Initial commit

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.RELEASE_TOKEN }}

.github/workflows/julia_ci.yml

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+name: Julia CI/CD
+
+on:
+  schedule:
+    - cron: 0 0 * * *
+  push:
+    branches: ["main"]
+    tags: ["*"]
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      action:
+        description: "Action"
+        required: true
+        default: "test"
+        type: choice
+        options:
+          - test
+          - release
+      version:
+        description: "Tag and release version:"
+        required: false
+
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  discussions: read
+  issues: read
+  packages: read
+  pages: read
+  pull-requests: write
+  repository-projects: read
+  security-events: read
+  statuses: read
+
+jobs:
+  CI:
+    if: github.event_name == 'pull_request' || github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.action == 'test')
+    uses: AlgebraicJulia/.github/.github/workflows/julia_ci.yml@main
+    secrets: inherit
+  CompatHelper:
+    if: github.event_name == 'schedule'
+    uses: AlgebraicJulia/.github/.github/workflows/julia_compat.yml@main
+    secrets: inherit
+  Release:
+    if: github.event_name == 'workflow_dispatch' && inputs.action == 'release' && inputs.version != ''
+    uses: AlgebraicJulia/.github/.github/workflows/julia_release.yml@main
+    secrets: inherit

.gitignore

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+# 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
+.vscode
+.ipynb_checkpoints

LICENSE

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+MIT License
+
+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
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

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+name = "AlgebraicTemplate"
+uuid = "b66562e1-fa90-4e8b-9505-c909188fab76"
+license = "MIT"
+authors = ["AlgebraicJulia Developer <[email protected]>"]
+version = "0.0.1"
+
+[deps]
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+
+[compat]
+Catlab = "^0.14"
+julia = "1.6"

README.md

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+# AlgebraicTemplate.jl
+
+[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicTemplate.jl/stable)
+[![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicTemplate.jl/dev)
+[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/AlgebraicTemplate.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/AlgebraicTemplatee.jl)
+[![CI/CD](https://github.com/AlgebraicJulia/AlgebraicTemplate.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/AlgebraicTemplate.jl/actions/workflows/julia_ci.yml)
+
+A template repository for making a new AlgebraicJulia package.
+
+## 🛠️ Usage
+
+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/AlgebraicTemplate.jl` to match the name of your new package (e.x. "AlgebraicX")
+   ```sh
+   mv src/AlgebraicTemplate.jl src/AlgebraicX.jl
+   ```
+6. Replace all instances of the word "AlgebraicTemplate" with your new package name (e.x. "AlgebraicX")
+   ```sh
+   # On linux
+   git grep -l 'AlgebraicTemplate' | xargs sed -i 's/AlgebraicTemplate/AlgebraicX/g'
+   # On Mac OS X
+   git grep -l 'AlgebraicTemplate' | xargs sed -i '' -e 's/AlgebraicTemplate/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

codecov.yml

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+coverage:
+  precision: 2
+  status:
+    patch:
+      default:
+        target: 0%
+        threshold: 100%
+    project:
+      default:
+        target: 0%
+        threshold: 100%

docs/.gitignore

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+build/
+src/generated/

docs/Project.toml

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+[deps]
+AlgebraicTemplate = "b66562e1-fa90-4e8b-9505-c909188fab76"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

docs/literate/literate_example.jl

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+# # 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 AlgebraicTemplate
+
+# ## Using `hello()`
+#
+# We provide the `hello(string)` method which prints "Hello, `string`!"
+
+hello("World")

docs/make.jl

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+using Documenter
+using Literate
+
+const literate_dir = joinpath(@__DIR__, "literate")
+const generated_dir = joinpath(@__DIR__, "src", "generated")
+
+@info "Loading AlgebraicTemplate"
+using AlgebraicTemplate
+
+const no_literate = "--no-literate" in ARGS
+if !no_literate
+  @info "Building Literate.jl docs"
+
+  # 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/AlgebraicTemplate.jl/blob/gh-pages/dev"
+    config["repo_root_url"] = "https://github.com/AlgebraicJulia/AlgebraicTemplate.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=[AlgebraicTemplate],
+  format=Documenter.HTML(),
+  sitename="AlgebraicTemplate.jl",
+  doctest=false,
+  checkdocs=:none,
+  pages=Any[
+    "AlgebraicTemplate.jl"=>"index.md",
+    "Examples"=>Any[
+      "generated/literate_example.md",
+    ],
+    "Library Reference"=>"api.md",
+  ]
+)
+
+@info "Deploying docs"
+deploydocs(
+  target="build",
+  repo="github.com/AlgebraicJulia/AlgebraicTemplate.jl.git",
+  branch="gh-pages"
+)

docs/src/api.md

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+# Library Reference
+
+```@autodocs
+Modules = [AlgebraicTemplate]
+```

docs/src/index.md

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+# AlgebraicTemplate.jl
+
+```@meta
+CurrentModule = AlgebraicTemplate
+```
+
+`AlgebraicTemplate.jl` is a Julia library for...

src/AlgebraicTemplate.jl

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+""" Some description of ths package
+"""
+module AlgebraicTemplate
+
+export hello
+
+using Catlab
+
+""" hello(name::String)
+
+Returns the string "Hello, <name>!" where `<name>` is replaced with the provided parameter
+"""
+hello(name::String) = string("Hello, ", name, "!")
+
+end

test/Project.toml

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+[deps]
+AlgebraicTemplate = "b66562e1-fa90-4e8b-9505-c909188fab76"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/core.jl

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+@test hello("World") == "Hello, World!"

test/runtests.jl

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+using Test
+
+using AlgebraicTemplate
+
+@testset "Core" begin
+  include("core.jl")
+end