cleanup codebase using pre-commit checks: ruff, codespell (#42)
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| name: Scribl Python package | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - '**.pdf' | |
| - '**.png' | |
| - 'CITATION.cff' | |
| - '.zenodo.json' | |
| - 'paper/**' | |
| - '.github/dependabot.yml' | |
| - '.github/release-drafter.yml' | |
| - '.github/ISSUE_TEMPLATE/**' | |
| - '.github/workflows/release-drafter.yml' | |
| - '.gitattributes' | |
| pull_request: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - '**.pdf' | |
| - '**.png' | |
| - 'CITATION.cff' | |
| - '.zenodo.json' | |
| - 'paper/**' | |
| - '.github/dependabot.yml' | |
| - '.github/release-drafter.yml' | |
| - '.github/ISSUE_TEMPLATE/**' | |
| - '.github/workflows/release-drafter.yml' | |
| - '.gitattributes' | |
| release: | |
| types: | |
| - published | |
| jobs: | |
| skip_publish_zenodo: | |
| name: Non publication, Zenodo skip | |
| runs-on: ubuntu-latest | |
| # FIXME: this is the default action, the logical inverse of the | |
| # below "if" in publish_zenodo: a bit hacky, but it works | |
| if: (github.event_name == 'release' && github.event.action == 'published' && github.event.release.prerelease == false) == false | |
| steps: | |
| - name: Skip Zenodo step unless publishing release | |
| run: | | |
| echo "Not a publication release, skipping Zenodo" | |
| echo "github.ref: ${{ toJson(github.ref) }}" | |
| echo "github.event_name: ${{ toJson(github.event_name) }}" | |
| echo "github.event.action: ${{ toJson(github.event.action) }}" | |
| publish_zenodo: | |
| name: Production release, Zenodo publication | |
| runs-on: ubuntu-latest | |
| # "else" we *are* publishing something, only works for non-pre-releases on the main branch | |
| # if: false | |
| if: github.event.release.target_commitish == 'main' && github.event_name == 'release' && github.event.action == 'published' && github.event.release.prerelease == false | |
| steps: | |
| - name: Checkout the contents of your repository | |
| uses: actions/checkout@v4 | |
| - name: Upsert the version and related ids in the metadata in .zenodo.json | |
| run: | | |
| echo "GITHUB_REF_NAME = $GITHUB_REF_NAME | GITHUB_REF = $GITHUB_REF | GITHUB_EVENT_PATH = $GITHUB_EVENT_PATH" | |
| echo "github.event.release.target_commitish = ${{ github.event.release.target_commitish }}" | |
| # convert semver to Python-style version | |
| VERSION_PYTHON_STYLE=$(GITHUB_REF_NAME=$GITHUB_REF_NAME python -c 'import os; from packaging import version; print(str(version.Version(os.getenv("GITHUB_REF_NAME"))))') | |
| echo "VERSION_PYTHON_STYLE = $VERSION_PYTHON_STYLE" | |
| # cp .zenodo.json .zenodo.orig.json | |
| # update the 'related_identifiers' to use exact tree and pypi packaage | |
| cat .zenodo.json | jq "(.related_identifiers[] | (select (.relation == \"isSourceOf\" and .resource_type == \"software\")) | select (.identifier | startswith(\"https://pypi.org/project/scribl\")).identifier) |= \"https://pypi.org/project/scribl/$VERSION_PYTHON_STYLE\"" | jq "(.related_identifiers[] | (select (.relation == \"isSupplementTo\" and .resource_type == \"software\")) | select (.identifier | startswith(\"https://github.com/amberbiology/scribl\")).identifier) |= \"https://github.com/amberbiology/scribl/tree/$GITHUB_REF_NAME\"" > .zenodo.mod.json | |
| # update the version number | |
| echo "{\"version\": \"$GITHUB_REF_NAME\"}" | cat .zenodo.mod.json - | jq -s add > .zenodo.json | |
| # debugging only | |
| cat .zenodo.json | |
| rm .zenodo.mod.json | |
| - name: Upsert the version in the metadata in CITATION.cff | |
| run: | | |
| yq -i ".version = \"$GITHUB_REF_NAME\"" CITATION.cff | |
| - name: Push changes back to repo files | |
| run: | | |
| git fetch origin | |
| git config --global user.name "ci-scribl" | |
