Update error message and docs for features argument to clarify CellProfiler default expectations and how to handle non-CellProfiler data
#325
Workflow file for this run
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| 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 | |
| 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" |