first cut at 0.7 compatibility (#848)

* using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test * first cut * Use mauro/SimpleTraits.jl/m3/where-fns in tests * Fix SimpleTraits checkout (#851) * Move up SimpleTraits checkout (#852) * Update runtests.jl * Update REQUIRE * Update REQUIRE
sbromberger · Jun 5, 2018 · 18d32d2 · 18d32d2
1 parent f8e0d46
commit 18d32d2
Show file tree

Hide file tree

Showing 28 changed files with 79 additions and 60 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -5,13 +5,9 @@ os:
 #  - osx
 
 julia:
- - 0.6
+#  - 0.6
  - nightly
 
-matrix:
-  allow_failures:
-    - julia: nightly
-
 notifications:
   email: false
 

diff --git a/REQUIRE b/REQUIRE
@@ -1,4 +1,4 @@
-julia 0.6
+julia 0.7-
 CodecZlib 0.4
 DataStructures 0.7
-SimpleTraits 0.4.0
+SimpleTraits 0.7.1
diff --git a/src/LightGraphs.jl b/src/LightGraphs.jl
@@ -1,15 +1,28 @@
 __precompile__(true)
 module LightGraphs
 
+using SharedArrays
+using Random
 import CodecZlib
 using DataStructures
 using SimpleTraits
 
+using SparseArrays
+using LinearAlgebra
+using IterativeEigensolvers
+using SharedArrays
+using Random
+using Markdown
+using DelimitedFiles
 import Base: write, ==, <, *, ≈, convert, isless, issubset, union, intersect,
-            reverse, reverse!, blkdiag, isassigned, getindex, setindex!, show,
-            print, copy, in, sum, size, sparse, eltype, length, ndims, transpose,
-            ctranspose, join, start, next, done, eltype, get, issymmetric, A_mul_B!,
-            Pair, Tuple, zero
+            reverse, reverse!, isassigned, getindex, setindex!, show,
+            print, copy, in, sum, size, eltype, length, ndims, transpose,
+            ctranspose, join, start, next, done, eltype, get, Pair, Tuple, zero
+import Random: GLOBAL_RNG
+import Distributed: @parallel, @sync
+import SparseArrays: sparse, blkdiag
+import LinearAlgebra: issymmetric, mul!
+
 export
 # Interface
 AbstractGraph, AbstractEdge, AbstractEdgeIter,

diff --git a/src/SimpleGraphs/SimpleGraphs.jl b/src/SimpleGraphs/SimpleGraphs.jl
@@ -1,5 +1,8 @@
 module SimpleGraphs
 
+using SparseArrays
+using LinearAlgebra
+
 import Base:
     eltype, show, ==, Pair, Tuple, copy, length, start, next, done, issubset, zero, in
 

diff --git a/src/community/clique_percolation.jl b/src/community/clique_percolation.jl
@@ -26,7 +26,7 @@ function clique_percolation end
     x[kcliques[i]] = false
   end
   components = connected_components(h)
-  communities = [IntSet() for i=1:length(components)]
+  communities = [BitSet() for i=1:length(components)]
   for (i,component) in enumerate(components)
     push!(communities[i], vcat(kcliques[component]...)...)
   end

diff --git a/src/community/cliques.jl b/src/community/cliques.jl
@@ -24,7 +24,7 @@ julia> maximal_cliques(g)
 """
 function maximal_cliques end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function maximal_cliques{T, AG<:AbstractGraph{T}}(g::AG::(!IsDirected))
+@traitfn function maximal_cliques(g::AG::(!IsDirected)) where {T, AG<:AbstractGraph{T}}
     # Cache nbrs and find first pivot (highest degree)
     maxconn = -1
     # uncomment this when https://github.com/JuliaLang/julia/issues/23618 is fixed

diff --git a/src/community/label_propagation.jl b/src/community/label_propagation.jl
@@ -12,7 +12,7 @@ the second is the convergence history for each node. Will return after
 function label_propagation(g::AbstractGraph{T}, maxiter=1000) where T
     n = nv(g)
     label = collect(one(T):n)
-    active_vs = IntSet(vertices(g))
+    active_vs = BitSet(vertices(g))
     c = NeighComm(collect(one(T):n), fill(-1, n), one(T))
     convergence_hist = Vector{Int}()
     random_order = Vector{T}(n)

