Update cookiecutter, adopt pyproject.toml

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/tjs/git/cookiecutter-pypackage",
-  "commit": "2fc25aaaf59ce346529c90c032c34baa30a45def",
+  "commit": "e67ba8180e050ffd1c29e38cf2ad3929004fdd8f",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -14,6 +14,7 @@
       "version": "0.7.20-beta",
       "use_pytest": "y",
       "use_black": "y",
+      "use_conda": "y",
       "add_pyup_badge": "n",
       "make_docs": "y",
       "command_line_interface": "Click",

.flake8

@@ -0,0 +1,32 @@
+[flake8]
+exclude =
+	.eggs,
+	.git,
+	build,
+	docs/conf.py,
+	tests
+ignore =
+	AZ100,
+	AZ200,
+	AZ300,
+	C,
+	D,
+	E,
+	F,
+	W503
+	W504
+per-file-ignores =
+	tests/*:E402
+rst-roles =
+	doc,
+	mod,
+	py:attr,
+	py:attribute,
+	py:class,
+	py:const,
+	py:data,
+	py:func,
+	py:meth,
+	py:mod,
+	py:obj,
+	py:ref

.github/labeler.yml

@@ -8,6 +8,7 @@
 CI:
   - .cruft.json
   - .editorconfig
+  - .flake8
   - .gitignore
   - .pre-commit-config.yaml
   - .readthedocs.yml

.github/workflows/actions-versions-updater.yml

@@ -0,0 +1,24 @@
+name: GitHub Actions Version Updater
+
+on:
+  schedule:
+    # 12:00 AM on the first of every month
+    - cron:  '0 0 1 * *'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        with:
+          # This requires a personal access token with the privileges to push directly to `main`
+          token: ${{ secrets.WORKFLOW_TOKEN }}
+          persist-credentials: true
+      - name: Run GitHub Actions Version Updater
+        uses: saadmk11/[email protected]
+        with:
+          token: ${{ secrets.WORKFLOW_TOKEN }}
+          committer_email: 'bumpversion[bot]@ouranos.ca'
+          committer_username: 'update-github-actions[bot]'
+          pull_request_title: '[bot] Update GitHub Action Versions'

.github/workflows/bump-version.yml

@@ -7,26 +7,30 @@ on:
     paths-ignore:
       - .cruft.json
       - .editorconfig
+      - .flake8
       - .github/**.yml
       - .gitignore
       - .gitlab-ci.yml
       - .gitmodules
       - .pre-commit-config.yaml
+      - .secrets.baseline
       - .yamllint.yaml
       - AUTHORS.rst
+      - CHANGES.rst
       - CONTRIBUTING.rst
-      - docs/notebooks
+      - MANIFEST.in
+      - Makefile
+      - conda/xscen/*.yaml
       - docs/*.py
       - docs/*.rst
+      - docs/notebooks
       - environment-dev.yml
       - environment.yml
-      - HISTORY.rst
-      - Makefile
-      - MANIFEST.in
-      - requirements_upstream.txt
+      - pyproject.toml
       - setup.cfg
       - setup.py
-      - tests/**.py
+      - templates
+      - tests/*.py
       - tox.ini
       - xscen/__init__.py
 
@@ -48,9 +52,9 @@ jobs:
         run: echo "current_version=$(grep -E '__version__'  xscen/__init__.py | cut -d ' ' -f3)"
       - name: Bump Patch Version
         run: |
-          python -m pip install bump2version
+          python -m pip install bump-my-version
           echo "Bumping version"
-          python -m bump2version patch
+          python -m bump-my-version bump patch
           echo "new_version=$(grep -E '__version__'  xscen/__init__.py | cut -d ' ' -f3)"
       - name: Push Changes
         uses: ad-m/github-push-action@master

.github/workflows/main.yml

@@ -5,19 +5,22 @@ on:
     branches:
       - main
     paths-ignore:
-      - HISTORY.rst
+      - CHANGES.rst
+      - README.rst
+      - pyproject.toml
       - setup.cfg
       - setup.py
       - xscen/__init__.py
   pull_request:
 
 jobs:
-  black:
-    name: Code Style Compliance
+  lint:
+    name: Lint (Python${{ matrix.python-version }})
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version:
+          - "3.x"
     steps:
       - name: Cancel previous runs
         uses: styfle/[email protected]
@@ -26,17 +29,17 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.x"
       - name: Install tox
         run: |
           python -m pip install tox
       - name: Run linting suite
         run: |
-          python -m tox -e black
+          python -m tox -e lint
 
