Merge branch 'main' into integrate

.buildkite/jobscript.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+pwd; hostname; date
+
+module load julia
+
+echo "Running Tests..."
+julia --project -t 16 -e 'using Pkg; Pkg.status(); Pkg.test()'
+
+echo "Building Documentation..."
+julia --project=docs -t 16 -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.status(); Pkg.instantiate(); include("docs/make.jl")'

.buildkite/pipeline.yml

@@ -0,0 +1,21 @@
+env:
+  JULIA_VERSION: "1.10.2"
+  GATAS_HOME: "$DEPOT"
+
+steps:
+
+  - label: ":hammer: Build Project"
+    command: 
+      - "module load julia"
+      - "julia --project=docs --color=yes -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate(); Pkg.precompile()'"
+
+  - wait 
+
+  - label: ":scroll: Build docs and run tests"
+    env:
+      JULIA_PROJECT: "docs/"
+    command:
+      - "srun --cpus-per-task=16 --mem=64G --time=1:00:00 --output=.buildkite/log_%j.log --unbuffered .buildkite/jobscript.sh"
+
+  - wait
+

README.md

@@ -4,7 +4,7 @@ Structural graph theorists and algorithmicists alike know that it's usually a sm
 
 ### But what happens if we want to compute on other kinds of mathematical structures?
 
-This project consists of an implementation of the category-theoretic notion of [structured decompositions][2]. These provide a formalism for decomposing decomposing arbitrary mathematical objects (not just graphs) and morphisms between them into smaller constituent parts. Since the definition of a structured decompositions is functorial, one can easily lift computational problems (defined as functors mapping inputs to solution spaces) to functors between from decompositions of the inputs to decompositions of solution spaces. This package allows one to leverage insights to solve decision problems that are encoded as [sheaves][3] efficiently (i.e. in [fixed-parameter-tractable][4] time parameterized by the width of the decompositions).
+This project consists of an implementation of the category-theoretic notion of [structured decompositions][2]. These provide a formalism for decomposing arbitrary mathematical objects (not just graphs) and morphisms between them into smaller constituent parts. Since the definition of a structured decompositions is functorial, one can easily lift computational problems (defined as functors mapping inputs to solution spaces) to functors between from decompositions of the inputs to decompositions of solution spaces. This package allows one to leverage insights to solve decision problems that are encoded as [sheaves][3] efficiently (i.e. in [fixed-parameter-tractable][4] time parameterized by the width of the decompositions).
 
   [1]: https://en.wikipedia.org/wiki/Tree_decomposition
   [2]: https://arxiv.org/abs/2207.06091

benchmarks/BenchmarkAgainstNauty.jl

@@ -0,0 +1,48 @@
+# This file shows benchmarks against the Nauty algorithm currently implemented in CSetAutomorphisms.jl
+
+using BenchmarkTools
+using PkgBenchmark
+using Profile
+using Test
+
+using CSetAutomorphisms
+using CSetAutomorphisms.NautyInterface: all_autos
+using CSetAutomorphisms.TestHelp: Labeled
+
+using StructuredDecompositions.Decompositions
+using StructuredDecompositions.DecidingSheaves
+using StructuredDecompositions.FunctorUtils
+
+using Catlab.Graphs
+using Catlab.ACSetInterface
+using Catlab.CategoricalAlgebra
+using Catlab.Graphics
+
+# The following structures and functions were pulled from DecidingSheaves.jl 
+
+struct Coloring
+    n     
+    func
+end
+
+K(n) = complete_graph(Graph, n)
+Coloring(n) = Coloring(n, g -> homomorphisms(g, K(n)))
+(c::Coloring)(X::Graph) = FinSet(c.func(X))
+function (c::Coloring)(f::ACSetTransformation)  
+    (G₁, G₂)   = (dom(f), codom(f)) 
+    (cG₁, cG₂) = (c(G₁), c(G₂))
+    FinFunction( λ₂ -> compose(f,λ₂), cG₂, cG₁ )
+end
+
+skeletalColoring(n) = skeleton ∘ Coloring(n)
+
+function colorability_test(n, the_test_case)
+  hom = is_homomorphic(ob(colimit(the_test_case)), K(n))
+  dec = decide_sheaf_tree_shape(skeletalColoring(n), the_test_case)[1]
+  if hom == dec
+    return hom
+  else
+    error("is_homomorphic != decide_sheaf_tree_shape")
+  end
+end
+