diff --git a/src/digraph/cycles/hadwick-james.jl b/src/digraph/cycles/hadwick-james.jl
@@ -9,7 +9,7 @@ of Hadwick & James.
 """
 function simplecycles_hadwick_james end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function simplecycles_hadwick_james{T, AG<:AbstractGraph{T}}(g::AG::IsDirected)
+@traitfn function simplecycles_hadwick_james(g::AG::IsDirected) where {T, AG<:AbstractGraph{T}}
     nvg = nv(g)
     B = Vector{T}[Vector{T}() for i in vertices(g)]
     blocked = zeros(Bool, nvg)
@@ -43,7 +43,7 @@ resetblocked!(blocked) = fill!(blocked, false)
 Find circuits in `g` recursively starting from v1.
 """
 function circuit_recursive! end
-@traitfn function circuit_recursive!{T<:Integer}(g::::IsDirected, v1::T, v2::T, blocked::AbstractVector, B::Vector{Vector{T}}, stack::Vector{T}, cycles::Vector{Vector{T}})
+@traitfn function circuit_recursive!(g::::IsDirected, v1::T, v2::T, blocked::AbstractVector, B::Vector{Vector{T}}, stack::Vector{T}, cycles::Vector{Vector{T}}) where T<:Integer
     f = false
     push!(stack, v2)
     blocked[v2] = true

diff --git a/src/digraph/cycles/johnson.jl b/src/digraph/cycles/johnson.jl
@@ -127,8 +127,8 @@ recursive version. Modify the vector of cycles, when needed.
 - [Johnson](http://epubs.siam.org/doi/abs/10.1137/0204007)
 """
 function circuit end
-@traitfn function circuit{T<:Integer}(v::T, dg::::IsDirected, vis::JohnsonVisitor{T}, 
-allcycles::Vector{Vector{T}}, vmap::Vector{T}, startnode::T = v)
+@traitfn function circuit(v::T, dg::::IsDirected, vis::JohnsonVisitor{T}, 
+allcycles::Vector{Vector{T}}, vmap::Vector{T}, startnode::T = v) where T<:Integer
     done = false
     push!(vis.stack, v)
     vis.blocked[v] = true
@@ -215,8 +215,8 @@ the same as v, otherwise it should be passed.
 - [Johnson](http://epubs.siam.org/doi/abs/10.1137/0204007)
 """
 function circuit_iter end
-@traitfn function circuit_iter{T<:Integer}(v::T, dg::::IsDirected, vis::JohnsonVisitor{T}, 
-vmap::Vector{T}, cycle::Channel, startnode::T = v)
+@traitfn function circuit_iter(v::T, dg::::IsDirected, vis::JohnsonVisitor{T}, 
+vmap::Vector{T}, cycle::Channel, startnode::T = v) where T<:Integer
     done = false
     push!(vis.stack, v)
     vis.blocked[v] = true

diff --git a/src/linalg/LinAlg.jl b/src/linalg/LinAlg.jl
@@ -1,13 +1,17 @@
 module LinAlg
 
 using SimpleTraits
+using SparseArrays
+using LinearAlgebra
+using IterativeEigensolvers
 using ..LightGraphs
 
 import LightGraphs: IsDirected, adjacency_matrix, laplacian_matrix, laplacian_spectrum, AbstractGraph, inneighbors,
 outneighbors, all_neighbors, is_directed, nv, ne, has_edge, vertices
 
-import Base: convert, sparse, size, diag, eltype, ndims, ==, *, .*, issymmetric, A_mul_B!, length, Diagonal
-
+import Base: convert, size, eltype, ndims, ==, *, .*, length
+import SparseArrays: sparse, diag
+import LinearAlgebra: issymmetric, mul!, Diagonal
 
 export convert,
     SparseMatrix,

diff --git a/src/linalg/graphmatrices.jl b/src/linalg/graphmatrices.jl
@@ -239,37 +239,37 @@ function *(adjmat::PunchedAdjacency{T}, x::AbstractVector{T}) where T<:Number
     return y - dot(adjmat.perron, y) * adjmat.perron
 end
 
-function A_mul_B!(Y, A::Adjacency, B)
+function mul!(Y, A::Adjacency, B)
     # we need to do 3 matrix products
-    # Y and B can't overlap in any one call to A_mul_B!
-    # The last call to A_mul_B! must be (Y, postscalefactor, tmp)
+    # Y and B can't overlap in any one call to mul!
+    # The last call to mul! must be (Y, postscalefactor, tmp)
     # so we need to write to tmp in the second step  must be (tmp, A.A, Y)
     # and the first step (Y, prescalefactor, B)
     tmp1 = Diagonal(prescalefactor(A)) * B
     tmp = similar(Y)
-    A_mul_B!(tmp, A.A, tmp1)
-    return A_mul_B!(Y, Diagonal(postscalefactor(A)), tmp)
+    mul!(tmp, A.A, tmp1)
+    return mul!(Y, Diagonal(postscalefactor(A)), tmp)
 end
 
