Lint And Test MacOS #95
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| name: Lint And Test MacOS | |
| # NOTE: Due to 10X minute multiplier, do NOT run on macos-latest on every push! | |
| # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers | |
| # Run on macos on a separate weekly schedule. | |
| on: | |
| # push: # Do NOT run on MacOS on every push! | |
| # pull_request: (either on origin or on upstream pull request) | |
| schedule: | |
| # Instead, run it every Tuesday at midnight. | |
| - cron: '0 0 * * 2' | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -l {0} # Invoke bash in login mode, NOT interactive mode. | |
| # This will cause bash to look for the startup file ~/.bash_profile, NOT ~/.bashrc | |
| # This is important since conda init writes to ~/.bashrc | |
| permissions: | |
| actions: read | |
| contents: read | |
| pull-requests: read | |
| jobs: | |
| lint_and_test: | |
| # See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#concurrency | |
| # This will prevent DOS attacks from people blasting the CI with rapid fire commits. | |
| concurrency: | |
| group: ${{ github.workflow }}-macos-latest-${{ github.ref }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout sophios | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ github.repository_owner }}/sophios | |
| ref: master | |
| path: sophios | |
| - name: Checkout biobb_adapters | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: vjaganat90/biobb_adapters | |
| ref: master | |
| path: biobb_adapters | |
| - name: Checkout mm-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ github.repository_owner }}/mm-workflows | |
| ref: main | |
| path: mm-workflows | |
| - name: Checkout image-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ github.repository_owner }}/image-workflows | |
| ref: main | |
| path: image-workflows | |
| - name: Setup miniforge (linux, macos) | |
| if: runner.os != 'Windows' | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: 24.7.1-2 | |
| environment-file: sophios/install/system_deps.yml | |
| activate-environment: wic | |
| use-mamba: true | |
| channels: conda-forge | |
| python-version: "3.11.*" | |
| - name: ShellCheck Script Quality | |
| if: always() | |
| # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ." | |
| run: shellcheck -e SC1017 $(find sophios/ -name "*.sh" -and -not -path "./3/*") | |
| - name: Install Sophios | |
| if: always() | |
| run: cd sophios/ && pip install ".[all_except_runner_src]" | |
| - name: Update Sophios Config | |
| if: always() | |
| run: cd sophios/ && python .github/update_sophios_config.py | |
| - name: Install Molecular Modeling Workflows | |
| if: always() | |
| # Also run mm-workflows command to generate | |
| # mm-workflows/autogenerated/schemas/config_schemas.json | |
| # NOTE: Use ".[test]" instead of ".[all_except_runner_src]" | |
| # We do not want or need to install the workflow_deps extra. | |
| # (Many of the packages conflict with pypy.) | |
| run: cd mm-workflows/ && pip install ".[test]" && mm-workflows --generate_schemas | |
| - name: Generate Sophios Python API Workflows (*.py -> *.wic) | |
| if: always() | |
| run: cd sophios/ && pytest -k test_compile_python_workflows | |
| - name: Generate Sophios Validation Jsonschema | |
| if: always() | |
| run: cd sophios/ && sophios --generate_schemas | |
| # Please read docs/validation.md#Property-Based-Testing | |
| # This is essentially an integration test for all of the | |
| # Sophios Python API workflows as well as the Sophios Python API itself. | |
| - name: Validate Sophios Python API Workflows (*.py -> *.wic) | |
| if: always() | |
| run: cd sophios/ && pytest -k test_compile_python_workflows | |
| - name: Build Documentation | |
| if: always() | |
| run: cd sophios/docs && make html | |
| - name: MyPy Check Type Annotations | |
| if: always() | |
| run: cd sophios/ && mypy src/ examples/ tests/ | |
| # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing: | |
| # src/sophios/__init__.py: error: Duplicate module named "wic" | |
| # (also at "./build/lib/sophios/__init__.py") | |
| - name: PyLint Check Code Quality | |
| if: always() | |
| run: cd sophios/ && pylint src/ examples/**/*.py tests/ | |
| # NOTE: See fail-under threshold in .pylintrc | |
| - name: PEP8 Code Formatting | |
| if: always() | |
| id: autopep8 | |
| run: cd sophios/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/ | |
| - name: Fail if autopep8 made changes | |
| if: steps.autopep8.outputs.exit-code == 2 | |
| run: exit 1 | |
| # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252 | |
| - name: PyTest CWL Embedding Independence | |
| if: always() | |
| run: cd sophios/ && pytest -k test_cwl_embedding_independence # --cov --cov-config=.coveragerc_serial | |
| # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout() | |
| timeout-minutes: 20 # backup timeout for windows | |
| - name: PyTest Inline Subworkflows | |
| if: always() | |
| run: cd sophios/ && pytest -k test_inline_subworkflows # --cov --cov-config=.coveragerc_serial | |
| # NOTE: This test MUST be run in serial! See is_isomorphic_with_timeout() | |
| timeout-minutes: 20 # backup timeout for windows |