update gromacs from 2021.4 to 2022.2 - jfennick/workflow-inference-compiler - update_gromacs #281
Workflow file for this run
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| name: Build 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 | |
| # 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.mm-workflows_ref}}" | |
| env: | |
| BUILD_TYPE: Release | |
| 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 }}-${{ github.ref }}-${{ inputs.sender_repo }}-${{ inputs.mm-workflows_ref}} | |
| cancel-in-progress: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout source code | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ inputs.wic_owner }}/workflow-inference-compiler | |
| ref: ${{ inputs.wic_ref }} | |
| submodules: recursive | |
| path: wic | |
| - name: Checkout mm-workflows | |
| if: always() | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ${{ inputs.mm-workflows_owner }}/mm-workflows | |
| ref: ${{ inputs.mm-workflows_ref }} | |
| submodules: recursive | |
| path: mm-workflows | |
| - name: Setup mamba (linux, macos) | |
| if: runner.os != 'Windows' | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| miniforge-variant: Mambaforge-pypy3 | |
| miniforge-version: latest | |
| environment-file: wic/system_deps.yml | |
| activate-environment: wic | |
| use-mamba: true | |
| channels: conda-forge | |
| python-version: "3.9.*" # pypy is not yet compatible with 3.10 and 3.11 | |
| - name: Setup conda (windows) | |
| if: runner.os == 'Windows' | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| miniforge-version: latest | |
| environment-file: wic/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 wic/ -name "*.sh" -not -path "./biobb/*" -and -not -path "./3/*") | |
| - name: Install Workflow Inference Compiler | |
| if: always() | |
| run: cd wic/ && pip install ".[all]" | |
| - 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 wic/docs && make html | |
| - name: MyPy Check Type Annotations | |
| if: always() | |
| run: cd wic/ && mypy --no-incremental src/ tests/ api.py auth/ | |
| # 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") | |
| # NOTE: We need to use --no-incremental because there is a bug in mypy. | |
| # This bug most often occurs when using ruamel library. | |
| # See https://github.com/python/mypy/issues/12664 | |
| - name: PyLint Check Code Quality | |
| if: always() | |
| run: cd wic/ && pylint src/ tests/ api.py auth/ | |
| # NOTE: See fail-under threshold in .pylintrc | |
| - name: Helm Lint Check Code Quality | |
| if: always() | |
| run: cd wic/ && helm lint deploy/helm/wic-api | |
| - name: PEP8 Code Formatting | |
| if: always() | |
| id: autopep8 | |
| run: cd wic/ && autopep8 --exit-code --recursive --diff --max-line-length 120 examples/ src/ tests/ api.py auth/ | |
| - 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 wic/ && 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 wic/ && 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 Fuzzy Compile | |
| if: always() | |
| run: cd wic/ && pytest -k test_fuzzy_compile | |
| - name: PyTest Scattering Scaling | |
| if: runner.os != 'Windows' # Cannot run on Windows (natively) yet | |
| run: cd wic/ && 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 | |
| id: generate_token | |
| uses: tibdex/github-app-token@b62528385c34dbc9f38e5f4225ac829252d1ea92 | |
| with: | |
| app_id: ${{ secrets.APP_ID }} | |
| private_key: ${{ secrets.APP_PRIVATE_KEY }} | |
| - name: Check actor's identity | |
| env: | |
| APP_TOKEN: ${{ steps.generate_token.outputs.token }} | |
| run: | | |
| if ! curl -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| -H "Authorization: Bearer $APP_TOKEN" \ | |
| https://api.github.com/repos/${{ github.repository }}/collaborators \ | |
| | jq '.[].login' | grep "${{ inputs.sender_repo_owner }}"; | |
| then | |
| echo "Account doesn't have enough permissions!" \ | |
| && false; | |
| fi | |
| - 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: ./wic/.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 }} |