Update with cookiecutter-snekpack

.cruft.json

@@ -0,0 +1,26 @@
+{
+  "template": "https://github.com/cthoyt/cookiecutter-snekpack",
+  "commit": "0618364d751132ea40c35ef4720a350dc028bcbe",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "package_name": "curies",
+      "package_name_stylized": "CURIEs",
+      "short_description": "Idiomatic conversion between URIs and compact URIs (CURIEs)",
+      "author_name": "Charles Tapley Hoyt",
+      "author_email": "[email protected]",
+      "github_organization_name": "biopragmatics",
+      "github_repository_name": "curies",
+      "command_line_interface": true,
+      "gitlab": false,
+      "runner": "tox",
+      "__runner": "tox -e",
+      "__runner_uv": "--with tox-uv tox -e",
+      "__runner_pip": "tox tox-uv",
+      "__runner_tests": "py",
+      "__gh_slug": "biopragmatics/curies",
+      "_template": "https://github.com/cthoyt/cookiecutter-snekpack"
+    }
+  },
+  "directory": null
+}

.github/CONTRIBUTING.md

@@ -8,7 +8,8 @@ This project uses the [GitHub Flow](https://guides.github.com/introduction/flow)
 model for code contributions. Follow these steps:
 
 1. [Create a fork](https://help.github.com/articles/fork-a-repo) of the upstream
-   repository at [`cthoyt/curies`](https://github.com/cthoyt/curies)
+   repository
+   at [`biopragmatics/curies`](https://github.com/biopragmatics/curies)
    on your GitHub account (or in one of your organizations)
 2. [Clone your fork](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
    with `git clone https://github.com/<your namespace here>/curies.git`
@@ -19,7 +20,8 @@ model for code contributions. Follow these steps:
 
 ### Merge Model
 
-This repository uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
+This repository
+uses [squash merges](https://docs.github.com/en/github/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-pull-request-commits)
 to group all related commits in a given pull request into a single commit upon
 acceptance and merge into the main branch. This has several benefits:
 
@@ -30,21 +32,21 @@ acceptance and merge into the main branch. This has several benefits:
 
 ### Code Style
 
+This project uses `tox` for running code quality checks. Start by installing
+it with `pip install tox tox-uv`.
+
 This project encourages the use of optional static typing. It
-uses [`mypy`](http://mypy-lang.org/) as a type checker
-and [`sphinx_autodoc_typehints`](https://github.com/agronholm/sphinx-autodoc-typehints)
-to automatically generate documentation based on type hints. You can check if
+uses [`mypy`](http://mypy-lang.org/) as a type checker. You can check if
 your code passes `mypy` with `tox -e mypy`.
 
-This project uses [`black`](https://github.com/psf/black) to automatically
-enforce a consistent code style. You can apply `black` and other pre-configured
-linters with `tox -e lint`.
+This project uses [`ruff`](https://docs.astral.sh/ruff/) to automatically
+enforce a consistent code style. You can apply `ruff format` and other pre-configured
+formatters with `tox -e format`.
 
-This project uses [`flake8`](https://flake8.pycqa.org) and several plugins for
+This project uses [`ruff`](https://docs.astral.sh/ruff/) and several plugins for
 additional checks of documentation style, security issues, good variable
-nomenclature, and more (
-see [`tox.ini`](tox.ini) for a list of flake8 plugins). You can check if your
-code passes `flake8` with `tox -e flake8`.
+nomenclature, and more (see `pyproject.toml` for a list of Ruff plugins). You can check if your
+code passes `ruff check` with `tox -e lint`.
 
 Each of these checks are run on each commit using GitHub Actions as a continuous
 integration service. Passing all of them is required for accepting a
@@ -56,7 +58,7 @@ comment, and we will help you.
 
 Python's builtin `print()` should not be used (except when writing to files),
 it's checked by the
-[`flake8-print`](https://github.com/jbkahn/flake8-print) plugin to `flake8`. If
+[`flake8-print` (T20)](https://docs.astral.sh/ruff/rules/#flake8-print-t20) plugin to `ruff`. If
 you're in a command line setting or `main()` function for a module, you can use
 `click.echo()`. Otherwise, you can use the builtin `logging` module by adding
 `logger = logging.getLogger(__name__)` below the imports at the top of your
@@ -65,8 +67,9 @@ file.
 ### Documentation
 
 All public functions (i.e., not starting with an underscore `_`) must be
-documented using the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
-The [`darglint`](https://github.com/terrencepreilly/darglint) plugin to `flake8`
+documented using
+the [sphinx documentation format](https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html#the-sphinx-docstring-format).
+The [`darglint2`](https://github.com/akaihola/darglint2) tool
 reports on functions that are not fully documented.
 
 This project uses [`sphinx`](https://www.sphinx-doc.org) to automatically build
@@ -78,8 +81,8 @@ build it locally with `tox -e docs`.
 
 Functions in this repository should be unit tested. These can either be written
 using the `unittest` framework in the `tests/` directory or as embedded
-doctests. You can check that the unit tests pass with `tox -e py` and that the
-doctests pass with `tox -e doctests`. These tests are required to pass for
+doctests. You can check that the unit tests pass with `tox -e py`
+and that the doctests pass with `tox -e doctests`. These tests are required to pass for
 accepting a contribution.
 
 ### Syncing your fork
@@ -89,23 +92,25 @@ resolve conflicts against the main branch. After cloning, you should add the
 upstream repository with
 
 ```shell
-$ git remote add cthoyt https://github.com/cthoyt/curies.git
+$ git remote add biopragmatics https://github.com/biopragmatics/curies.git
 ```
 
 Then, you can merge upstream code into your branch. You can also use the GitHub
-UI to do this by following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).
+UI to do this by
+following [this tutorial](https://docs.github.com/en/github/collaborating-with-pull-requests/working-with-forks/syncing-a-fork).
 
