fix(study_locus_valiation): ensure the the transQtlColumn is missing … #85
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| name: Release | |
| "on": | |
| push: | |
| branches: ["main", "release/**", "dev"] | |
| concurrency: | |
| group: deploy | |
| cancel-in-progress: false # prevent hickups with semantic-release | |
| env: | |
| PYTHON_VERSION_DEFAULT: "3.11.11" | |
| jobs: | |
| release: | |
| runs-on: ubuntu-latest | |
| concurrency: release | |
| outputs: | |
| released: ${{ steps.semrelease.outputs.released }} | |
| permissions: | |
| # NOTE: this enables trusted publishing. | |
| # See https://github.com/pypa/gh-action-pypi-publish/tree/release/v1#trusted-publishing | |
| # and https://blog.pypi.org/posts/2023-04-20-introducing-trusted-publishers/ | |
| id-token: write | |
| contents: write | |
| steps: | |
| # NOTE: commits using GITHUB_TOKEN does not trigger workflows | |
| - uses: actions/create-github-app-token@v1 | |
| id: trigger-token | |
| with: | |
| app-id: ${{ vars.TRIGGER_WORKFLOW_GH_APP_ID}} | |
| private-key: ${{ secrets.TRIGGER_WORKFLOW_GH_APP_KEY }} | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| repository: opentargets/gentropy | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| persist-credentials: false | |
| - name: Python Semantic Release | |
| id: semrelease | |
| uses: python-semantic-release/python-semantic-release@v9.16.1 | |
| with: | |
| github_token: ${{ steps.trigger-token.outputs.token }} | |
| - name: Publish package to GitHub Release | |
| uses: python-semantic-release/upload-to-gh-release@main | |
| # NOTE: semrelease output is a string, so we need to compare it to a string | |
| if: steps.semrelease.outputs.released == 'true' | |
| with: | |
| # NOTE: allow to start the workflow when push action on tag gets executed | |
| # requires using GH_APP to authenitcate, otherwise push authorised with | |
| # the GITHUB_TOKEN does not trigger the tag artifact workflow. | |
| # see https://github.com/actions/create-github-app-token | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| tag: ${{ steps.semrelease.outputs.tag }} | |
| - name: Store the distribution packages | |
| if: steps.semrelease.outputs.released == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: python-package-distributions | |
| path: dist/ | |
| publish-to-pypi: | |
| needs: release | |
| name: Publish 📦 in PyPI | |
| if: github.ref == 'refs/heads/main' && needs.release.outputs.released == 'true' | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: pypi | |
| url: https://pypi.org/p/gentropy | |
| permissions: | |
| id-token: write # IMPORTANT: mandatory for trusted publishing | |
| steps: | |
| - name: Download all the dists | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: python-package-distributions | |
| path: dist/ | |
| - name: Publish distribution 📦 to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| publish-to-testpypi: | |
| name: Publish 📦 in TestPyPI | |
| needs: release | |
| if: github.ref == 'refs/heads/main' && needs.release.outputs.released == 'true' | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: testpypi | |
| url: https://test.pypi.org/p/gentropy | |
| permissions: | |
| id-token: write # IMPORTANT: mandatory for trusted publishing | |
| steps: | |
| - name: Download all the dists | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: python-package-distributions | |
| path: dist/ | |
| - name: Publish distribution 📦 to TestPyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| repository-url: https://test.pypi.org/legacy/ | |
| documentation: | |
| needs: release | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/main' && needs.release.outputs.released == 'true' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION_DEFAULT }} | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v5 | |
| - name: Load cached venv | |
| id: cached-dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: .venv | |
| key: | | |
| venv-${{ runner.os }}-\ | |
| ${{ env.PYTHON_VERSION_DEFAULT }}-\ | |
| ${{ hashFiles('**/uv.lock') }} | |
| - name: Install dependencies | |
| if: steps.cached-dependencies.outputs.cache-hit != 'true' | |
| run: uv sync --group docs | |
| - name: Publish docs | |
| run: uv run mkdocs gh-deploy --force |