-A_mul_B!(Y, A::CombinatorialAdjacency, B) = A_mul_B!(Y, A.A, B)
+mul!(Y, A::CombinatorialAdjacency, B) = mul!(Y, A.A, B)
 
 # You can compute the StochasticAdjacency product without allocating a similar of Y.
 # This is true for all Adjacency where the postscalefactor is a Noop
 # at time of writing this is just StochasticAdjacency and CombinatorialAdjacency
-function A_mul_B!(Y, A::StochasticAdjacency, B)
+function mul!(Y, A::StochasticAdjacency, B)
     tmp = Diagonal(prescalefactor(A)) * B
-    A_mul_B!(Y, A.A, tmp)
+    mul!(Y, A.A, tmp)
     return Y
 end
 
-function A_mul_B!(Y, adjmat::PunchedAdjacency, x)
+function mul!(Y, adjmat::PunchedAdjacency, x)
     y = adjmat.A * x
     Y[:] = y - dot(adjmat.perron, y) * adjmat.perron
     return Y
 end
 
-function A_mul_B!(Y, lapl::Laplacian, B)
-	A_mul_B!(Y, lapl.A, B)
+function mul!(Y, lapl::Laplacian, B)
+	mul!(Y, lapl.A, B)
 	z = diag(lapl) .* B
 	Y[:] = z - Y[:]
 	return Y
@@ -284,7 +284,7 @@ Return a symmetric version of graph (represented by sparse matrix `A`) as a spar
 """
 function symmetrize(A::SparseMatrix, which=:or)
 	if which == :or
-		M = A + A'
+		M = A + sparse(A')
 		M.nzval[M.nzval .== 2] = 1
 		return M
     end
@@ -298,7 +298,7 @@ function symmetrize(A::SparseMatrix, which=:or)
     else
         throw(ArgumentError("$which is not a supported method of symmetrizing a matrix"))
     end
-	M = T + T'
+	M = T + sparse(T')
 	return M
 end
 
@@ -317,7 +317,7 @@ symmetrize(adjmat::CombinatorialAdjacency, which=:or) =
 
 
 # per #564
-@deprecate A_mul_B!(Y, A::Noop, B) None
+@deprecate mul!(Y, A::Noop, B) None
 @deprecate convert(::Type{Adjacency}, lapl::Laplacian) None
 @deprecate convert(::Type{SparseMatrix}, adjmat::CombinatorialAdjacency) sparse(adjmat)
 

diff --git a/src/linalg/nonbacktracking.jl b/src/linalg/nonbacktracking.jl
@@ -100,7 +100,7 @@ function *(nbt::Nonbacktracking, x::Vector{T}) where T<:Number
     end
     return y
 end
-function A_mul_B!(C, nbt::Nonbacktracking, B)
+function mul!(C, nbt::Nonbacktracking, B)
     # computs C = A * B
     for i in 1:size(B, 2)
         C[:, i] = nbt * B[:, i]

diff --git a/src/linalg/spectral.jl b/src/linalg/spectral.jl
@@ -73,14 +73,14 @@ for a graph `g`, indexed by `[u, v]` vertices. `T` defaults to `Int` for both gr
 ### Optional Arguments
 `dir=:unspec`: `:unspec`, `:both`, :in`, and `:out` are currently supported.
 For undirected graphs, `dir` defaults to `:out`; for directed graphs,
-`dir` defaults to `:both`. 
+`dir` defaults to `:both`.
 """
 function laplacian_matrix(g::AbstractGraph{U}, T::DataType=Int; dir::Symbol=:unspec) where U
     if dir == :unspec
         dir = is_directed(g) ? :both : :out
     end
     A = adjacency_matrix(g, T; dir=dir)
-    D = convert(SparseMatrixCSC{T, U}, spdiagm(sum(A, 2)[:]))
+    D = convert(SparseMatrixCSC{T, U}, Diagonal(sparse(sum(A, 2)[:])))
     return D - A
 end
 