-  testing-tox:
+  test-pypi:
     name: Test with Python${{ matrix.python-version }} (PyPI/tox)
-    needs: black
+    needs: lint
     runs-on: ubuntu-latest
     env:
       COVERALLS_PARALLEL: true
@@ -100,9 +103,9 @@ jobs:
 #          COVERALLS_PARALLEL: true
 #          COVERALLS_SERVICE_NAME: github
 
-  testing-conda:
+  test-conda:
     name: Test with Python${{ matrix.python-version }} (Anaconda)
-    needs: black
+    needs: lint
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -127,14 +130,14 @@ jobs:
       - name: Compile catalogs and install xscen
         run: |
           make translate
-          python -m pip install --no-deps --editable .
+          python -m pip install --no-deps .
       - name: Check versions
         run: |
           conda list
           python -m pip check || true
       - name: Test with pytest
         run: |
-          python -m pytest tests
+          python -m pytest --cov xscen
       - name: Report coverage
         run: |
           python -m coveralls
@@ -146,15 +149,15 @@ jobs:
 
   finish:
     needs:
-      - testing-tox
-      - testing-conda
+      - test-pypi
+      - test-conda
     runs-on: ubuntu-latest
     container: python:3-slim
     steps:
       - name: Coveralls Finished
         run: |
-          pip install --upgrade coveralls
-          coveralls --finish
+          python -m pip install --upgrade coveralls
+          python -m coveralls --finish
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_SERVICE_NAME: github

.github/workflows/publish-pypi.yml

@@ -9,20 +9,22 @@ jobs:
   build-n-publish-pypi:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
+    environment: production
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python3
         uses: actions/setup-python@v4
         with:
           python-version: "3.x"
       - name: Install packaging libraries
         run: |
-          python -m pip install build wheel
+          python -m pip install babel build setuptools wheel
       - name: Build a binary wheel and a source tarball
         run: |
+          make translate
           python -m build --sdist --wheel
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tag-testpypi.yml

@@ -3,28 +3,49 @@ name: "Publish Python 🐍 distributions 📦 to TestPyPI"
 on:
   push:
     tags:
-      - '*'
+      - 'v*.*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
 jobs:
-  build-n-publish-testpypi:
+  release:
+    name: Create Release from tag
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v') && endsWith(github.ref, '.0')
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Create Release
+        uses: softprops/action-gh-release@v1
+        env:
+          # This token is provided by Actions, you do not need to create your own token
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          name: Release ${{ github.ref }}
+          draft: true
+          prerelease: false
+
+  deploy-testpypi:
     name: Build and publish Python 🐍 distributions 📦 to TestPyPI
     runs-on: ubuntu-latest
+    environment: staging
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python3
         uses: actions/setup-python@v4
         with:
           python-version: "3.x"
       - name: Install packaging libraries
         run: |
-          python -m pip install build wheel
+          python -m pip install babel build setuptools wheel
       - name: Build a binary wheel and a source tarball
         run: |
+          make translate
           python -m build --sdist --wheel
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
           skip_existing: true

.pre-commit-config.yaml

@@ -20,35 +20,38 @@ repos:
       - id: pretty-format-json
         args: [ '--autofix', '--no-ensure-ascii', '--no-sort-keys' ]
         exclude: .ipynb
+      - id: check-toml
       - id: check-yaml
         args: [ '--allow-multiple-documents' ]
         exclude: conda/xscen/meta.yaml
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
       - id: rst-inline-touching-normal
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.11.0
     hooks:
       - id: black
         exclude: ^docs/
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [ 'flake8-rst-docstrings' ]
-        args: [ '--config=setup.cfg' ]
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
-        args: [ '--settings-file=setup.cfg' ]
         exclude: ^docs/
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.4
     hooks:
-      - id: pydocstyle
-        args: [ '--config=setup.cfg' ]
+      - id: ruff
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [ 'flake8-alphabetize', 'flake8-rst-docstrings' ]
+        args: [ '--config=.flake8' ]
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
@@ -70,7 +73,6 @@ repos:
         args: [ '--target-version=py39' ]
         additional_dependencies: [ 'black==23.11.0' ]
       - id: nbqa-isort
-        args: [ "--settings-file=setup.cfg" ]
         additional_dependencies: [ 'isort==5.12.0' ]
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
@@ -83,11 +85,11 @@ repos:
       - id: detect-secrets
         exclude: .cruft.json|docs/notebooks
         args: [ '--baseline=.secrets.baseline' ]
-#  Currently commented because Git needs to be updated on our work environment.
-#  - repo: https://github.com/mgedmin/check-manifest
-#    rev: "0.49"
-#    hooks:
-#      - id: check-manifest
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.27.1
+    hooks:
+      - id: check-github-workflows
+      - id: check-readthedocs
   - repo: meta
     hooks:
       - id: check-hooks-apply