Added fixes for Julia 1.0 (#19)

* added fixes for Julia 1.0

* changed .travis.yml to julia version 0.7, 1.0 and nightly

* updated appveyor script

* added using InteractiveUtils so versioninfo() can still be used

* replaced content of appveyor.yml with new version from README

* forgot to uncomment a line

* changed indentation

* added using Pkg to appveyor script

* added second using Pkg to appveyor.yml

* changed Clp requirement in test to v0.5

* changed Clp requirement in test to v0.5

Author: simonschoelly

.travis.yml

@@ -4,7 +4,8 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 
 matrix:
@@ -34,4 +35,4 @@ after_success:
   - julia -e 'cd(Pkg.dir("LightGraphsFlows")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
   # Build documentation
   - julia -e 'Pkg.add("Documenter")'
-  - julia -e 'cd(Pkg.dir("LightGraphsFlows")); include(joinpath("docs", "make.jl"))'
+  - julia -e 'cd(Pkg.dir("LightGraphsFlows")); include(joinpath("docs", "make.jl"))'

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.6
-LightGraphs 0.12
+julia 0.7
+LightGraphs 1.1.0
 SimpleTraits 0.6
 MathProgBase 0.7

appveyor.yml

@@ -1,16 +1,18 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
-
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1
+  - julia_version: nightly
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+matrix:
+   allow_failures:
+   - julia_version: nightly
 
 branches:
   only:
@@ -24,24 +26,19 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
 # Need to convert from shallow to complete for Pkg.clone to work
   - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"LightGraphsFlows\"); Pkg.build(\"LightGraphsFlows\")"
+  - C:\julia\bin\julia -e "using InteractiveUtils, Pkg; versioninfo();
+        Pkg.clone(pwd(), \"LightGraphsFlows\"); Pkg.build(\"LightGraphsFlows\")"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"LightGraphsFlows\")"
+    - C:\julia\bin\julia -e "using Pkg; Pkg.test(\"LightGraphsFlows\")"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"

src/LightGraphsFlows.jl

@@ -8,7 +8,10 @@ import SimpleTraits
 using MathProgBase.HighLevelInterface: linprog
 using MathProgBase.SolverInterface: AbstractMathProgSolver
 
-import Base: getindex, size, transpose, ctranspose
+using SparseArrays: spzeros
+using Markdown: @doc_str
+
+import Base: getindex, size, transpose, adjoint
 
 include("maximum_flow.jl")
 include("edmonds_karp.jl")

src/boykov_kolmogorov.jl

@@ -16,12 +16,12 @@ Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision.
 """
 function boykov_kolmogorov_impl end
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function boykov_kolmogorov_impl{T, U, AG<:lg.AbstractGraph{U}}(
-    residual_graph::AG::lg.IsDirected,    # the input graph
-    source::Integer,                      # the source vertex
-    target::Integer,                      # the target vertex
-    capacity_matrix::AbstractMatrix{T}    # edge flow capacities
-    )
+@traitfn function boykov_kolmogorov_impl(
+        residual_graph::AG::lg.IsDirected,    # the input graph
+        source::Integer,                      # the source vertex
+        target::Integer,                      # the target vertex
+        capacity_matrix::AbstractMatrix{T}    # edge flow capacities
+    ) where {T, U, AG<:lg.AbstractGraph{U}}
     n = lg.nv(residual_graph)
 
     flow = 0
@@ -53,7 +53,7 @@ function boykov_kolmogorov_impl end
 end
 
 # see https://github.com/mauro3/SimpleTraits.jl/issues/47#issuecomment-327880153 for syntax
-@traitfn function find_path!{T, AG<:lg.AbstractGraph{T}}(
+@traitfn function find_path!(
         residual_graph::AG::lg.IsDirected, # the input graph
         source::Integer,                   # the source vertex
         target::Integer,                   # the target vertex
@@ -62,7 +62,7 @@ end
         PARENT::Vector,                    # parent table
         TREE::Vector,                      # tree table
         A::Vector                          # active set
-    )
+    ) where {T, AG<:lg.AbstractGraph{T}}
     tree_cap(p, q) = TREE[p] == one(T) ? capacity_matrix[p, q] - flow_matrix[p, q] :
     capacity_matrix[q, p] - flow_matrix[q, p]
     while !isempty(A)
@@ -72,7 +72,7 @@ end
                 if TREE[q] == zero(T)
                     TREE[q] = TREE[p]
                     PARENT[q] = p
-                    unshift!(A, q)
+                    pushfirst!(A, q)
                 end
                 if TREE[q] ≠ zero(T) && TREE[q] ≠ TREE[p]
                     # p -> source
@@ -134,19 +134,19 @@ function augment!(
         if flow_matrix[p, q] == capacity_matrix[p, q]
             if TREE[p] == TREE[q] == one(T)
                 PARENT[q] = zero(T)
-                unshift!(O, q)
+                pushfirst!(O, q)
             end
             if TREE[p] == TREE[q] == 2
                 PARENT[p] = zero(T)
-                unshift!(O, p)
+                pushfirst!(O, p)
             end
         end
     end
 