@@ -179,7 +179,7 @@ If `k` is ommitted, uses full spectrum.
 function spectral_distance end
 
 # can't use Traitor syntax here (https://github.com/mauro3/SimpleTraits.jl/issues/36)
-@traitfn function spectral_distance{G<:AbstractGraph; !IsDirected{G}}(G₁::G, G₂::G, k::Integer)
+@traitfn function spectral_distance(G₁::G, G₂::G, k::Integer) where {G<:AbstractGraph; !IsDirected{G}}
     A₁ = adjacency_matrix(G₁)
     A₂ = adjacency_matrix(G₂)
 
@@ -190,7 +190,7 @@ function spectral_distance end
 end
 
 # can't use Traitor syntax here (https://github.com/mauro3/SimpleTraits.jl/issues/36)
-@traitfn function spectral_distance{G<:AbstractGraph; !IsDirected{G}}(G₁::G, G₂::G)
+@traitfn function spectral_distance(G₁::G, G₂::G) where {G<:AbstractGraph; !IsDirected{G}}
     nv(G₁) == nv(G₂) || throw(ArgumentError("Spectral distance not defined for |G₁| != |G₂|"))
     return spectral_distance(G₁, G₂, nv(G₁))
 end
diff --git a/src/operators.jl b/src/operators.jl
@@ -211,7 +211,7 @@ in the generated graph exceeds the eltype.
 """
 function crosspath end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function crosspath{T, AG<:AbstractGraph{T}}(len::Integer, g::AG::(!IsDirected))
+@traitfn function crosspath(len::Integer, g::AG::(!IsDirected)) where {T, AG<:AbstractGraph{T}}
     p = PathGraph(len)
     h = Graph{T}(p)
     return cartesian_product(h, g)

diff --git a/src/spanningtrees/kruskal.jl b/src/spanningtrees/kruskal.jl
@@ -40,10 +40,10 @@ distance matrix `distmx` using [Kruskal's algorithm](https://en.wikipedia.org/wi
 """
 function kruskal_mst end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function kruskal_mst{T<:Real, U, AG<:AbstractGraph{U}}(
+@traitfn function kruskal_mst(
     g::AG::(!IsDirected),
     distmx::AbstractMatrix{T} = weights(g)
-)
+) where {T<:Real, U, AG<:AbstractGraph{U}}
 
     edge_list = Vector{KruskalHeapEntry{T}}()
     mst = Vector{Edge}()

diff --git a/src/spanningtrees/prim.jl b/src/spanningtrees/prim.jl
@@ -13,10 +13,10 @@ distance matrix `distmx` using [Prim's algorithm](https://en.wikipedia.org/wiki/
 Return a vector of edges.
 """
 function prim_mst end
-@traitfn function prim_mst{T<:Real, U, AG<:AbstractGraph{U}}(
+@traitfn function prim_mst(
     g::AG::(!IsDirected),
     distmx::AbstractMatrix{T} = weights(g)
-    )
+    ) where {T<:Real, U, AG<:AbstractGraph{U}}
     pq = Vector{PrimHeapEntry{T}}()
     mst = Vector{Edge}()
     marked = zeros(Bool, nv(g))

diff --git a/src/traversals/dfs.jl b/src/traversals/dfs.jl
@@ -12,7 +12,7 @@ Uses DFS.
 function is_cyclic end
 @traitfn is_cyclic(g::::(!IsDirected)) = ne(g) > 0
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function is_cyclic{T,AG<:AbstractGraph{T}}(g::AG::IsDirected)
+@traitfn function is_cyclic(g::AG::IsDirected) where {T, AG<:AbstractGraph{T}}
     vcolor = zeros(UInt8, nv(g))
     for v in vertices(g)
         vcolor[v] != 0 && continue
@@ -50,7 +50,7 @@ graph `g` as a vector of vertices in topological order.
 """
 function toplogical_sort_by_dfs end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function topological_sort_by_dfs{T, AG<:AbstractGraph{T}}(g::AG::IsDirected)
+@traitfn function topological_sort_by_dfs(g::AG::IsDirected) where {T, AG<:AbstractGraph{T}}
     vcolor = zeros(UInt8, nv(g))
     verts = Vector{T}()
     for v in vertices(g)

diff --git a/src/traversals/diffusion.jl b/src/traversals/diffusion.jl
@@ -27,7 +27,7 @@ function diffusion(g::AbstractGraph{T},
 
