copy & paste cwl-docker-extract code from main.py - jfennick/workflow-inference-compiler - python_api_cwl_docker_extract #465
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| name: Lint And Test | |
| on: | |
| workflow_dispatch: | |
| # Have to declare parameters here for those that will be sent through 'workflow-dispatch' | |
| # event in branch_dispatch.yml. Otherwise, there'll be github API errors: | |
| # '"message": "Unexpected inputs provided: ...",' | |
| inputs: | |
| event_type: | |
| description: An arbitrary string used to dispatch steps | |
| required: true | |
| type: string | |
| commit_message: | |
| description: The commit message | |
| required: true | |
| type: string | |
| sender_repo: | |
| description: The repository which initiated the workflow dispatch | |
| required: true | |
| type: string | |
| sender_repo_owner: | |
| description: The account name of the repository initiated the workflow dispatch | |
| required: true | |
| type: string | |
| wic_owner: | |
| description: The account name of the wic repository | |
| required: true | |
| type: string | |
| wic_ref: | |
| description: The branch name within the wic repository | |
| required: true | |
| type: string | |
| mm-workflows_owner: | |
| description: The account name of the mm-workflows repository | |
| required: true | |
| type: string | |
| mm-workflows_ref: | |
| description: The branch name within the mm-workflows repository | |
| required: true | |
| type: string | |
| image-workflows_owner: | |
| description: The account name of the image-workflows repository | |
| required: true | |
| type: string | |
| image-workflows_ref: | |
| description: The branch name within the image-workflows repository | |
| required: true | |
| type: string | |
| # See https://github.com/orgs/community/discussions/15690 | |
| # For workflow_dispatch, the commit message, repo, and branch name are not displayed by default. | |
| run-name: "${{ inputs.commit_message}} - ${{ inputs.sender_repo }} - ${{ inputs.wic_ref }}" | |
| 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: | |
| 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: ${{ github.workflow }}-${{ matrix.os }}-${{ github.ref }}-${{ inputs.sender_repo }}-${{ inputs.mm-workflows_ref}} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # 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. | |
| os: [ubuntu-latest, windows-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout workflow-inference-compiler | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ inputs.wic_owner }}/workflow-inference-compiler | |
| ref: ${{ inputs.wic_ref }} | |
| path: workflow-inference-compiler | |
| - name: Checkout biobb_adapters | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| # NOTE: temporarily hardcode jfennick & master because we can only | |
| # have up to 10 input parameters for workflow_dispatch... | |
| repository: jfennick/biobb_adapters | |
| ref: master | |
| path: biobb_adapters | |
| - name: Checkout mm-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ inputs.mm-workflows_owner }}/mm-workflows | |
| ref: ${{ inputs.mm-workflows_ref }} | |
| path: mm-workflows | |
| - name: Checkout image-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ inputs.image-workflows_owner }}/image-workflows | |
| ref: ${{ inputs.image-workflows_ref }} | |
| path: image-workflows | |
| # NOTE: pypy actually decreases performance for lint_and_test.yml (by a factor of ~2) | |
| # - name: Append pypy to conda environment files | |
| # if: runner.os != 'Windows' | |
| # run: cd workflow-inference-compiler/install/ && echo " - pypy" >> system_deps.yml | |
| # - name: Append pypy to conda environment files | |
| # if: runner.os == 'Windows' | |
| # run: cd workflow-inference-compiler/install/ && echo " - pypy" >> system_deps_windows.yml | |
| - name: Setup mamba (linux, macos) | |
| if: runner.os != 'Windows' | |
| uses: conda-incubator/setup-miniconda@v3.0.1 | |
| with: | |
| miniforge-variant: Mambaforge-pypy3 | |
| miniforge-version: latest | |
| environment-file: workflow-inference-compiler/install/system_deps.yml | |
| activate-environment: wic | |
| 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/setup-miniconda@v3.0.1 | |
| with: | |
| miniforge-variant: Mambaforge-pypy3 | |
| miniforge-version: latest | |
| environment-file: workflow-inference-compiler/install/system_deps_windows.yml | |
| activate-environment: wic | |