     return Δ
 end
 
-@traitfn function adopt!{T, AG<:lg.AbstractGraph{T}}(
+@traitfn function adopt!(
         residual_graph::AG::lg.IsDirected,  # the input graph
         source::Integer,                    # the source vertex
         target::Integer,                    # the target vertex
@@ -156,7 +156,7 @@ end
         TREE::Vector,                       # tree table
         A::Vector,                          # active set
         O::Vector                           # orphan set
-    )
+    ) where {T, AG<:lg.AbstractGraph{T}}
     tree_cap(p, q) = TREE[p] == 1 ? capacity_matrix[p, q] - flow_matrix[p, q] :
     capacity_matrix[q, p] - flow_matrix[q, p]
     while !isempty(O)
@@ -183,11 +183,11 @@ end
             for q in lg.neighbors(residual_graph, p)
                 if TREE[q] == TREE[p]
                     if tree_cap(q, p) > 0
-                        unshift!(A, q)
+                        pushfirst!(A, q)
                     end
                     if PARENT[q] == p
                         PARENT[q] = zero(T)
-                        unshift!(O, q)
+                        pushfirst!(O, q)
                     end
                 end
             end

src/dinic.jl

@@ -7,12 +7,12 @@ with edge flow capacities in `capacity_matrix` using
 Return the value of the maximum flow as well as the final flow matrix.
 """
 function dinic_impl end
-@traitfn function dinic_impl{T}(
-    residual_graph::::lg.IsDirected,               # the input graph
-    source::Integer,                       # the source vertex
-    target::Integer,                       # the target vertex
-    capacity_matrix::AbstractMatrix{T}    # edge flow capacities
-    )
+@traitfn function dinic_impl(
+        residual_graph::::lg.IsDirected,               # the input graph
+        source::Integer,                       # the source vertex
+        target::Integer,                       # the target vertex
+        capacity_matrix::AbstractMatrix{T}    # edge flow capacities
+    ) where {T}
     n = lg.nv(residual_graph)                     # number of vertexes
     flow_matrix = zeros(T, n, n)           # initialize flow matrix
     P = zeros(Int, n)                      # Sharable parent vector
@@ -36,14 +36,14 @@ end
 Like `blocking_flow`, but requires a preallocated parent vector `P`.
 """
 function blocking_flow! end
-@traitfn function blocking_flow!{T}(
+@traitfn function blocking_flow!(
         residual_graph::::lg.IsDirected,     # the input graph
         source::Integer,                     # the source vertex
         target::Integer,                     # the target vertex
         capacity_matrix::AbstractMatrix{T},  # edge flow capacities
         flow_matrix::AbstractMatrix,         # the current flow matrix
         P::AbstractVector{Int}               # Parent vector to store Level Graph
-    )
+    ) where {T}
     n = lg.nv(residual_graph)                # number of vertexes
     fill!(P, -1)
     P[source] = -2
@@ -56,7 +56,7 @@ function blocking_flow! end
         for v in lg.outneighbors(residual_graph, u)
             if P[v] == -1 && capacity_matrix[u, v] > flow_matrix[u, v]
                 P[v] = u
-                unshift!(Q, v)
+                pushfirst!(Q, v)
             end
         end
     end

src/edmonds_karp.jl

@@ -7,12 +7,12 @@ Compute the maximum flow in flow graph `residual_graph` between `source` and
 Return the value of the maximum flow as well as the final flow matrix.
 """
 function edmonds_karp_impl end
-@traitfn function edmonds_karp_impl{T}(
+@traitfn function edmonds_karp_impl(
         residual_graph::::lg.IsDirected,               # the input graph
         source::Integer,                       # the source vertex
         target::Integer,                       # the target vertex
         capacity_matrix::AbstractMatrix{T}    # edge flow capacities
-    )
+    ) where {T}
     n = lg.nv(residual_graph)                     # number of vertexes
     flow = 0
     flow_matrix = zeros(T, n, n)           # initialize flow matrix
@@ -111,7 +111,7 @@ function fetch_path! end
                 if capacity_matrix[u, v] - flow_matrix[u, v] > 0 && P[v] == -1
                     P[v] = u
                     if S[v] == -1
-                        unshift!(Q_f, v)
+                        pushfirst!(Q_f, v)
                     else
                         return v, P, S, 0 # 0 indicates success
                     end
@@ -126,7 +126,7 @@ function fetch_path! end
                     S[u] = v
                     P[u] != -1 && return u, P, S, 0 # 0 indicates success
 
-                    unshift!(Q_r, u)
+                    pushfirst!(Q_r, u)
                 end
 
             end

src/ext_multiroute_flow.jl

@@ -1,3 +1,4 @@
+# EMRF (Extended Multiroute Flow) algorithms
 """
     emrf(flow_graph, source, target, capacity_matrix, flow_algorithm, routes=0)
 
