Inheriting code from decapodes

.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
+

Project.toml

@@ -1,18 +1,19 @@
-name = "DiagrammaticEquations.jl"
-uuid = "b66562e1-fa90-4e8b-9505-c909188fab76"
+name = "DiagrammaticEquations"
+uuid = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
 license = "MIT"
-authors = authors = [
-  "James Fairbanks",
-  "Andrew Baas",
-  "Evan Patterson",
-  "Luke Morris",
-  "George Rauta",
-]
+authors = ["James Fairbanks", "Andrew Baas", "Evan Patterson", "Luke Morris", "George Rauta"]
 version = "0.0.1"
 
 [deps]
-Catlab = "d3509f1a-f4fe-4f63-b9c2-a8cefdb22603"
+AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [compat]
-Catlab = "^0.14"
+AlgebraicRewriting = "0.2"
+Catlab = "0.15"
+DataStructures = "0.18.13"
+MLStyle = "0.4.17"
 julia = "1.6"

README.md

@@ -1,83 +1,13 @@
-# AlgebraicX.jl
+# DiagrammaticEquations.jl
 
-[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicX.jl/stable)
-[![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicX.jl/dev)
-[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/AlgebraicX.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/AlgebraicXe.jl)
-[![CI/CD](https://github.com/AlgebraicJulia/AlgebraicX.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/AlgebraicX.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)
 
-A template repository for making a new AlgebraicJulia package.
+`DiagrammaticEquations.jl` is a Julia library implementing category theory to reason formally about diagrammatic representations of systems of algebraic and differential equations. 
 
-## 🛠️ Usage
+Currently DiagrammaticEquations.jl contains two submodules, `Deca` and `Learn` for supporting `Decapodes.jl` and `AlgebraicLearning.jl` functionality. 
 