| git config --global user.email "username@users.noreply.github.com" | |
| git checkout -b $GITHUB_REF_NAME-with-upserting-changes-pre-upload | |
| git add .zenodo.json CITATION.cff | |
| git commit -m "Upserted version into CITATION.cff and into .zenodo.json" | |
| git checkout ${{ github.event.release.target_commitish }} | |
| git merge $GITHUB_REF_NAME-with-upserting-changes-pre-upload | |
| git push origin ${{ github.event.release.target_commitish }} | |
| # FIXME: removing files marked with 'export-ignore' 'set' in .gitattributes | |
| # before zenodraft creates the zipball using https://stackoverflow.com/a/30573319 | |
| # to ensure that we handle filenames with potential ':' or newlines | |
| git ls-files -z|git check-attr --stdin -z export-ignore |sed -zne 'x;n;n;s/^set$//;t print;b;:print;x;p'|xargs --null rm | |
| # FIXME: need to also remove orphaned empty directories resulting from above | |
| find . -empty -type d -delete | |
| - name: Create a draft snapshot of your repository contents as a new | |
| version in test collection on Zenodo using metadata | |
| from repository file .zenodo.json | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODO_SCRIBL_ACCESS_TOKEN }} | |
| uses: zenodraft/action@0.13.3 | |
| # uses: alexlancaster/zenodraft-action@0.10.2 | |
| with: | |
| concept: 12728362 | |
| metadata: .zenodo.json | |
| publish: false | |
| sandbox: false | |
| compression: zip | |
| upsert-doi: true | |
| upsert-location: doi | |
| verbose: true | |
| ci_build: | |
| needs: [publish_zenodo, skip_publish_zenodo] | |
| if: always() && !cancelled() && !failure() | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| allow-prereleases: true | |
| - name: Build wheel and sdist | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build flake8 pytest | |
| python -m build | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| # force use of bash on all platforms, so wildcard expansion works on Windows | |
| # (otherwise would use powershell on Windows, which fails) | |
| shell: bash | |
| run: | | |
| pip install --only-binary ":all:" --no-binary sgmllib3k,bibtexparser dist/scribl*.whl | |
| pytest -v tests | |
| # skip uploading separate files for each CI run (need just one wheel/dist done in 'dist' job, below) | |
| #- name: Upload artifact | |
| # | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: scribl-wheels-${{ matrix.os }}-python-${{ matrix.python-version }} | |
| # path: dist/*.whl | |
| dist: | |
| name: Create wheel and sdist for distribution | |
| needs: [ci_build] # make sure it passes the CI first | |
| runs-on: ubuntu-latest | |
| if: always() && !cancelled() && !failure() | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: hynek/build-and-inspect-python-package@v2 | |
| upload_test_pypi: | |
| name: Upload to Test_PyPI | |
| needs: [dist] | |
| runs-on: ubuntu-latest | |
| environment: test_pypi | |
| permissions: | |
| id-token: write | |
| # drop requirement of 'main', release to test_pypi to test releases | |
| #if: false | |
| if: github.event_name == 'release' && github.event.action == 'published' && always() && !cancelled() && !failure() | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| merge-multiple: true | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| repository-url: https://test.pypi.org/legacy/ | |
| upload_pypi: | |
| name: Upload to PyPI | |
| needs: [dist] | |
| runs-on: ubuntu-latest | |
| environment: pypi | |
| permissions: | |
| id-token: write | |
| if: github.event.release.target_commitish == 'main' && github.event_name == 'release' && github.event.action == 'published' && always() && !cancelled() && !failure() | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| merge-multiple: true | |
| - name: Publish package distributions to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 |