fix onionnet_featuriz bug #308
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| name: Build And Test | |
| on: | |
| push: | |
| 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 | |
| # https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions#jobs | |
| # Rather than use a single job with a linear pipeline of steps, you may be | |
| # tempted to make each step into a separate job and specify the dependencies | |
| # using the `needs` syntax for more parallelism. | |
| # However, data cannot be shared between jobs because each job will be run on a | |
| # different runner. Even on a self-hosted runner, the `needs` syntax does not | |
| # guarantee that the data can be shared! | |
| # Using if: always() allows all steps to run, while still properly reporting failure. | |
| # See https://stackoverflow.com/questions/62045967/github-actions-is-there-a-way-to-continue-on-error-while-still-getting-correct | |
| permissions: | |
| actions: read | |
| contents: read | |
| pull-requests: read | |
| jobs: | |
| build_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: ${{ github.workflow }}-${{ matrix.os }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout mm-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| path: mm-workflows | |
| - name: Checkout biobb_adapters | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: vjaganat90/biobb_adapters # TODO: use check_existence | |
| ref: master | |
| path: biobb_adapters | |
| - name: Setup mamba (linux, macos) | |
| if: runner.os != 'Windows' | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Miniforge-pypy3 | |
| miniforge-version: latest | |
| environment-file: mm-workflows/install/system_deps.yml | |
| activate-environment: mm | |
| channels: conda-forge | |
| python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11 | |
| - name: Setup mamba (windows) | |
| if: runner.os == 'Windows' | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Miniforge-pypy3 | |
| miniforge-version: latest | |
| environment-file: mm-workflows/install/system_deps_windows.yml | |
| activate-environment: mm | |
| channels: conda-forge | |
| python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11 | |
| - name: ShellCheck Script Quality | |
| if: always() | |
| # "SC1017 (error): Literal carriage return. Run script through tr -d '\r' ." | |
| run: shellcheck -e SC1017 $(find mm-workflows/ -name "*.sh" -not -path "./biobb_adapters/*" -and -not -path "./3/*") | |
| - name: Install Molecular Modeling Workflows | |
| if: always() | |
| # Also run mm-workflows command to generate | |
| # mm-workflows/autogenerated/schemas/config_schemas.json | |
| run: cd mm-workflows/ && pip install ".[all]" && mm-workflows | |
| - name: Build Documentation | |
| if: always() | |
| run: cd mm-workflows/docs && make html | |
| - name: MyPy Check Type Annotations | |
| if: always() | |
| run: cd mm-workflows/ && mypy src/ examples/ cwl_adapters/ | |
| # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing: | |
| # src/wic/__init__.py: error: Duplicate module named "wic" (also at "./build/lib/wic/__init__.py") | |
| - name: PyLint Check Code Quality | |
| if: always() | |
| run: cd mm-workflows/ && pylint src/ examples/**/*.py | |
| # NOTE: See fail-under threshold in .pylintrc | |
| - name: PEP8 Code Formatting | |
| if: always() | |
| id: autopep8 | |
| run: cd mm-workflows/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ | |
| - name: Fail if autopep8 made changes | |
| if: steps.autopep8.outputs.exit-code == 2 | |
| run: exit 1 |