-1. Use the "Use this template" dropdown to select "Create a new repository"
-2. In the new page select "AlgebraicJulia" as the owner, give the repository a name such as "AlgebraicX.jl", and create a new repository from the template
-3. Set up Codecov credentials for code coverage (If you have trouble, reach out to an AlgebraicJulia organization owner to help with this)
-
-   1. Log into [Codecov](https://codecov.io) with your GitHub account (this requires that you are a member of the AlgebraicJulia organization)
-   2. Navigate to the [AlgebraicJulia organization](https://app.codecov.io/gh/AlgebraicJulia)
-   3. Select your new repository from the list (e.x. "AlgebraicX")
-   4. Note down the `CODECOV_TOKEN` value (It may be in the "Settings" tab if it doesn't show up immediately)
-   5. Navigate back to your new GitHub repository and go to the Settings tab
-   6. Go to "Security", "Secrets and variables", and "Actions" and click the "New repository secret" button
-   7. Give the secret name `CODECOV_TOKEN` and the Secret value is the value you noted from the Codecov settings
-   8. Click "Add secret"
-
-4. Clone the new repository, for example in the terminal:
-   ```sh
-   git clone https://github.com/AlgebraicJulia/AlgebraicX.jl.git
-   cd AlgebraicX.jl
-   ```
-5. Rename the file `src/AlgebraicX.jl` to match the name of your new package (e.x. "AlgebraicX")
-   ```sh
-   mv src/AlgebraicX.jl src/AlgebraicX.jl
-   ```
-6. Replace all instances of the word "AlgebraicX" with your new package name (e.x. "AlgebraicX")
-   ```sh
-   # On linux
-   git grep -l 'AlgebraicX' | xargs sed -i 's/AlgebraicX/AlgebraicX/g'
-   # On Mac OS X
-   git grep -l 'AlgebraicX' | xargs sed -i '' -e 's/AlgebraicX/AlgebraicX/g'
-   ```
-7. Generate a new random version 4 UUID (you can get one here: https://www.uuidgenerator.net/version4)
-   - We will assume for this example that your new UUID is `<UUID>`
-8. Replace all instances of the template's UUID, "b66562e1-fa90-4e8b-9505-c909188fab76", with your new UUID (e.x. "<UUID>")
-   ```sh
-   # On linux
-   git grep -l 'b66562e1-fa90-4e8b-9505-c909188fab76' | xargs sed -i 's/b66562e1-fa90-4e8b-9505-c909188fab76/<UUID>/g'
-   # On Mac OS X
-   git grep -l 'b66562e1-fa90-4e8b-9505-c909188fab76' | xargs sed -i '' -e 's/b66562e1-fa90-4e8b-9505-c909188fab76/<UUID>/g'
-   ```
-9. Commit these new changes to your repository
-   ```sh
-   git commit -am "Set up skeleton for AlgebraicX.jl"
-   git push
-   ```
-10. Go back to your repository and wait until the tests have passed, you can check the status by going to the "Actions" tab in the repository
-
-### 📔 Set Up GitHub Pages (Public Repos Only)
-
-1. Follow the Usage steps above to set up a new template, make sure all initial GitHub Actions have passed
-2. Navigate to the repository settings and go to "Code and automation", "Pages"
-3. Make sure the "Source" dropdown is set to "Deploy from a branch"
-4. Set the "Branch" dropdown to "gh-pages", make sure the folder is set to "/ (root)", and click "Save"
-5. Go back to the main page of your repository and click the gear to the right of the "About" section in the right side column
-6. Under "Website" check the checkbox that says "Use your GitHub Pages website" and click "Save changes"
-7. You will now see a URL in the "About" section that will link to your package's documentation
-
-### 🛡️ Set Up Branch Protection (Public Repos Only)
-
-1. Follow the Usage steps above to set up a new template, make sure all initial GitHub Actions have passed
-2. Navigate to the repository settings and go to "Code and automation", "Branches"
-3. Click "Add branch protection rule" to start adding branch protection
-4. Under "Branch name pattern" put `main`, this will add protection to the main branch
-5. Make sure to set the following options:
-   - Check the "Require a pull request before merging"
-   - Check the "Request status checks to pass before merging" and make sure the following status checks are added to the required list:
-     - CI / Documentation
-     - CI / Julia 1 - ubuntu-latest - x64 - push
-     - CI / Julia 1 - ubuntu-latest - x86 - push
-     - CI / Julia 1 - windows-latest - x64 - push
-     - CI / Julia 1 - windows-latest - x86 - push
-     - CI / Julia 1 - macOS-latest - x64 - push
-   - Check the "Restrict who can push to matching branches" and add `algebraicjuliabot` to the list of people with push access
-6. Click "Save changes" to enable the branch protection
+## Relevant Work
+* Patterson, E., Baas, A., Hosgood, T., & Fairbanks, J. (2022). A diagrammatic view of differential equations in physics. arXiv preprint arXiv:2204.01843.

docs/literate/literate_example.jl

@@ -1,13 +1,6 @@
 # # Code Example
 #
-# This is an example of adding a code example compiled with Literate.jl in the docs.
-#
-# First we want to load our package with `using`
 
 using DiagrammaticEquations
 
-# ## Using `hello()`
-#
-# We provide the `hello(string)` method which prints "Hello, `string`!"
 
-hello("World")

docs/make.jl

@@ -14,8 +14,8 @@ if !no_literate
   # 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/AlgebraicX.jl/blob/gh-pages/dev"
-    config["repo_root_url"] = "https://github.com/AlgebraicJulia/AlgebraicX.jl/blob/main/docs"
+    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)
@@ -36,11 +36,11 @@ end
 makedocs(
   modules=[DiagrammaticEquations],
   format=Documenter.HTML(),
-  sitename="AlgebraicX.jl",
+  sitename="DE.jl",
   doctest=false,
   checkdocs=:none,
   pages=Any[
-    "AlgebraicX.jl"=>"index.md",
+    "DiagrammaticEquations.jl"=>"index.md",
     "Examples"=>Any[
       "generated/literate_example.md",
     ],

