Clean up code from decapodes and begin ground work for DiagrammaticEq…

…uations.jl

.buildkite/pipeline.yml

@@ -0,0 +1,22 @@
+env:
+  JULIA_VERSION: "1.9.3"
+
+steps:
+
+  - label: ":hammer: Build Project"
+    command: 
+      - "module load julia"
+      - "julia --project --color=yes -e 'using Pkg; Pkg.instantiate()'"
+      - "julia --project=docs/ --color=yes -e 'using Pkg; Pkg.instantiate()'"
+      - "julia --project=docs/ --color=yes -e 'using Pkg; Pkg.precompile()'"
+
+  - wait 
+
+  - label: ":scroll: Build docs"
+    command:
+      - "srun --mem=8G --time=1:00:00 --output=log_%j.log jobscript.sh"
+    env:
+      JULIA_PROJECT: "docs/"
+
+  - wait
+

.gitignore

@@ -1,6 +1,29 @@
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# Files generated by benchmarktools
+.benchmarkci
+benchmark/*.json
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml
+
+# Misc. System Files
 .DS_Store
-.ipynb_checkpoints
-/Manifest.toml
-/dev/
-*.mem
 .vscode
+.ipynb_checkpoints

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 AlgebraicJulia
+Copyright (c) 2023 AlgebraicJulia
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -1,52 +1,19 @@
-name = "Decapodes"
-uuid = "679ab3ea-c928-4fe6-8d59-fd451142d391"
+name = "DiagrammaticEquations"
+uuid = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
+license = "MIT"
 authors = ["James Fairbanks", "Andrew Baas", "Evan Patterson", "Luke Morris", "George Rauta"]
-version = "0.5.0"
+version = "0.0.1"
 
 [deps]
-ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
-Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [compat]
-ACSets = "0.2"
-Artifacts = "1"
-Catlab = "0.15, 0.16"
-CombinatorialSpaces = "0.5, 0.6"
-ComponentArrays = "0.15"
+AlgebraicRewriting = "0.2"
+Catlab = "0.15"
 DataStructures = "0.18.13"
-Distributions = "0.25"
-FileIO = "1.16"
-GeometryBasics = "0.4.2"
-JLD2 = "0.4"
-JSON = "0.21"
-LinearAlgebra = "1.9"
 MLStyle = "0.4.17"
-OrdinaryDiffEq = "6.47"
-PreallocationTools = "0.4"
-Requires = "1.3"
-Unicode = "1.9"
-julia = "1.9"
-
-[extras]
-AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["AlgebraicPetri", "Distributions", "Test", "Random", "GeometryBasics"]
+julia = "1.6"

README.md

@@ -1,18 +1,13 @@
-# Decapodes.jl
+# DiagrammaticEquations.jl
 
-[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/Decapodes.jl/stable)
-[![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/Decapodes.jl/dev)
-[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/Decapodes.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/Decapodes.jl)
-[![CI/CD](https://github.com/AlgebraicJulia/Decapodes.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/Decapodes.jl/actions/workflows/julia_ci.yml)
+[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/DiagrammaticEquations.jl/stable)
+[![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/DiagrammaticEquations.jl/dev)
+[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/DiagrammaticEquations.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/DiagrammaticEquations.jl)
+[![CI/CD](https://github.com/AlgebraicJulia/DiagrammaticEquations.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/DiagrammaticEquations.jl/actions/workflows/julia_ci.yml)
 
-Decapodes are a graphical tool for the composition of physical systems.
-Ultimately, this library will include tooling which takes advantage of the
-formalization of physical theories described by DEC provided by
-[CombinatorialSpaces.jl](https://algebraicjulia.github.io/CombinatorialSpaces.jl/dev/).
+`DiagrammaticEquations.jl` is a Julia library implementing category theory to reason formally about diagrammatic representations of systems of algebraic and differential equations. 
 
-# NOTE
+Currently DiagrammaticEquations.jl contains two submodules, `Deca` and `Learn` for supporting `Decapodes.jl` and `AlgebraicLearning.jl` functionality. 
 
-This library is currently under active development, and so is not yet at a
-point where a constant API/behavior can be assumed. That being said, if this
-project looks interesting/relevant please contact us and
-[let us know](https://www.algebraicjulia.org/#contributing)!
+## Relevant Work
+* Patterson, E., Baas, A., Hosgood, T., & Fairbanks, J. (2022). A diagrammatic view of differential equations in physics. arXiv preprint arXiv:2204.01843.

