Update to 5 loci to allow tests to pass #1462
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| name: Build PyPop | |
| 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' | |
| - '.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' | |
| - '.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 == \"isDerivedFrom\" 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 "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 | |
| # git tag -d $GITHUB_REF_NAME | |
| # git push --follow-tags origin :$GITHUB_REF | |
| # git tag $GITHUB_REF_NAME | |
| # git push origin $GITHUB_REF | |
| # git ls-remote origin $GITHUB_REF | |
| - 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/action@0.10.0 | |
| uses: alexlancaster/zenodraft-action@0.10.1 | |
| with: | |
| collection: 10080667 | |
| metadata: .zenodo.json | |
| publish: false | |
| sandbox: false | |
| compression: zip | |
| upsert-doi: true | |
| upsert-location: doi | |
| verbose: true | |
| # | |
| # FIXME: disabled the rest of these steps (already done by zenodraft) | |
| # | |
| - name: Get existing release | |
| if: false | |
| id: get_existing_release | |
| uses: cardinalby/git-get-release-action@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| with: | |
| releaseId: ${{ github.event.release.id }} | |
| - name: Delete old release | |
| if: false | |
| uses: liudonghua123/delete-release-action@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| with: | |
| release_id: ${{ github.event.release.id }} | |
| - name: Recreate release with new tag | |
| if: false | |
| id: recreate_release | |
| uses: joutvhu/create-release@v1 | |
| with: | |
| tag_name: ${{ github.event.release.tag_name }} | |
| name: ${{ steps.get_existing_release.outputs.name }} | |
| body: ${{ steps.get_existing_release.outputs.body }} | |
| # FIXME: have to set these both to false, because not copied | |
| # from the original release properly | |
| # draft: ${{ steps.get_existing_release.outputs.draft }} | |
| # prerelease: ${{ steps.get_existing_release.outputs.draft }} | |
| draft: false | |
| prerelease: false | |
| target_commitish: ${{ steps.get_existing_release.outputs.target_commitish }} | |
| on_release_exists: update | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # GITHUB_TOKEN: ${{ secrets.PYPOP_RELEASE_TOKEN }} | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.os }} | |
| # 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] | |
| # 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: | |
| matrix: | |
| os: [ubuntu-20.04, macos-11, windows-2019] | |
| 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: Build and test wheels | |
| uses: pypa/cibuildwheel@v2.16.2 | |
| with: | |
| package-dir: . | |
| output-dir: wheelhouse | |
| config-file: "{package}/pyproject.toml" | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| 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@v3 | |
| with: | |
| 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@v3 | |
| with: | |
| # unpacks default artifact into dist/ | |
| # if `name: artifact` is omitted, the action will create extra parent dir | |
| name: artifact | |
| path: dist | |
| - uses: softprops/action-gh-release@v1 | |
| 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@v3 | |
| with: | |
| # unpacks default artifact into dist/ | |
| # if `name: artifact` is omitted, the action will create extra parent dir | |
| name: artifact | |
| path: dist | |
| - 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@v3 | |
| with: | |
| # unpacks default artifact into dist/ | |
| # if `name: artifact` is omitted, the action will create extra parent dir | |
| name: artifact | |
| path: dist | |
| - name: Publish package distributions to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 |