bump: version 1.0.1 → 1.1.0 #109
Workflow file for this run
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| name: Integration Workflow | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| tags: ["*"] | |
| 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-latest | |
| 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-latest | |
| - ubuntu-latest | |
| 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" | |
| 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-latest') && (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 | |
| continue-on-error: true | |
| if: (matrix.os == 'ubuntu-latest') && (matrix.python-version == env.TARGET_PYTHON_VERSION ) | |
| uses: codecov/codecov-action@v3 | |
| 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 | |
| - name: Run pytest | |
| # For every other version and/or OS, run pytest without coverage | |
| if: (matrix.os != 'ubuntu-latest') || (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-latest | |
| 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 |