@@ -13,7 +14,6 @@ multiroute flow function.
 ### References
 - [Extended Multiroute Flow algorithm](http://dx.doi.org/10.1016/j.disopt.2016.05.002)
 """
-# EMRF (Extended Multiroute Flow) algorithms
 function emrf(
         flow_graph::lg.AbstractGraph,          # the input graph
         source::Integer,                       # the source vertex
@@ -104,12 +104,12 @@ Calculates the breaking of the restricted max-flow from a set of auxiliary point
 for `flow_graph` from `source to `target` using capacities in `capacity_matrix`.
 """
 function breakingPoints end
-@traitfn function breakingPoints{T}(
+@traitfn function breakingPoints(
         flow_graph::::lg.IsDirected,                   # the input graph
         source::Integer,                           # the source vertex
         target::Integer,                           # the target vertex
         capacity_matrix::AbstractMatrix{T}   # edge flow capacities
-    )
+    ) where {T}
     auxpoints = auxiliaryPoints(flow_graph, source, target, capacity_matrix)
     λ = length(auxpoints) - 1
     left_index = 1
@@ -131,6 +131,9 @@ function breakingPoints end
     return breakingpoints
 end
 
+# Function to get the nonzero min and max function of a Matrix
+# note: this is more efficient than maximum() / minimum() / extrema()
+#       since we have to ignore zero values.
 """
     minmaxCapacity(capacity_matrix)
 
@@ -139,10 +142,6 @@ Return the nonzero min and max function of `capacity_matrix`.
 Note: this is more efficient than maximum() / minimum() / extrema()
 since we have to ignore zero values.
 """
-
-# Function to get the nonzero min and max function of a Matrix
-# note: this is more efficient than maximum() / minimum() / extrema()
-#       since we have to ignore zero values.
 function minmaxCapacity(
     capacity_matrix::AbstractMatrix{T}    # edge flow capacities
     ) where T

src/maximum_flow.jl

@@ -48,7 +48,7 @@ getindex(d::DefaultCapacity{T}, s::Integer, t::Integer) where T = if lg.has_edge
 # isassigned{T<:Integer}(d::DefaultCapacity{T}, u::T, v::T) = (u in 1:d.nv) && (v in 1:d.nv)
 size(d::DefaultCapacity) = (Int(d.nv), Int(d.nv))
 transpose(d::DefaultCapacity) = DefaultCapacity(reverse(d.flow_graph))
-ctranspose(d::DefaultCapacity) = DefaultCapacity(reverse(d.flow_graph))
+adjoint(d::DefaultCapacity) = DefaultCapacity(reverse(d.flow_graph))
 
 """
     residual(flow_graph)

src/push_relabel.jl

@@ -8,12 +8,12 @@ FIFO push relabel algorithm with gap heuristic.
 Takes approximately ``\\mathcal{O}(|V|^{3})`` time.
 """
 function push_relabel end
-@traitfn function push_relabel{T}(
+@traitfn function push_relabel(
         residual_graph::::lg.IsDirected,       # the input graph
         source::Integer,                       # the source vertex
         target::Integer,                       # the target vertex
         capacity_matrix::AbstractMatrix{T}     # edge flow capacities
-    )
+    ) where {T}
 
     n = lg.nv(residual_graph)
     flow_matrix = zeros(T, n, n)
@@ -55,7 +55,6 @@ end
 Push inactive node `v` into queue `Q` and activates it. Requires preallocated
 `active` and `excess` vectors.
 """
-
 function enqueue_vertex!(
         Q::AbstractVector,
         v::Integer,                   # input vertex
@@ -64,7 +63,7 @@ function enqueue_vertex!(
     )
     if !active[v] && excess[v] > 0
         active[v] = true
-        unshift!(Q, v)
+        pushfirst!(Q, v)
     end
     return nothing
 end

test/REQUIRE

@@ -1 +1 @@
-Clp 0.4
+Clp 0.5

test/maximum_flow.jl

@@ -44,7 +44,7 @@
             @test d[s, t] == 0
             @test size(d) == (nvertices, nvertices)
             @test typeof(transpose(d)) <: LightGraphsFlows.DefaultCapacity
-            @test typeof(ctranspose(d)) <: LightGraphsFlows.DefaultCapacity
+            @test typeof(adjoint(d)) <: LightGraphsFlows.DefaultCapacity
 
             # Test all algorithms - type instability in PushRelabel #553
             for ALGO in [EdmondsKarpAlgorithm, DinicAlgorithm, BoykovKolmogorovAlgorithm, PushRelabelAlgorithm]

test/mincost.jl

@@ -1,4 +1,5 @@
 using Clp: ClpSolver
+using SparseArrays: spzeros
 
 @testset "Minimum-cost flow" begin
 

test/runtests.jl

@@ -1,9 +1,11 @@
 using LightGraphsFlows
-using Base.Test
+using Test
 import LightGraphs
 import SimpleTraits
 const lg = LightGraphs
 
+using LinearAlgebra: diag
+
 const testdir = dirname(@__FILE__)
 
 testgraphs(g) = [g, lg.Graph{UInt8}(g), lg.Graph{Int16}(g)]