Merge remote-tracking branch 'origin/main' into replace_pval_extensio… #2366
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| name: Build PyPop | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }} | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - 'CITATION.cff' | |
| - '.zenodo.json' | |
| - 'website/**' | |
| - '.github/dependabot.yml' | |
| - '.github/release-drafter.yml' | |
| - '.github/ISSUE_TEMPLATE/**' | |
| - '.github/workflows/documentation.yaml' | |
| - '.github/workflows/buildjet_arm64.yml' | |
| - '.github/workflows/release-drafter.yml' | |
| - '.github/workflows/codeql.yml' | |
| - '.gitattributes' | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - 'CITATION.cff' | |
| - '.zenodo.json' | |
| - 'website/**' | |
| - '.github/dependabot.yml' | |
| - '.github/release-drafter.yml' | |
| - '.github/ISSUE_TEMPLATE/**' | |
| - '.github/workflows/documentation.yaml' | |
| - '.github/workflows/buildjet_arm64.yml' | |
| - '.github/workflows/release-drafter.yml' | |
| - '.github/workflows/codeql.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: 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 = $VERSION_PYTHON_STYLE" | |
| # cp .zenodo.json .zenodo.orig.json | |
| # update the 'related_identifiers' to use exact tree and pypi packaage | |
| cat .zenodo.json | jq "(.related_identifiers[] | (select (.relation == \"isSourceOf\" and .resource_type == \"software\")) | select (.identifier | startswith(\"https://pypi.org/project/pypop-genomics\")).identifier) |= \"https://pypi.org/project/pypop-genomics/$VERSION_PYTHON_STYLE\"" | jq "(.related_identifiers[] | (select (.relation == \"isSupplementTo\" and .resource_type == \"software\")) | select (.identifier | startswith(\"https://github.com/alexlancaster/pypop\")).identifier) |= \"https://github.com/alexlancaster/pypop/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-pypop" | |
| git config --global user.email "[email protected]" | |
| 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_ACCESS_TOKEN }} | |
| uses: zenodraft/[email protected] | |
| # uses: alexlancaster/[email protected] | |
| with: | |
| concept: 10080667 | |
| metadata: .zenodo.json | |
| publish: false | |
| sandbox: false | |
| compression: zip | |
| upsert-doi: true | |
| upsert-location: doi | |
| verbose: true | |
| generate-wheels-matrix: | |
| # Create a matrix of all architectures & versions to build. | |
| # This enables the next step to run cibuildwheel in parallel. | |
| # From https://iscinumpy.dev/post/cibuildwheel-2-10-0/#only-210 | |
| name: Generate wheels matrix | |
| runs-on: ubuntu-latest | |
| outputs: | |
| include: ${{ steps.set-matrix.outputs.include }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install cibuildwheel | |
| # Nb. keep cibuildwheel version pin consistent with job below | |
| run: pipx install cibuildwheel==2.21.3 | |
| - id: set-matrix | |
| run: | | |
| echo "CI_ONLY" $CI_ONLY | |
| if [ "$CI_ONLY" == "true" ]; then | |
| MATRIX="[{'only':'cp313-manylinux_x86_64','os':'ubuntu-20.04'},{'only':'cp313-win_amd64','os':'windows-2019'}, {'only':'cp313-macosx_x86_64','os':'macos-13'}, {'only':'cp313-macosx_arm64','os':'macos-14'}]" | |
| else | |
| MATRIX=$( | |
| { | |
| cibuildwheel --print-build-identifiers --platform linux \ | |
| | jq -nRc '{"only": inputs, "os": "ubuntu-20.04"}' \ | |
| && cibuildwheel --print-build-identifiers --platform macos --archs x86_64 \ | |
| | jq -nRc '{"only": inputs, "os": "macos-13"}' \ | |
| && cibuildwheel --print-build-identifiers --platform macos --archs arm64 \ | |
| | jq -nRc '{"only": inputs, "os": "macos-14"}' \ | |
| && cibuildwheel --print-build-identifiers --platform windows \ | |
| | jq -nRc '{"only": inputs, "os": "windows-2019"}' | |
| } | jq -sc | |
| ) | |
| fi | |
| echo "include=$MATRIX" >> $GITHUB_OUTPUT | |
| echo "platform matrix:" $MATRIX | |
| env: | |
| # only generate all wheels on releases, pull requests or commits to the main branch | |
| # otherwise just generate a test wheel Python 3.12 for 4 platform | |
| CI_ONLY: ${{ github.event_name != 'release' && github.event_name != 'pull_request' && github.ref_name != 'main' && github.event_name != 'workflow_dispatch' }} | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.only }} | |
| # depend on zenodo, to make sure updated CITATION.cff gets into builds | |
| # this only results in changes upon production releases | |
| needs: [publish_zenodo, skip_publish_zenodo, generate-wheels-matrix] | |
| # trying solution here: https://github.com/actions/runner/issues/491#issuecomment-1507495166 | |
