ci(dependabot): enable auto poetry updates #364
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Integration Workflow | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| tags: ["*"] | |
| schedule: | |
| # runs every Wednesday at 7 AM UTC | |
| - cron: "0 7 * * 3" | |
| workflow_dispatch: | |
| inputs: | |
| pytest_addopts: | |
| description: Extra options for pytest; use -vv for full details; see | |
| https://docs.pytest.org/en/latest/example/simple.html#how-to-change-command-line-options-defaults | |
| required: false | |
| default: "" | |
| env: | |
| LANG: "en_US.utf-8" | |
| LC_ALL: "en_US.utf-8" | |
| PIP_CACHE_DIR: ${{ github.workspace }}/.cache/pip | |
| POETRY_CACHE_DIR: ${{ github.workspace }}/.cache/pypoetry | |
| POETRY_VIRTUALENVS_IN_PROJECT: "true" | |
| PRE_COMMIT_HOME: ${{ github.workspace }}/.cache/pre-commit | |
| PYTEST_ADDOPTS: ${{ github.event.inputs.pytest_addopts }} | |
| PYTHONIOENCODING: "UTF-8" | |
| TARGET_PYTHON_VERSION: "3.9" | |
| jobs: | |
| quality-test: | |
| # This job is used to run pre-commit checks to ensure that all files are | |
| # are formatted correctly. | |
| name: Pre-commit checks | |
| # Runs pre-commit checks on all files | |
| # This job doesn't fail fast to ensure that feedback on function is still provided | |
| strategy: | |
| fail-fast: false | |
| runs-on: ubuntu-22.04 | |
| if: github.event_name != 'schedule' | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| # Full history required for branch-based pre-commit checks | |
| fetch-depth: 0 | |
| - name: Setup python, and check pre-commit cache | |
| uses: ./.github/actions/setup-env | |
| with: | |
| python-version: ${{ env.TARGET_PYTHON_VERSION }} | |
| cache-pre-commit: true | |
| cache-venv: false | |
| setup-poetry: false | |
| install-deps: false | |
| - name: Run pre-commit checks on all files | |
| uses: pre-commit/[email protected] | |
| with: | |
| extra_args: --all-files | |
| python-type-checks: | |
| # This job is used to check Python types | |
| name: Python type checks | |
| # Avoid fail-fast to retain output | |
| strategy: | |
| fail-fast: false | |
| runs-on: ubuntu-22.04 | |
| if: github.event_name != 'schedule' | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Setup python, and check pre-commit cache | |
| uses: ./.github/actions/setup-env | |
| with: | |
| python-version: ${{ env.TARGET_PYTHON_VERSION }} | |
| cache-pre-commit: false | |
| cache-venv: true | |
| setup-poetry: true | |
| install-deps: true | |
| - name: Run mypy | |
| run: | | |
| poetry run mypy . | |
| integration-test: | |
| name: Pytest (Python ${{ matrix.python-version }} on ${{ matrix.os }}) | |
| # Runs pytest on all tested versions of python and OSes | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - macos-13 | |
| - ubuntu-22.04 | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| OS: ${{ matrix.os }} | |
| # This is needed to avoid a warning from SQLAlchemy | |
| # https://sqlalche.me/e/b8d9 | |
| # We can remove this once we upgrade to SQLAlchemy >= 2.0 | |
| SQLALCHEMY_SILENCE_UBER_WARNING: "1" | |
| if: github.event_name != 'schedule' | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Setup python, and load cache | |
| uses: ./.github/actions/setup-env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache-pre-commit: false | |
| cache-venv: true | |
| setup-poetry: true | |
| install-deps: true | |
| - name: Run pytest and generate coverage report | |
| # For the target version and ubuntu, run pytest and generate coverage report | |
| if: (matrix.os == 'ubuntu-22.04') && (matrix.python-version == env.TARGET_PYTHON_VERSION) | |
| run: poetry run pytest --cov=./ --cov-report=xml ${{ github.event.inputs.pytest_addopts }} | |
| - name: Upload coverage to Codecov | |
| # For the target version and ubuntu, upload coverage to Codecov | |
| if: (matrix.os == 'ubuntu-22.04') && (matrix.python-version == env.TARGET_PYTHON_VERSION ) | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python-version }} | |
| with: | |
| file: ./coverage.xml | |
| files: ./coverage1.xml,./coverage2.xml | |
| directory: ./coverage/reports/ | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: true | |
| flags: unittests | |
| name: pycytominer | |
| # Adds codecov token. See the link below for more information: | |
| # https://docs.codecov.com/docs/adding-the-codecov-token | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Run pytest | |
| # For every other version and/or OS, run pytest without coverage | |
| if: (matrix.os != 'ubuntu-22.04') || (matrix.python-version != env.TARGET_PYTHON_VERSION ) | |
| run: poetry run pytest ${{ github.event.inputs.pytest_addopts }} | |
| build: | |
| name: Build versioned package | |
| # This job is used to build the package and upload the artifacts to GitHub Actions workflow results. | |
| # See https://github.com/actions/upload-artifact?tab=readme-ov-file#where-does-the-upload-go | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| version: ${{ steps.get_version.outputs.version }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup python, and load cache | |
