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 merging the two functions, having
MolecularGraph add new methods to the Graphs function. Currently, this
PR should be viewed as a "trial balloon" because there is a major
problem: solving the problem this way is piracy. There are several
alternatives, including (1) renaming MolecularGraph's function to
something else, (2) scoping calls to `MolecularGraph.maximum_clique` in
the test suite, or (3) defining a new function in MolecularGraph that
calls Graphs' function and then does some post-processing. Let me know
your preferred solution and I can implement it.

Because this was introducing piracy, I also took the liberty of adding
Aqua tests. Currently this highlights quite a few failures (not just the
piracy I introduced), so I marked the test as broken. Fixing these
should be the subject of a future PR.

Author: timholy

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 = "0.22.1"
 
 [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"
@@ -49,8 +50,9 @@ julia = "1.9"
 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/graph/clique.jl

@@ -138,16 +138,16 @@ all_maximal_cliques(g::SimpleGraph{T}; kwargs...
 
 Calculate maximum clique.
 """
-function maximum_clique(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U}
-    state = MaxCliqueState{T,U}(g; kwargs...)
+function Graphs.maximum_clique(::Type{U}, g::SimpleGraph{T}; kwargs...) where {T,U}
+    state = MaxCliqueState{T,U}(g; kwargs...)  # FIXME: this is piracy
     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...)
+Graphs.maximum_clique(g::SimpleGraph{T}; kwargs...
+    ) where T = maximum_clique(Vector{T}, g; kwargs...)  # FIXME: this is piracy
 
 
 

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
+    # Aqua.test_unbound_args(MolecularGraph)  # broken
+    # Aqua.test_undefined_exports(MolecularGraph) # broken
+    Aqua.test_project_extras(MolecularGraph)
+    Aqua.test_stale_deps(MolecularGraph)
+    # Aqua.test_deps_compat(MolecularGraph) # broken
+    # Aqua.test_piracies(MolecularGraph) # broken
+    Aqua.test_persistent_tasks(MolecularGraph)
+    Aqua.test_undocumented_names(MolecularGraph)
+end