Weekly global Tool Linting and Tests #614
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Weekly global Tool Linting and Tests | |
| on: | |
| schedule: | |
| # Run at midnight every monday | |
| - cron: '0 0 * * 1' | |
| repository_dispatch: | |
| types: [run-all-tool-tests-command] | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_24.1 | |
| MAX_CHUNKS: 40 | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| if: ${{ github.repository_owner == 'galaxyproject' }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| fork: ${{ steps.get-fork-branch.outputs.fork }} | |
| branch: ${{ steps.get-fork-branch.outputs.branch }} | |
| repository-list: ${{ steps.discover.outputs.repository-list }} | |
| chunk-count: ${{ steps.discover.outputs.chunk-count }} | |
| chunk-list: ${{ steps.discover.outputs.chunk-list }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Add reaction | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
| comment-id: ${{ github.event.client_payload.github.payload.comment.id }} | |
| reactions: hooray | |
| - name: Set galaxy fork and branch | |
| id: get-fork-branch | |
| run: | | |
| TMP="${{ github.event.client_payload.slash_command.args.named.fork }}" | |
| echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT | |
| TMP="${{ github.event.client_payload.slash_command.args.named.branch }}" | |
| echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| # Install the `wheel` package so that when installing other packages which | |
| # are not available as wheels, pip will build a wheel for them, which can be cached. | |
| - name: Install wheel | |
| run: pip install wheel | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: discover | |
| with: | |
| create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }} | |
| galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }} | |
| galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show repository list | |
| run: echo '${{ steps.discover.outputs.repository-list }}' | |
| - name: Show chunks | |
| run: | | |
| echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' | |
| lint: | |
| name: Check for missing containers | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Planemo lint | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: lint | |
| with: | |
| mode: lint | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| tool-list: ${{ needs.setup.outputs.tool-list }} | |
| additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Tool linting output' | |
| path: lint_report.txt | |
| test: | |
| name: Test tools | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} | |
| python-version: ['3.11'] | |
| services: | |
| postgres: | |
| image: postgres:11 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| # checkout the repository | |
| # and use it as the current working directory | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v2 | |
| id: cpu-cores | |
| - name: Clean dotnet folder for space | |
| run: rm -Rf /usr/share/dotnet | |
| - run: python -m pip install pillow tifffile | |
| - name: Planemo test | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: test | |
| with: | |
| mode: test | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: ${{ needs.setup.outputs.fork }} | |
| galaxy-branch: ${{ needs.setup.outputs.branch }} | |
| chunk: ${{ matrix.chunk }} | |
| chunk-count: ${{ needs.setup.outputs.chunk-count }} | |
| galaxy-slots: ${{ steps.cpu-cores.outputs.count }} | |
| # Limit each test to 15 minutes | |
| test_timeout: 900 | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'Tool test output ${{ matrix.chunk }}' | |
| path: upload | |
| # - combine the results of the test chunks (which will never fail due | |
| # to `|| true`) and create a global test report as json and html which | |
| # is provided as artifact | |
| # - check if any tool test actually failed (by lookup in the combined json) | |
| # and fail this step if this is the case | |
| combine_outputs: | |
| name: Combine chunked test results | |
| needs: [setup, test] | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Combine outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY | |
| - name: Create URL to the run output | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| id: vars | |
| run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT | |
| - name: Create comment | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
| issue-number: ${{ github.event.client_payload.github.payload.issue.number }} | |
| body: | | |
| Summary: | |
| ${{ steps.combine.outputs.statistics }} | |
| [Find all tool test results here][1] | |
| [1]: ${{ steps.vars.outputs.run-url }} | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check |