| # so that it works if either job in "needs" completes | |
| if: always() && !cancelled() && !failure() | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # FIXME: if on a release, use the tag name, not original SHA because it might be changed (somewhat hacky) | |
| ref: ${{ (github.event_name == 'release' && github.event.action == 'published') && github.ref_name || '' }} | |
| - name: Set up QEMU | |
| if: runner.os == 'Linux' | |
| uses: docker/setup-qemu-action@v3 | |
| with: | |
| platforms: all | |
| - name: Install a recent stable Python to handle Python deps | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Query version with setuptools_scm | |
| id: version | |
| shell: bash | |
| run: | | |
| python -m pip install setuptools_scm | |
| VERSION=$(python -c "from src.PyPop import __version_scheme__; import setuptools_scm; print(setuptools_scm.get_version(version_scheme=__version_scheme__))") | |
| echo "VERSION=${VERSION}" | |
| echo "VERSION=${VERSION}" >> $GITHUB_ENV | |
| - name: Install toml and remove cffconvert from pyproject.toml | |
| run: | | |
| python -m pip install toml | |
| python -c " | |
| import toml | |
| with open('pyproject.toml', 'r') as f: | |
| config = toml.load(f) | |
| if 'build-system' in config and 'requires' in config['build-system']: | |
| config['build-system']['requires'] = [ | |
| dep for dep in config['build-system']['requires'] if 'cffconvert' not in dep.lower() | |
| ] | |
| with open('pyproject.toml', 'w') as f: | |
| toml.dump(config, f) | |
| " | |
| - name: Generate citation formats | |
| run: | | |
| python --version | |
| python -m pip install git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert | |
| python src/PyPop/citation.py | |
| - name: Build and test wheels | |
| uses: pypa/[email protected] | |
| env: | |
| # FIXME: only run the slow tests when doing regular pushes, or manual - not for PRs | |
| CIBW_TEST_COMMAND: "pytest -v {package}/tests ${{ (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && '--runslow' || '' }}" | |
| SETUPTOOLS_SCM_PRETEND_VERSION: ${{ env.VERSION }} | |
| CIBW_ENVIRONMENT_PASS_LINUX: SETUPTOOLS_SCM_PRETEND_VERSION | |
| with: | |
| only: ${{ matrix.only }} | |
| package-dir: . | |
| output-dir: wheelhouse | |
| config-file: "{package}/pyproject.toml" | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-${{ matrix.only }} | |
| path: ./wheelhouse/*.whl | |
| # path: ./wheelhouse/* use if more than wheels are wanted | |
| build_sdist: | |
| name: Build source distribution | |
| # depend on zenodo, to make sure updated CITATION.cff gets into builds | |
| needs: [publish_zenodo, skip_publish_zenodo] | |
| if: always() && !cancelled() && !failure() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: # FIXME: if on a release, use the tag name, not original SHA because it might be changed (somewhat hacky) | |
| ref: ${{ (github.event_name == 'release' && github.event.action == 'published') && github.ref_name || '' }} | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/*.tar.gz | |
| upload_gh_release: | |
| name: Upload binary wheels and sdist to GH release page | |
| needs: [build_wheels, build_sdist] | |
| runs-on: ubuntu-latest | |
| # alternatively, to publish when a GitHub Release is created, use the following rule: | |
| if: github.event_name == 'release' && github.event.action == 'published' && always() && !cancelled() && !failure() | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| # unpacks default artifact into dist/ | |
| path: dist | |
| merge-multiple: true | |
| - uses: softprops/action-gh-release@v2 | |
| name: Uploading binaries to release page | |
| with: | |
| files: dist/* | |
| upload_test_pypi: | |
| name: Upload to Test_PyPI | |
| needs: [build_wheels, build_sdist] | |
| runs-on: ubuntu-latest | |
| environment: test_pypi | |
| permissions: | |
| id-token: write | |
| # drop requirement of 'main', release to test_pypi to test releases | |
| if: github.event_name == 'release' && github.event.action == 'published' && always() && !cancelled() && !failure() | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| # unpacks default artifact into dist/ | |
| 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: [build_wheels, build_sdist] | |
| 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: | |
| # unpacks default artifact into dist/ | |
| path: dist | |
| merge-multiple: true | |
| - name: Publish package distributions to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 |