Add JET.jl to testsuite (#249)

* Add JET.jl to testsuite

* Add JET to extras and target in Project.toml
* Add a file ./test/jet_test.jl
* Include this test in runtests.jl conditioned on Julia version >= 1.7

* Fix JET warnings and use JET.test_package

* using JET

* Fix JET bug

* Fix most warnings from JET and linter

* Fix LinAlg deprecation to None

* Only one JET error remains on fadj/badj

* Custom hack for SimpleDiGraph equality to satisfy JET

* Fix tests

* Upgrate JET to 0.8.2

* Check JET version before testing (>= 0.8.3 on Julia 1.9)

* Fix test dependencies

* Make sure that JET runs on Julia >= 1.9

---------

Co-authored-by: Guillaume Dalle <[email protected]>

Author: jlapeyre

Project.toml

@@ -16,7 +16,7 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-Aqua = "0.5"
+Aqua = "0.6"
 ArnoldiMethod = "0.1, 0.2"
 Compat = "3.40, 4"
 DataStructures = "0.17, 0.18"
@@ -32,9 +32,15 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "Base64", "DelimitedFiles", "Documenter", "JuliaFormatter", "StableRNGs", "Test"]
+test = ["Aqua", "Base64", "DelimitedFiles", "Documenter", "JET", "JuliaFormatter", "LinearAlgebra", "Pkg", "Random", "SparseArrays", "StableRNGs", "Statistics", "Test"]

src/Experimental/vf2.jl

@@ -658,7 +658,7 @@ function all_isomorph(
     edge_relation::Union{Nothing,Function}=nothing,
 )::Channel{Vector{Tuple{eltype(g1),eltype(g2)}}}
     T = Vector{Tuple{eltype(g1),eltype(g2)}}
-    !could_have_isomorph(g1, g2) && return Channel(_ -> return, ctype = T)  # TODO: fix problem with JuliaFormatter, right now the whole file is ignored
+    !could_have_isomorph(g1, g2) && return Channel(_ -> nothing, ctype = T)  # TODO: fix problem with JuliaFormatter, right now the whole file is ignored
     make_callback(c) = vmap -> (put!(c, collect(zip(vmap, 1:length(vmap)))), return true)
     ch::Channel{T} = Channel(; ctype=T) do c
         vf2(

src/SimpleGraphs/SimpleGraphs.jl

@@ -142,7 +142,7 @@ edges(g::AbstractSimpleGraph) = SimpleEdgeIter(g)
 fadj(g::AbstractSimpleGraph) = g.fadjlist
 fadj(g::AbstractSimpleGraph, v::Integer) = g.fadjlist[v]
 
-badj(x...) = _NI("badj")
+function badj end
 
 # handles single-argument edge constructors such as pairs and tuples
 has_edge(g::AbstractSimpleGraph, x) = has_edge(g, edgetype(g)(x))