| 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 workflow-inference-compiler/ -name "*.sh" -and -not -path "./3/*") | |
| - name: Install Workflow Inference Compiler | |
| if: always() | |
| run: cd workflow-inference-compiler/ && pip install ".[all_except_runner_src]" | |
| - 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 workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' | |
| - name: Generate Sophios Validation Jsonschema | |
| if: always() | |
| run: cd workflow-inference-compiler/ && 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 workflow-inference-compiler/ && python -c 'import sophios; import sophios.plugins; sophios.plugins.blindly_execute_python_workflows()' | |
| - name: Build Documentation | |
| if: always() | |
| run: cd workflow-inference-compiler/docs && make html | |
| - name: MyPy Check Type Annotations | |
| if: always() | |
| run: cd workflow-inference-compiler/ && mypy src/ examples/ tests/ | |
| # NOTE: Do not use `mypy .` because then mypy will check both src/ and build/ causing: | |
| # src/workflow-inference-compiler/__init__.py: error: Duplicate module named "wic" | |
| # (also at "./build/lib/workflow-inference-compiler/__init__.py") | |
| - name: PyLint Check Code Quality | |
| if: always() | |
| run: cd workflow-inference-compiler/ && pylint src/ examples/**/*.py tests/ | |
| # NOTE: See fail-under threshold in .pylintrc | |
| - name: PEP8 Code Formatting | |
| if: always() | |
| id: autopep8 | |
| run: cd workflow-inference-compiler/ && 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 workflow-inference-compiler/ && 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: 5 # backup timeout for windows | |
| - name: PyTest Inline Subworkflows | |
| if: always() | |
| run: cd workflow-inference-compiler/ && 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: 5 # backup timeout for windows | |
| - name: PyTest Scattering Scaling | |
| if: runner.os == 'Linux' | |
| # Avoid Windows and macOS due to 2X and 10X minute multipliers. | |
| # https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#minute-multipliers | |
| # Also, cannot run on Windows (natively) yet | |
| run: cd workflow-inference-compiler/ && pytest -k test_scattering_scaling | |
| # NOTE: The steps below are for repository_dispatch only. For all other steps, please insert above | |
| # this comment. | |
| # Need to store success value in environment variable, rather than using 'success()' in-line inside a run tag. | |
| # Otherwise: "The workflow is not valid. ... Unrecognized function: 'success'." | |
| # https://github.com/actions/runner/issues/834#issuecomment-889484016 | |
| - name: The workflow has succeeded | |
| if: success() | |
| run: | | |
| echo 'workflow_success=true' >> "$GITHUB_ENV" | |
| # It is not clear from the documentation, but the 'success()' and 'failure()' functions | |
| # do not consider skipped steps. Specifically, the above 'success()' function will not | |
| # affect the 'failure()' function here. | |
| # https://docs.github.com/en/actions/learn-github-actions/expressions#status-check-function | |
| - name: The workflow has failed | |
| if: failure() | |
| run: | | |
| echo 'workflow_success=false' >> "$GITHUB_ENV" | |
| # See token.md | |
| - name: Generate a token | |
| if: always() | |
| id: generate_token | |
| uses: tibdex/github-app-token@b62528385c34dbc9f38e5f4225ac829252d1ea92 | |
| with: | |
| app_id: ${{ secrets.APP_ID }} | |
| private_key: ${{ secrets.APP_PRIVATE_KEY }} | |
| - name: Reply CI results to sender | |
| # In case of failure, we still need to return the failure status to the original repository. | |
| # Use 'always()' so this step runs even if there's a failure and use an internal if-statement | |
| # to only run this step only if the repository_dispatch sends the signal. | |
| # https://github.com/actions/runner/issues/834#issuecomment-907096707 | |
| # Use inputs.sender_repo to reply the original sender. | |
| if: always() | |
| uses: ./workflow-inference-compiler/.github/my_actions/reply_sender/ # Must start with ./ | |
| with: | |
| github_repository: ${{ github.repository }} | |
| event_type: ${{ inputs.event_type }} | |
| sender_repo: ${{ inputs.sender_repo }} | |
| operating_system: ${{ matrix.os }} | |
| commit_message: ${{ inputs.commit_message }} | |
| mm_workflows_ref: ${{ inputs.mm-workflows_ref }} | |
| workflow_success: ${{ env.workflow_success }} | |
| access_token: ${{ steps.generate_token.outputs.token }} |