codecov.yml

@@ -0,0 +1,11 @@
+coverage:
+  precision: 2
+  status:
+    patch:
+      default:
+        target: 0%
+        threshold: 100%
+    project:
+      default:
+        target: 0%
+        threshold: 100%

docs/.gitignore

@@ -0,0 +1,2 @@
+build/
+src/generated/

docs/Project.toml

@@ -1,21 +1,4 @@
 [deps]
-AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DiagrammaticEquations = "b66562e1-fa90-4e8b-9505-c909188fab76"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

docs/literate/literate_example.jl

@@ -0,0 +1,6 @@
+# # Code Example
+#
+
+using DiagrammaticEquations
+
+

docs/make.jl

@@ -1,66 +1,56 @@
 using Documenter
 using Literate
 
-@info "Loading Decapodes"
-using Decapodes
-using Catlab
-using Catlab.WiringDiagrams
-using AlgebraicPetri
-using CairoMakie
+const literate_dir = joinpath(@__DIR__, "literate")
+const generated_dir = joinpath(@__DIR__, "src", "generated")
 
-# Set Literate.jl config if not being compiled on recognized service.
-config = Dict{String,String}()
-if !(haskey(ENV, "GITHUB_ACTIONS") || haskey(ENV, "GITLAB_CI"))
-  config["nbviewer_root_url"] = "https://nbviewer.jupyter.org/github/AlgebraicJulia/Decapodes.jl/blob/gh-pages/dev"
-  config["repo_root_url"] = "https://github.com/AlgebraicJulia/Decapodes.jl/blob/main/docs"
-end
+@info "Loading DiagrammaticEquations"
+using DiagrammaticEquations
+
+const no_literate = "--no-literate" in ARGS
+if !no_literate
+  @info "Building Literate.jl docs"
 
-#const literate_dir = joinpath(@__DIR__, "..", "examples")
-#const generated_dir = joinpath(@__DIR__, "src", "examples")
-#
-#for (root, dirs, files) in walkdir(literate_dir)
-#  out_dir = joinpath(generated_dir, relpath(root, literate_dir))
-#  for file in files
-#    f,l = splitext(file)
-#    if l == ".jl" && !startswith(f, "_")
-#      Literate.markdown(joinpath(root, file), out_dir;
-#        config=config, documenter=true, credit=false)
-#      Literate.notebook(joinpath(root, file), out_dir;
-#        execute=true, documenter=true, credit=false)
-#    end
-#  end
-#end
+  # Set Literate.jl config if not being compiled on recognized service.
+  config = Dict{String,String}()
+  if !(haskey(ENV, "GITHUB_ACTIONS") || haskey(ENV, "GITLAB_CI"))
+    config["nbviewer_root_url"] = "https://nbviewer.jupyter.org/github/AlgebraicJulia/DiagrammaticEquations.jl/blob/gh-pages/dev"
+    config["repo_root_url"] = "https://github.com/AlgebraicJulia/DiagrammaticEquations.jl/blob/main/docs"
+  end
+
+  for (root, dirs, files) in walkdir(literate_dir)
+    out_dir = joinpath(generated_dir, relpath(root, literate_dir))
+    for file in files
+      f, l = splitext(file)
+      if l == ".jl" && !startswith(f, "_")
+        Literate.markdown(joinpath(root, file), out_dir;
+          config=config, documenter=true, credit=false)
+        Literate.notebook(joinpath(root, file), out_dir;
+          execute=true, documenter=true, credit=false)
+      end
+    end
+  end
+end
 
 @info "Building Documenter.jl docs"
 makedocs(
-  modules   = [Decapodes],
-  format    = Documenter.HTML(
-    assets = ["assets/analytics.js"],
-  ),
-  sitename  = "Decapodes.jl",
-  doctest   = false,
-  checkdocs = :none,
-  pages     = Any[
-    "Decapodes.jl" => "index.md",
-    "Overview" => "overview.md",
-    "Equations" => "equations.md",
-    "ASCII Operators" => "ascii.md",
-    "Misc Features" => "bc_debug.md",
-    "Pipe Flow" => "poiseuille.md",
-    "Glacial Flow" => "ice_dynamics.md",
-    "Grigoriev Ice Cap" => "grigoriev.md",
-    "Budyko-Sellers-Halfar" => "budyko_sellers_halfar.md",
-#    "Examples" => Any[
-#      "examples/cfd_example.md"
-#    ],
-    "Library Reference" => "api.md"
+  modules=[DiagrammaticEquations],
+  format=Documenter.HTML(),
+  sitename="DE.jl",
+  doctest=false,
+  checkdocs=:none,
+  pages=Any[
+    "DiagrammaticEquations.jl"=>"index.md",
+    "Examples"=>Any[
+      "generated/literate_example.md",
+    ],
+    "Library Reference"=>"api.md",
   ]
 )
 
 @info "Deploying docs"
 deploydocs(
-  target = "build",
-  repo   = "github.com/AlgebraicJulia/Decapodes.jl.git",
-  branch = "gh-pages",
-  devbranch = "main"
+  target="build",
+  repo="github.com/AlgebraicJulia/DiagrammaticEquations.jl.git",
+  branch="gh-pages"
 )

docs/src/api.md

@@ -1,7 +1,5 @@
 # Library Reference
 
-## Decapodes
 ```@autodocs
-Modules = [ Decapodes ]
-Private = false
+Modules = [DiagrammaticEquations, DiagrammaticEquations.Deca, DiagrammaticEquations.Learn]
 ```