src/SimpleGraphs/generators/deprecations.jl

@@ -1,45 +1,45 @@
-@deprecate BullGraph bull_graph
-@deprecate ChvatalGraph chvatal_graph
-@deprecate CubicalGraph cubical_graph
-@deprecate DesarguesGraph desargues_graph
-@deprecate DiamondGraph diamond_graph
-@deprecate DodecahedralGraph dodecahedral_graph
-@deprecate FruchtGraph frucht_graph
-@deprecate HeawoodGraph heawood_graph
-@deprecate HouseGraph house_graph
-@deprecate HouseXGraph house_x_graph
-@deprecate IcosahedralGraph icosahedral_graph
-@deprecate KarateGraph karate_graph
-@deprecate KrackhardtKiteGraph krackhardt_kite_graph
-@deprecate MoebiusKantorGraph moebius_kantor_graph
-@deprecate OctahedralGraph octahedral_graph
-@deprecate PappusGraph pappus_graph
-@deprecate PetersenGraph petersen_graph
-@deprecate SedgewickMazeGraph sedgewick_maze_graph
-@deprecate TetrahedralGraph tetrahedral_graph
-@deprecate TruncatedCubeGraph truncated_cube_graph
-@deprecate TruncatedTetrahedronGraph truncated_tetrahedron_graph
-@deprecate TruncatedTetrahedronDiGraph truncated_tetrahedron_digraph
-@deprecate TutteGraph tutte_graph
-@deprecate CompleteGraph complete_graph
-@deprecate CompleteBipartiteGraph complete_bipartite_graph
-@deprecate CompleteMultipartiteGraph complete_multipartite_graph
-@deprecate TuranGraph turan_graph
-@deprecate CompleteDiGraph complete_digraph
-@deprecate StarGraph star_graph
-@deprecate StarDigraph star_digraph
-@deprecate PathGraph path_graph
-@deprecate PathDiGraph path_digraph
-@deprecate CycleGraph cycle_graph
-@deprecate CycleDiGraph cycle_digraph
-@deprecate WheelGraph wheel_graph
-@deprecate WheelDiGraph wheel_digraph
-@deprecate Grid grid
-@deprecate BinaryTree binary_tree
-@deprecate Doublebinary_tree double_binary_tree
-@deprecate RoachGraph roach_graph
-@deprecate CliqueGraph clique_graph
-@deprecate LadderGraph ladder_graph
-@deprecate Circularladder_graph circular_ladder_graph
-@deprecate BarbellGraph barbell_graph
-@deprecate LollipopGraph lollipop_graph
+@deprecate BullGraph() bull_graph()
+@deprecate ChvatalGraph() chvatal_graph()
+@deprecate CubicalGraph() cubical_graph()
+@deprecate DesarguesGraph() desargues_graph()
+@deprecate DiamondGraph() diamond_graph()
+@deprecate DodecahedralGraph() dodecahedral_graph()
+@deprecate FruchtGraph() frucht_graph()
+@deprecate HeawoodGraph() heawood_graph()
+@deprecate HouseGraph() house_graph()
+@deprecate HouseXGraph() house_x_graph()
+@deprecate IcosahedralGraph() icosahedral_graph()
+@deprecate KarateGraph() karate_graph()
+@deprecate KrackhardtKiteGraph() krackhardt_kite_graph()
+@deprecate MoebiusKantorGraph() moebius_kantor_graph()
+@deprecate OctahedralGraph() octahedral_graph()
+@deprecate PappusGraph() pappus_graph()
+@deprecate PetersenGraph() petersen_graph()
+@deprecate SedgewickMazeGraph() sedgewick_maze_graph()
+@deprecate TetrahedralGraph() tetrahedral_graph()
+@deprecate TruncatedCubeGraph() truncated_cube_graph()
+@deprecate TruncatedTetrahedronGraph() truncated_tetrahedron_graph()
+@deprecate TruncatedTetrahedronDiGraph() truncated_tetrahedron_digraph()
+@deprecate TutteGraph() tutte_graph()
+@deprecate CompleteGraph(n) complete_graph(n)
+@deprecate CompleteBipartiteGraph(n1, n2) complete_bipartite_graph(n1, n2)
+@deprecate CompleteMultipartiteGraph(partitions) complete_multipartite_graph(partitions)
+@deprecate TuranGraph(n, r) turan_graph(n, r)
+@deprecate CompleteDiGraph(n) complete_digraph(n)
+@deprecate StarGraph(n) star_graph(n)
+@deprecate StarDigraph(n) star_digraph(n)
+@deprecate PathGraph(n) path_graph(n)
+@deprecate PathDiGraph(n) path_digraph(n)
+@deprecate CycleGraph(n) cycle_graph(n)
+@deprecate CycleDiGraph(n) cycle_digraph(n)
+@deprecate WheelGraph(n) wheel_graph(n)
+@deprecate WheelDiGraph(n) wheel_digraph(n)
+@deprecate Grid(dims; periodic=false) grid(dims; periodic=false)
+@deprecate BinaryTree(k) binary_tree(k)
+@deprecate Doublebinary_tree(k) double_binary_tree(k)
+@deprecate RoachGraph(k) roach_graph(k)
+@deprecate CliqueGraph(k, n) clique_graph(k, n)
+@deprecate LadderGraph(n) ladder_graph(n)
+@deprecate Circularladder_graph(n) circular_ladder_graph(n)
+@deprecate BarbellGraph(n1, n2) barbell_graph(n1, n2)
+@deprecate LollipopGraph(n1, n2) lollipop_graph(n1, n2)

src/deprecations.jl

@@ -2,7 +2,7 @@
 # for which the deprecation should be removed.
 
