Update CI tests and add pre-commit #7
Workflow file for this run
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| name: Model integrity | |
| on: | |
| pull_request: | |
| branches: 'main' | |
| paths: 'HTAN.model.csv' | |
| workflow_dispatch: | |
| concurrency: | |
| # cancel the current running workflow from the same branch, PR when a new workflow is triggered | |
| # when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group | |
| # {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows | |
| # {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag | |
| # {{ github.sha }}: full commit sha | |
| # credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml | |
| group: >- | |
| ${{ github.workflow }}-${{ github.ref_type }}- | |
| ${{ github.sha }} | |
| cancel-in-progress: true | |
| jobs: | |
| component_requirements_check: | |
| name: Check component requirements | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_components.py | |
| attributes_exist_check: | |
| name: Check attributes exist | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_exist.py | |
| attributes_used_check: | |
| name: Check attributes are used | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_are_used.py | |
| attributes_unique_check: | |
| name: Check attributes are unique | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_are_unique.py |