Fix Lattice system class for coarse-grained molecules
#442
Workflow file for this run
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| name: pytest | |
| on: | |
| push: | |
| # Action will run when any changes to these paths are pushed or pr'ed to master | |
| branches: [ main ] | |
| paths: | |
| - flowermd/** | |
| - environment-dev.yml | |
| - .github/workflows/pytest.yml | |
| pull_request: | |
| branches: [ main ] | |
| paths: | |
| - flowermd/** | |
| - environment-dev.yml | |
| - .github/workflows/pytest.yml | |
| issue_comment: | |
| types: [created] | |
| branches: [ main ] | |
| paths: | |
| - flowermd/** | |
| - environment-dev.yml | |
| - .github/workflows/pytest.yml | |
| workflow_dispatch: | |
| jobs: | |
| pytest: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macOS-latest, ubuntu-latest] | |
| python-version: ['3.10', '3.11'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Build environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment-dev.yml | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 4.9.2-4 | |
| use-mamba: true | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: pip install . | |
| - name: Run pytest with coverage report | |
| shell: bash -l {0} | |
| run: python -m pytest -rs -v --cov=./ --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| test-tutorials: | |
| if: ${{ github.event.issue.pull_request && github.event.comment.body== '/testtutorials'}} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Put a reaction to the comment | |
| run: gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}" | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NODE_ID: ${{ github.event.comment.node_id }} | |
| - name: Check if PR is open | |
| run: | | |
| STATE=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json state --jq .state) | |
| if [ "$STATE" != "OPEN" ]; then | |
| echo "Cannot build for closed PRs" | |
| ( | |
| echo "**${{ github.workflow }}**" | |
| echo "Cannot build Kuby for a closed PR. Use the `latest` version (built for the `master` branch) or create a new PR." | |
| ) | \ | |
| gh pr comment "${PR_NUMBER}" --repo ${{ github.repository }} -F - | |
| gh api graphql --silent --raw-field query="mutation AddReaction {addReaction(input:{subjectId:\"$NODE_ID\",content:THUMBS_DOWN}){reaction{content}subject{id}}}" | |
| gh api graphql --silent --raw-field query="mutation RemoveReaction {removeReaction(input:{subjectId:\"$NODE_ID\",content:EYES}){reaction{content}subject{id}}}" | |
| exit 1 | |
| fi | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.issue.number }} | |
| NODE_ID: ${{ github.event.comment.node_id }} | |
| - name: Get PR HEAD Ref | |
| id: getRef | |
| run: echo "pr_ref=$(gh pr view $PR_NUMBER --repo ${{ github.repository }} --json headRefOid | jq -r '.headRefOid')" >> $GITHUB_OUTPUT | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| PR_NUMBER: ${{ github.event.issue.number }} | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Build environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment-dev.yml | |
| miniforge-variant: Mambaforge | |
| miniforge-version: 4.9.2-4 | |
| use-mamba: true | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: pip install . | |
| - name: Run pytest on tutorials | |
| shell: bash -l {0} | |
| run: python -m pytest -rs -v --nbmake tutorials/ |