 # Deprecated to fix spelling. Can be removed for version 2.0.
-@deprecate simplecycles_hadwick_james simplecycles_hawick_james
+@deprecate simplecycles_hadwick_james(g) simplecycles_hawick_james(g)
 
 # Deprecated for more explicit function name. Can be removed for version 2.0.
 @deprecate saw self_avoiding_walk

src/graphcut/normalized_cut.jl

@@ -115,7 +115,7 @@ function _partition_weightmx(cut, W::SparseMatrixCSC)
     return (W1, W2, vmap1, vmap2)
 end
 
-function _recursive_normalized_cut(W, thres=thres, num_cuts=num_cuts)
+function _recursive_normalized_cut(W, thres, num_cuts)
     m, n = size(W)
     D = Diagonal(vec(sum(W; dims=2)))
 

src/linalg/graphmatrices.jl

@@ -306,8 +306,8 @@ function symmetrize(adjmat::CombinatorialAdjacency, which=:or)
 end
 
 # per #564
-# @deprecate mul!(Y, A::Noop, B) None
-@deprecate convert(::Type{Adjacency}, lapl::Laplacian) None
+# @deprecate mul!(Y, A::Noop, B) nothing
+@deprecate convert(::Type{Adjacency}, lapl::Laplacian) nothing
 @deprecate convert(::Type{SparseMatrix}, adjmat::GraphMatrix) sparse(adjmat)
 
 """

src/operators.jl

@@ -394,7 +394,7 @@ function crosspath end
     len::Integer, g::AG::(!IsDirected)
 ) where {T,AG<:AbstractGraph{T}}
     p = path_graph(len)
-    h = Graph{T}(p)
+    h = SimpleGraph{T}(p)
     return cartesian_product(h, g)
 end
 

test/runtests.jl

@@ -3,6 +3,7 @@ using Documenter
 using Graphs
 using Graphs.SimpleGraphs
 using Graphs.Experimental
+using JET
 using JuliaFormatter
 using Graphs.Test
 using Test
@@ -14,9 +15,26 @@ using Base64
 using Random
 using Statistics: mean, std
 using StableRNGs
+using Pkg
 
 const testdir = dirname(@__FILE__)
 
+function get_pkg_version(name::AbstractString)
+    for dep in values(Pkg.dependencies())
+        if dep.name == name
+            return dep.version
+        end
+    end
+    return error("Dependency not available")
+end
+
+@testset "Code quality (JET.jl)" begin
+    if VERSION >= v"1.9"
+        @assert get_pkg_version("JET") >= v"0.8.3"
+        JET.test_package(Graphs; target_defined_modules=true)
+    end
+end
+
 @testset verbose = true "Code quality (Aqua.jl)" begin
     Aqua.test_all(Graphs; ambiguities=false)
 end

test/simplegraphs/simplegraphs.jl

@@ -9,7 +9,7 @@ using Random: Random
     @test @inferred(eltype(SimpleGraph(adjmx1))) == Int
     @test_throws ArgumentError SimpleGraph(adjmx2)
 
-    @test_throws Graphs.NotImplementedError badj(DummySimpleGraph())
+    @test_throws MethodError badj(DummySimpleGraph())
 
     @test @inferred(ne(SimpleGraph(path_digraph(5)))) == 4
     @test @inferred(!is_directed(SimpleGraph))
@@ -498,4 +498,15 @@ using Random: Random
     end
     # codecov for has_edge(::AbstractSimpleGraph, x, y)
     @test @inferred has_edge(DummySimpleGraph(), 1, 2)
+
+    # Test for SimpleDiGraph equality #249
+    @test SimpleGraph(1) != SimpleGraph(0)
+    @test SimpleGraph(1) != SimpleGraph(2)
+    @test SimpleGraph(2) != SimpleDiGraphFromIterator(Edge.([(1, 2)]))
+    @test SimpleDiGraphFromIterator(Edge.([(1, 2)])) !=
+        SimpleDiGraphFromIterator(Edge.([(2, 1)]))
+    @test SimpleDiGraphFromIterator(Edge.([(1, 2), (2, 3)])) !=
+        SimpleDiGraphFromIterator(Edge.([(1, 2), (3, 2)]))
+    @test SimpleDiGraphFromIterator(Edge.([(1, 2), (2, 3)])) !=
+        SimpleDiGraphFromIterator(Edge.([(1, 2), (1, 3)]))
 end