docs/src/api.md

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

docs/src/index.md

@@ -4,4 +4,5 @@
 CurrentModule = DiagrammaticEquations
 ```
 
-`DiagrammaticEquations.jl` is a Julia library for...
+`DiagrammaticEquations.jl` is a Julia library implementing category-theoretic formally reasoning about systems of algebraic and differential equations with diagrams. 
+

jobscript.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+#SBATCH --job-name=daemon_job_test    # Job name
+#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH [email protected] # Where to send mail	
+#SBATCH --ntasks=1                    # Run on a single CPU
+#SBATCH --mem=8gb                     # Job memory request
+#SBATCH --time=00:05:00               # Time limit hrs:min:sec
+#SBATCH --output=daemon_test_%j.log   # Standard output and error log
+pwd; hostname; date
+
+module load gcc/12.2.0 openmpi/4.1.5 julia
+
+echo "Running docs build..."
+
+julia --project=docs/ -e 'using Pkg; Pkg.status()'
+julia --project=docs/ -e 'using Pkg; Pkg.instantiate(); include("docs/make.jl")'
+# julia --project -e 'using Pkg; Pkg.status; Pkg.test()' > log_test.md
+# ./job.sh
+
+# mpiexec -np 1 julia --project -e test/runtests.jl
+
+date
+
+

src/DiagrammaticEquations.jl

@@ -0,0 +1,67 @@
+""" Some description of ths package
+"""
+module DiagrammaticEquations
+
+export 
+DerivOp, append_dot, normalize_unicode, infer_states,
+# Deca
+recursive_delete_parents, findname, spacename,
+op1_inf_rules_1D, op2_inf_rules_1D, op1_inf_rules_2D, op2_inf_rules_2D, op1_res_rules_1D, op2_res_rules_1D, op1_res_rules_2D, op2_res_rules_2D, varname,
+## collages
+Collage, collate,
+## composition
+oapply, unique_by, unique_by!, OpenSummationDecapodeOb, OpenSummationDecapode, Open,
+## acset
+unicode!,
+SchDecapode, SchNamedDecapode, AbstractDecapode, AbstractNamedDecapode, NamedDecapode, SummationDecapode,
+contract_operators, add_constant!, add_parameter, vec_to_dec!, infer_types!,
+fill_names!,  dot_rename!, expand_operators, infer_state_names, recognize_types,
+resolve_overloads!,
+## language
+@decapode, Term, parse_decapode, term, Eq, DecaExpr,
+# ~~~~~
+Plus, AppCirc1, AppCirc2, Var, Tan, App1, App2, Judgment, 
+## visualization
+to_graphviz_property_graph, typename,
+## rewrite
+average_rewrite
+
+
+using Catlab
+using Catlab.Theories
+import Catlab.Theories: otimes, oplus, compose, ⊗, ⊕, ⋅, associate, associate_unit, Ob, Hom, dom, codom
+using Catlab.Programs
+using Catlab.CategoricalAlgebra
+using Catlab.WiringDiagrams
+using Catlab.WiringDiagrams.DirectedWiringDiagrams
+using Catlab.ACSetInterface
+using MLStyle
+import Unicode
+
+# using .Deca
+# import .Deca: to_graphviz_property_graph 
+
+
+## TODO:
+## generate schema from a _theory_
+## from presentation in the theory determine what to slice over
+## Pavel S., Hypergraph theory string diagram
+
+normalize_unicode(s::String) = Unicode.normalize(s, compose=true, stable=true, chartransform=Unicode.julia_chartransform)
+normalize_unicode(s::Symbol)  = Symbol(normalize_unicode(String(s)))
+
+DerivOp = Symbol("∂ₜ")
+append_dot(s::Symbol) = Symbol(string(s)*'\U0307')
+
+
+include("acset.jl")
+include("language.jl")
+include("composition.jl")
+include("collages.jl")
+include("visualization.jl")
+include("rewrite.jl")
+
+include("deca/Deca.jl")
+include("learn/Learn.jl")
+
+end