Fix name collision in maximum_clique

Graphs v1.14.0 started exporting `maximum_clique`, which is a function
that MolecularGraph also exports. The two names collide, which causes
problems for MolecularGraph's test suite.

This fixes the problem by renaming MolecularGraph's `maximum_clique` to
`maximum_clique_mg`.

This also adds a bunch of Aqua tests to check for piracy, etc.

Author: timholy

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
 Manifest.toml
+Manifest-v*.toml
 
 _temp

Project.toml

@@ -1,16 +1,16 @@
 name = "MolecularGraph"
 uuid = "6c89ec66-9cd8-5372-9f91-fabc50dd27fd"
 authors = ["Seiji Matsuoka <ms0ae8ti1sj2ui@gmail.com"]
-version = "0.22.0"
+version = "0.23.0"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
@@ -30,13 +30,14 @@ CairoExt = "Cairo"
 RDKitExt = "RDKitMinimalLib"
 
 [compat]
+Aqua = "0.8"
 Cairo = "1.1"
 Colors = "0.13"
 DelimitedFiles = "1"
+EzXML = "1"
 GeometryBasics = "0.5"
 Graphs = "1.12"
 JSON = "1"
-EzXML = "1"
 MakieCore = "0.9,0.10"
 OrderedCollections = "1.8"
 RDKitMinimalLib = "1.2"
@@ -46,11 +47,16 @@ Test = "1"
 YAML = "0.4"
 coordgenlibs_jll = "3.0.2"
 julia = "1.9"
+Dates = "1"
+LinearAlgebra = "1"
+Printf = "1"
+Logging = "1"
 libinchi_jll = "1.5"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "Logging"]
+test = ["Test", "Aqua", "Logging"]

src/MolecularGraph.jl

@@ -77,7 +77,7 @@ export
 
 export
     maxcardmap, maxcard,
-    all_maximal_cliques, maximum_clique,
+    all_maximal_cliques, maximum_clique_mg,
     all_maximal_conn_cliques, maximum_conn_clique,
     approx_maximum_clique,
     mincyclebasis, edgemincyclebasis, disjoint_union,

src/graph/clique.jl

@@ -134,21 +134,26 @@ all_maximal_cliques(g::SimpleGraph{T}; kwargs...
 
 
 """
-    maximum_clique(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U} -> (U, Symbol)
+    maximum_clique_mg(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U} -> (U, Symbol)
 
 Calculate maximum clique.
+
+This is a molecular-mining-oriented variant of `Graphs.maximum_clique`: it accepts
+`timeout` and `targetsize` keyword arguments and reports a status alongside the
+result, both of which are needed in practice for the substructure-matching tasks in
+this package. The `_mg` suffix marks it as intentionally distinct from the like-named
+`Graphs.jl` function (#146).
 """
-function maximum_clique(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U}
+function maximum_clique_mg(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U}
     state = MaxCliqueState{T,U}(g; kwargs...)
     expand!(state, Set(vertices(g)), Set(vertices(g)))
     if state.status == :ongoing
         state.status = :done
     end
     return state.maxsofar, state.status
 end
-maximum_clique(g::SimpleGraph{T}; kwargs...
-    ) where T = maximum_clique(Vector{T}, g; kwargs...)
-
+maximum_clique_mg(g::SimpleGraph{T}; kwargs...
+    ) where T = maximum_clique_mg(Vector{T}, g; kwargs...)
 
 
 # Connected cliques (c-cliques)

src/graph/isomorphism_clique.jl

@@ -247,7 +247,7 @@ function maximum_common_subgraph(
     if connected
         maxclique, status = maximum_conn_clique(prod, connfunc=connfuncgen(prod, g, h); kwargs...)
     else
-        maxclique, status = maximum_clique(prod; kwargs...)
+        maxclique, status = maximum_clique_mg(prod; kwargs...)
     end
     # modprod reverse mapping
     nmap = Dict(div(i - 1, h.nv) + 1 => mod(i - 1, h.nv) + 1 for i in maxclique)
@@ -270,7 +270,7 @@ function maximum_common_subgraph(
             Dict{Edge{T},Edge{T}}, prod, connfunc=connfuncgen(prod, g, h),
             postprocess=mces_postprocess(g, h); kwargs...)
     else
-        return maximum_clique(
+        return maximum_clique_mg(
             Dict{Edge{T},Edge{T}}, prod, postprocess=mces_postprocess(g, h); kwargs...)
     end
 end

test/graph/clique.jl

@@ -7,31 +7,31 @@
 
 @testset "max_clique" begin
     nullg = SimpleGraph()
-    @test maximum_clique(nullg)[1] == []
+    @test maximum_clique_mg(nullg)[1] == []
 
     noedges = SimpleGraph(5)
     @test length(all_maximal_cliques(noedges)[1]) == 5
-    @test length(maximum_clique(noedges)[1]) == 1
+    @test length(maximum_clique_mg(noedges)[1]) == 1
 
     p7 = path_graph(7)
     @test length(all_maximal_cliques(p7)[1]) == 6
-    @test length(maximum_clique(p7)[1]) == 2
+    @test length(maximum_clique_mg(p7)[1]) == 2
 
     k5 = complete_graph(5)
     @test length(all_maximal_cliques(k5)[1]) == 1
-    @test length(maximum_clique(k5)[1]) == 5
+    @test length(maximum_clique_mg(k5)[1]) == 5
 
     w8 = wheel_graph(8)
     @test length(all_maximal_cliques(w8)[1]) == 7
-    @test length(maximum_clique(w8)[1]) == 3
+    @test length(maximum_clique_mg(w8)[1]) == 3
 
     petersen = smallgraph(:petersen)
     @test length(all_maximal_cliques(petersen)[1]) == 15
-    @test length(maximum_clique(petersen)[1]) == 2
+    @test length(maximum_clique_mg(petersen)[1]) == 2
 
     karate = smallgraph(:karate)
     @test length(all_maximal_cliques(karate)[1]) == 36
-    @test length(maximum_clique(karate)[1]) == 5
+    @test length(maximum_clique_mg(karate)[1]) == 5
 
 end
 

test/runtests.jl

@@ -107,3 +107,19 @@ include("./draw/svg.jl")
 include("./draw/3d.jl")
 
 end
+
+using MolecularGraph
+using Aqua
+using Test
+
+@testset "Aqua" begin
+    Aqua.test_ambiguities(MolecularGraph; broken=true)
+    Aqua.test_unbound_args(MolecularGraph; broken=true)
+    Aqua.test_undefined_exports(MolecularGraph; broken=true)
+    Aqua.test_project_extras(MolecularGraph)
+    Aqua.test_stale_deps(MolecularGraph)
+    Aqua.test_deps_compat(MolecularGraph)
+    Aqua.test_piracies(MolecularGraph)
+    Aqua.test_persistent_tasks(MolecularGraph)
+    Aqua.test_undocumented_names(MolecularGraph; broken=true)
+end