| uses: ./.github/actions/setup-env | |
| with: | |
| python-version: ${{ env.TARGET_PYTHON_VERSION }} | |
| cache-pre-commit: false | |
| cache-venv: true | |
| setup-poetry: true | |
| install-deps: true | |
| - name: Build | |
| run: poetry build | |
| - name: Get pycytominer version | |
| id: get_version | |
| run: | | |
| echo "version=$(poetry version | cut -d' ' -f2 )" >> "$GITHUB_OUTPUT" | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheel | |
| path: dist/*.whl | |
| if-no-files-found: error | |
| retention-days: 90 | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/*.tar.gz | |
| if-no-files-found: error | |
| retention-days: 90 | |
| docker-image-test-and-push: | |
| runs-on: ubuntu-22.04 | |
| # set a dependency sequence to occur after build job completion | |
| needs: build | |
| env: | |
| version: ${{ needs.build.outputs.version }} | |
| sdist_filename: pycytominer-${{ needs.build.outputs.version}}.tar.gz | |
| sdist_extracted_name: pycytominer-${{ needs.build.outputs.version}} | |
| steps: | |
| # checks out selected files for docker image build testing | |
| - name: Checkout selected files | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: | | |
| build/docker/Dockerfile | |
| tests | |
| sparse-checkout-cone-mode: false | |
| - name: Download sdist artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: sdist | |
| # gather the sdist tar.gz name (which varies) | |
| # unzips the sdist | |
| - name: Extract sdist | |
| run: | | |
| tar -xzvf "${{ env.sdist_filename}}" | |
| # note: roughly follows Docker documentation on GitHub Actions usage | |
| # found on the following https://github.com/docker/build-push-action | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # attempts to build a test image for observing test behavior | |
| # and modeling a production image build. Version label | |
| # assumes pwd of, for example: pycytominer-1.0.1.post37.dev0+55690e4, | |
| # where we attempt to use 1.0.1.post37.dev0+55690e4 as a version label. | |
| - name: Build docker image for testing | |
| run: | | |
| cd "${{ env.sdist_extracted_name }}" && \ | |
| cp -r ../tests . && \ | |
| docker build -f ../build/docker/Dockerfile \ | |
| -t pycytominer:testing \ | |
| --label version="${{ env.version }}" \ | |
| --target testing \ | |
| . | |
| # runs pytest for pycytominer within a docker container based on the image above | |
| - name: Run tests through docker image | |
| run: | | |
| docker run pycytominer:testing pytest | |
| # Gather and prepare the dynamic version and other vars for use with work below. | |
| # For example, 1.1.0.post6.dev0+bc093ef becomes 1.1.0.post6.dev0_bc093ef | |
| - name: Gather dynamic version and set env var | |
| if: (github.event_name == 'push'|| github.event_name == 'schedule') && github.ref == 'refs/heads/main' | |
| id: env-vars | |
| run: >- | |
| echo "CLEAN_VERSION=$(echo ${{ env.sdist_extracted_name }} | tr '+' '_' )" >> "$GITHUB_OUTPUT" && | |
| echo "DATE_TAG=$(date +'%y%m%d')" >> "$GITHUB_OUTPUT" | |
| - name: Login to Docker Hub | |
| # only run this task if we have a pull request merged or the schedule triggers from main | |
| if: (github.event_name == 'push'|| github.event_name == 'schedule') && github.ref == 'refs/heads/main' | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USER }} | |
| password: ${{ secrets.DOCKER_TOKEN }} | |
| # Docker image push based on weekly schedule | |
| - name: Schedule-based docker image push | |
| # only run this task if we have a schedule trigger from main on cytomining/pycytominer | |
| if: github.event_name == 'schedule' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: "${{ env.sdist_extracted_name }}" | |
| push: true | |
| file: ./build/docker/Dockerfile | |
| target: production | |
| tags: cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }}_${{ steps.env-vars.outputs.DATE_TAG }} | |
| # Docker image push based on GitHub pushes to main | |
| - name: Push-based docker image push | |
| # only run this task if we have a pull request which is merged | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: "${{ env.sdist_extracted_name }}" | |
| push: true | |
| file: ./build/docker/Dockerfile | |
| target: production | |
| tags: cytomining/pycytominer:latest,cytomining/pycytominer:${{ steps.env-vars.outputs.CLEAN_VERSION }} | |
| # update docker hub description using readme on merge | |
| - name: Update Docker Hub repository description from readme | |
| # only run this task if we have a pull request which is merged | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'cytomining/pycytominer' | |
| uses: peter-evans/dockerhub-description@v4 | |
| with: | |
| username: ${{ secrets.DOCKER_USER }} | |
| password: ${{ secrets.DOCKER_TOKEN }} | |
| repository: cytomining/pycytominer | |
| readme-filepath: "${{ env.sdist_extracted_name }}/README.md" |