
@@ -29,7 +30,7 @@ function loadgml(io::IO, gname::String)
 end
 
 function loadgml_mult(io::IO)
-    p = GML.parse_dict(readstring(io))
+    p = GML.parse_dict(read(io, String))
     graphs = Dict{String,LightGraphs.AbstractGraph}()
     for gs in p[:graph]
         dir = Bool(get(gs, :directed, 0))

src/graph6.jl

@@ -1,7 +1,7 @@
 struct Graph6Format <: AbstractGraphFormat end
 
 function _bv2int(x::BitVector)
-  assert(length(x) <= 8 * sizeof(Int))
+  @assert(length(x) <= 8 * sizeof(Int))
   acc = 0
   for i = 1:length(x)
     acc = acc << 1 + x[i]
@@ -10,7 +10,7 @@ function _bv2int(x::BitVector)
 end
 
 function _int2bv(n::Int, k::Int)
-  bitstr = lstrip(bits(n), '0')
+  bitstr = lstrip(bitstring(n), '0')
   l = length(bitstr)
   padding = k - l
   bv = falses(k)
@@ -25,7 +25,7 @@ function _g6_R(_x::BitVector)::Vector{UInt8}
   padding = cld(k, 6) * 6 - k
   x = vcat(_x, falses(padding))
   nbytes = div(length(x), 6)
-  bytevec = Vector{UInt8}(nbytes)   # uninitialized data!
+  bytevec = Vector{UInt8}(undef, nbytes)   # uninitialized data!
   for i = 1:nbytes
     xslice  = x[((i - 1) * 6 + 1):(i * 6)]
 
@@ -71,15 +71,15 @@ end
 
 
 """
-    \_graphToG6String(g)
+    _graphToG6String(g)
 
 Given a graph `g`, create the corresponding Graph6 string.
 """
 function _graphToG6String(g::LightGraphs.Graph)
   A = adjacency_matrix(g, Bool)
   n = nv(g)
   nbits = div(n * (n - 1), 2)
-  x  = BitVector(nbits)
+  x  = BitVector(undef, nbits)
 
   ind = 0
   for col = 2:n, row = 1:(col - 1)

src/graphml.jl

@@ -17,7 +17,7 @@ function _graphml_read_one_graph(reader::EzXML.StreamReader, isdirected::Bool)
                 tar = reader["target"]
                 push!(xedges, LightGraphs.Edge(nodes[src], nodes[tar]))
             else
-                warn("Skipping unknown node '$(elname)' - further warnings will be suppressed", once=true, key="unknode")
+                @warn "Skipping unknown node '$(elname)' - further warnings will be suppressed" maxlog=1 _id=:unknode
             end
         end
     end
@@ -51,7 +51,7 @@ function loadgraphml(io::IO, gname::String)
             elseif elname == "node" || elname == "edge"
                 # ok
             else
-                warn("Skipping unknown XML element '$(elname)' - further warnings will be suppressed", once=true, key="unkel")
+                @warn "Skipping unknown XML element '$(elname)' - further warnings will be suppressed" maxlog=1 _id=:unkel
             end
         end
     end
@@ -78,7 +78,7 @@ function loadgraphml_mult(io::IO)
                 end
                 graphs[graphname] = _graphml_read_one_graph(reader, directed)
             else
-                warn("Skipping unknown XML element '$(elname)' - further warnings will be suppressed", once=true, key="unkelmult")
+                @warn "Skipping unknown XML element '$(elname)' - further warnings will be suppressed" maxlog=1 _id=:unkelmult
             end
         end
     end

src/net.jl

@@ -32,30 +32,30 @@ function loadnet(io::IO, gname::String = "graph")
     while startswith(line, "%")
         line = readline(io)
     end
-    n = parse(Int, matchall(r"\d+", line)[1])
+    n = parse(Int, match(r"\d+", line).match)
     for ioline in eachline(io)
         line = ioline
-        (ismatch(r"^\*Arcs", line) || ismatch(r"^\*Edges", line)) && break
+        (occursin(r"^\*Arcs", line) || occursin(r"^\*Edges", line)) && break
     end
-    if ismatch(r"^\*Arcs", line)
+    if occursin(r"^\*Arcs", line)
         g = LightGraphs.DiGraph(n)
     else
         g = LightGraphs.Graph(n)
     end
-    while ismatch(r"^\*Arcs", line)
+    while occursin(r"^\*Arcs", line)
         for ioline in eachline(io)
             line = ioline
-            m = matchall(r"\d+", line)
-            length(m) < 2 && break
-            add_edge!(g, parse(Int, m[1]), parse(Int, m[2]))
+            ms = collect(m.match for m in eachmatch(r"\d+", line, overlap=false))
+            length(ms) < 2 && break
+            add_edge!(g, parse(Int, ms[1]), parse(Int, ms[2]))
         end
     end
-    while ismatch(r"^\*Edges", line) # add edges in both directions
+    while occursin(r"^\*Edges", line) # add edges in both directions
         for ioline in eachline(io)
             line = ioline
-            m = matchall(r"\d+", line)
-            length(m) < 2 && break
-            i1, i2 = parse(Int, m[1]), parse(Int, m[2])
+            ms = collect(m.match for m in eachmatch(r"\d+", line, overlap=false))
+            length(ms) < 2 && break
+            i1, i2 = parse(Int, ms[1]), parse(Int, ms[2])
             add_edge!(g, i1, i2)
             add_edge!(g, i2, i1)
         end

test/graphio.jl

@@ -82,8 +82,8 @@ end
     end
     fname = joinpath(testdir, "testdata", "warngraph.graphml")
 
-    @test_warn "Skipping unknown node 'warnnode' - further warnings will be suppressed" loadgraphs(fname, GraphMLFormat())
-    @test_warn "Skipping unknown XML element 'warnelement' - further warnings will be suppressed" loadgraph(fname, "graph", GraphMLFormat())
+    @test_logs (:warn, "Skipping unknown node 'warnnode' - further warnings will be suppressed") match_mode=:any loadgraphs(fname, GraphMLFormat())
+    @test_logs (:warn, "Skipping unknown XML element 'warnelement' - further warnings will be suppressed") match_mode=:any loadgraph(fname, "graph", GraphMLFormat())
     d = loadgraphs(fname, GraphMLFormat())
     write_test(GraphMLFormat(), d)
 end
@@ -145,6 +145,7 @@ end
     @test length(loadgraphs(fname, NETFormat())) == 1
 end
 
+#=
 @testset "JLD" begin
     using JLD
 
@@ -182,6 +183,7 @@ end
         rm(path)
     end
 end
+=#
 
 @testset "CDF" begin
 #test CDFFormat()

test/runtests.jl

@@ -1,6 +1,6 @@
 using GraphIO
 using LightGraphs
-using Base.Test
+using Test
 
 testdir = dirname(@__FILE__)