 ### Python Version Compatibility
 
 This project aims to support all versions of Python that have not passed their
 end-of-life dates. After end-of-life, the version will be removed from the Trove
-qualifiers in the [`setup.cfg`](setup.cfg) and from the GitHub Actions testing
+qualifiers in the `pyproject.toml` and from the GitHub Actions testing
 configuration.
 
 See https://endoflife.date/python for a timeline of Python release and
 end-of-life dates.
 
-## Acknowledgements 
+## Acknowledgements
 
-These code contribution guidelines are derived from the [cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
+These code contribution guidelines are derived from
+the [cthoyt/cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
 Python package template. They're free to reuse and modify as long as they're properly acknowledged.

codecov.yml → .github/codecov.yml

@@ -1,3 +1,4 @@
+# see https://docs.codecov.com/v4.6/docs/codecov-yaml
 ignore:
   - "src/curies/__main__.py"
   - "src/curies/cli.py"

.github/workflows/cruft.yml

@@ -0,0 +1,79 @@
+# from https://cruft.github.io/cruft/#automating-updates-with-github-actions
+
+name: Update repository with Cruft
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 2 * * 1" # Every Monday at 2am
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - add-paths: .
+            body: Use this to merge the changes to this repository.
+            branch: cruft/update
+            commit-message: "chore: accept new Cruft update"
+            title: New updates detected with Cruft
+          - add-paths: .cruft.json
+            body: Use this to reject the changes in this repository.
+            branch: cruft/reject
+            commit-message: "chore: reject new Cruft update"
+            title: Reject new updates detected with Cruft
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Cruft
+        run: pip3 install cruft
+
+      - name: Check if update is available
+        continue-on-error: false
+        id: check
+        run: |
+          CHANGES=0
+          if [ -f .cruft.json ]; then
+            if ! cruft check; then
+              CHANGES=1
+            fi
+          else
+            echo "No .cruft.json file"
+          fi
+
+          echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
+
+      - name: Run update if available
+        if: steps.check.outputs.has_changes == '1'
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub"
+
+          cruft update --skip-apply-ask --refresh-private-variables
+          git restore --staged .
+
+      - name: Create pull request
+        if: steps.check.outputs.has_changes == '1'
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          add-paths: ${{ matrix.add-paths }}
+          commit-message: ${{ matrix.commit-message }}
+          branch: ${{ matrix.branch }}
+          delete-branch: true
+          branch-suffix: timestamp
+          title: ${{ matrix.title }}
+          body: |
+            This is an autogenerated PR. ${{ matrix.body }}
+
+            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.github/workflows/tests.yml

@@ -19,38 +19,41 @@ jobs:
         python-version: [ "3.12", "3.9" ]
         tox-command: ["manifest", "lint", "pyroma", "mypy"]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+      - name: "Run command"
         run: |
-          pip install tox tox-uv
-      - name: Run command
-        run: tox -e ${{ matrix.tox-command }}
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e ${{ matrix.tox-command }}
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     strategy:
       matrix:
+        # We only test documentation on the latest version
+        # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
+        # a year early, which prompted re-thinking about this.
         python-version: [ "3.12" ]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
       - name: Install dependencies
         run: |
-          pip install tox tox-uv
           sudo apt-get install graphviz
       - name: Check RST conformity with doc8
-        run: tox -e doc8
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e doc8
       - name: Check docstring coverage
-        run: tox -e docstr-coverage
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docstr-coverage
       - name: Check documentation build with Sphinx
-        run: tox -e docs-test
+        run: uvx -p ${{ matrix.python-version }} --with tox-uv tox -e docs-test
   tests:
     name: Tests
     runs-on: ${{ matrix.os }}
@@ -59,18 +62,17 @@ jobs:
         os: [ ubuntu-latest ]
         python-version: [ "3.12", "3.9" ]
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - name: "Install uv"
+        uses: "astral-sh/setup-uv@v3"
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: pip install tox tox-uv
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
       - name: Test with pytest and generate coverage file
         run:
-          tox -e py
+          uvx -p ${{ matrix.python-version }} --with tox-uv tox -e py
       - name: Upload coverage report to codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         if: success()
         with:
           file: coverage.xml

.gitignore

@@ -899,5 +899,3 @@ FodyWeavers.xsd
 # End of https://www.toptal.com/developers/gitignore/api/macos,linux,windows,python,jupyternotebooks,jetbrains,pycharm,vim,emacs,visualstudiocode,visualstudio
 
 scratch/
-*.jnl
-*.jar

.readthedocs.yml

@@ -7,8 +7,10 @@ version: 2
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-20.04
+  apt_packages:
+    - graphviz
   tools:
-    python: "3.9"
+    python: "3.12"
 
 python:
   install:

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Charles Tapley Hoyt
+Copyright (c) 2024 Charles Tapley Hoyt
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -3,17 +3,9 @@ graft tests
 prune scripts
 prune notebooks
 prune tests/.pytest_cache
+prune docs
 
-prune docs/build
-prune docs/source/api
-
-recursive-include docs/source *.py
-recursive-include docs/source *.rst
-recursive-include docs/source *.png
-recursive-include docs/source *.svg
-
-global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle .idea/**
 
 include README.md LICENSE
-exclude tox.ini .flake8 .bumpversion.cfg .readthedocs.yml codecov.yml
-exclude docs/make_schema.py docs/schema.json
+exclude tox.ini .readthedocs.yml .cruft.json