     # Initialize
     watch_set = Set{T}(watch)
-    infected_vertices = IntSet(initial_infections)
+    infected_vertices = BitSet(initial_infections)
     vertices_per_step::Vector{Vector{T}} = [Vector{T}() for i in 1:n]
 
     # Record initial infection

diff --git a/src/traversals/randomwalks.jl b/src/traversals/randomwalks.jl
@@ -29,7 +29,7 @@ vector of vertices visited in order.
 """
 function non_backtracking_randomwalk end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function non_backtracking_randomwalk{T, AG<:AbstractGraph{T}}(g::AG::(!IsDirected), s::Integer, niter::Integer)
+@traitfn function non_backtracking_randomwalk(g::AG::(!IsDirected), s::Integer, niter::Integer) where {T, AG<:AbstractGraph{T}}
     s in vertices(g) || throw(BoundsError())
     visited = Vector{T}()
     sizehint!(visited, niter)
@@ -61,7 +61,7 @@ function non_backtracking_randomwalk end
 end
 
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function non_backtracking_randomwalk{T, AG<:AbstractGraph{T}}(g::AG::IsDirected, s::Integer, niter::Integer)
+@traitfn function non_backtracking_randomwalk(g::AG::IsDirected, s::Integer, niter::Integer) where {T, AG<:AbstractGraph{T}}
     s in vertices(g) || throw(BoundsError())
     visited = Vector{T}()
     sizehint!(visited, niter)

diff --git a/src/utils.jl b/src/utils.jl
@@ -42,7 +42,7 @@ Unlike [`sample!`](@ref), does not produce side effects.
 """
 sample(a::UnitRange, k::Integer; exclude = ()) = sample!(getRNG(), collect(a), k; exclude = exclude)
 
-getRNG(seed::Integer = -1) = seed >= 0 ? MersenneTwister(seed) : Base.Random.GLOBAL_RNG
+getRNG(seed::Integer = -1) = seed >= 0 ? MersenneTwister(seed) : GLOBAL_RNG
 
 """
     insorted(item, collection)
@@ -53,4 +53,3 @@ Return true if `item` is in sorted collection `collection`.
 Does not verify that `collection` is sorted.
 """
 insorted(item, collection) = !isempty(searchsorted(collection, item))
-
diff --git a/test/centrality/betweenness.jl b/test/centrality/betweenness.jl
@@ -7,7 +7,7 @@
 
     gint = loadgraph(joinpath(testdir, "testdata", "graph-50-500.jgz"), "graph-50-500")
 
-    c = vec(readcsv(joinpath(testdir, "testdata", "graph-50-500-bc.txt")))
+    c = vec(readdlm(joinpath(testdir, "testdata", "graph-50-500-bc.txt"), ','))
     for g in testdigraphs(gint)
         z  = @inferred(betweenness_centrality(g))
         zp = @inferred(parallel_betweenness_centrality(g))

diff --git a/test/centrality/radiality.jl b/test/centrality/radiality.jl
@@ -1,7 +1,7 @@
 @testset "Radiality" begin
     gint = loadgraph(joinpath(testdir, "testdata", "graph-50-500.jgz"), "graph-50-500")
 
-    c = vec(readcsv(joinpath(testdir, "testdata", "graph-50-500-rc.txt")))
+    c = vec(readdlm(joinpath(testdir, "testdata", "graph-50-500-rc.txt"), ','))
     for g in testdigraphs(gint)
         z  = @inferred(radiality_centrality(g))
         zp = @inferred(parallel_radiality_centrality(g))

diff --git a/test/centrality/stress.jl b/test/centrality/stress.jl
@@ -1,7 +1,7 @@
 @testset "Stress" begin
     gint = loadgraph(joinpath(testdir, "testdata", "graph-50-500.jgz"), "graph-50-500")
 
-    c = vec(readcsv(joinpath(testdir, "testdata", "graph-50-500-sc.txt")))
+    c = vec(readdlm(joinpath(testdir, "testdata", "graph-50-500-sc.txt"), ','))
     for g in testdigraphs(gint)
         z  = @inferred(stress_centrality(g))
         zp = @inferred(parallel_stress_centrality(g))

diff --git a/test/community/clique_percolation.jl b/test/community/clique_percolation.jl
@@ -1,6 +1,6 @@
 @testset "Clique percolation" begin
     function setofsets(array_of_arrays)
-        Set(map(IntSet, array_of_arrays))
+        Set(map(BitSet, array_of_arrays))
     end
 
     function test_cliques(graph, expected)