Create minimal markdown report if too large #218
Workflow file for this run
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
| on: [push, pull_request] | |
| name: 'Test action for tools' | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: master | |
| MAX_CHUNKS: 4 | |
| jobs: | |
| setup-pr-tools: | |
| name: Setup as in PR for tools | |
| runs-on: ubuntu-latest | |
| outputs: | |
| galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| repository-list: ${{ steps.discover.outputs.repository-list }} | |
| tool-list: ${{ steps.discover.outputs.tool-list }} | |
| chunk-count: ${{ steps.discover.outputs.chunk-count }} | |
| chunk-list: ${{ steps.discover.outputs.chunk-list }} | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| steps: | |
| - name: Print github context properties | |
| run: | | |
| echo 'event: ${{ github.event_name }}' | |
| echo 'sha: ${{ github.sha }}' | |
| echo 'ref: ${{ github.ref }}' | |
| echo 'head_ref: ${{ github.head_ref }}' | |
| echo 'base_ref: ${{ github.base_ref }}' | |
| echo 'event.before: ${{ github.event.before }}' | |
| echo 'event.after: ${{ github.event.after }}' | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v3 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ 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@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Introduce a change on test tool1 | |
| run: | | |
| git config --global user.name "Arthur Dent" | |
| git config --global user.email "[email protected]" | |
| echo "" >> test/tools/tool1/tool1.xml | |
| git commit -m bump test/tools/tool1/tool1.xml | |
| - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks | |
| uses: ./ | |
| id: discover | |
| with: | |
| create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }} | |
| galaxy-fork: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check commit range | |
| run: if ! grep "\.\." <<<$(echo ${{ steps.discover.outputs.commit-range }}); then echo "wrong commit range"; exit 1; fi | |
| - name: Check content of repository list | |
| run: | | |
| if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in repo list"; exit 1; fi | |
| if grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must not be in repo list"; exit 1; fi | |
| - name: Check content of tool list | |
| run: | | |
| if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in tool list"; exit 1; fi | |
| if grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must not be in tool list"; exit 1; fi | |
| - name: Check number of chunks | |
| run: if [ "${{ steps.discover.outputs.chunk-count }}" != "1" ]; then echo "wrong chunk-count"; exit 1; fi | |
| setup-ci-tools: | |
| name: Setup as in CI for tools | |
| 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: ${{ steps.discover.outputs.chunk-list }} | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| steps: | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: Artificially exclude workflows (because ci_find_repos discovers tool and workflow repos) | |
| run: echo 'test/workflows/' > .tt_skip | |
| - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks | |
| uses: ./ | |
| id: discover | |
| env: | |
| GITHUB_EVENT_NAME: schedule | |
| with: | |
| create-cache: true | |
| galaxy-fork: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| github-event-name-override: 'schedule' | |
| - name: Check for empty commit range | |
| run: if [ -n "${{ steps.discover.outputs.commit-range }}" ]; then exit 1; fi | |
| # note: ci_find_repos will find all tools and workflows | |
| - name: Check that all tools an workflows are in the repository list | |
| run: | | |
| if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in the repo list"; exit 1; fi | |
| if ! grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must be in the repo list"; exit 1; fi | |
| if grep -q "example3" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example3 must not be in the repo list"; exit 1; fi | |
| if grep -q "example4" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "example4 must not be in the repo list"; exit 1; fi | |
| # note: ci_find_tools will find onlytools | |
| - name: Check that all tools are in the tool list | |
| run: | | |
| if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in the repo list"; exit 1; fi | |
| if ! grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must be in the repo list"; exit 1; fi | |
| # chunk-count will only consider tools/workflows depending on the workflow input to the action | |
| - name: Check that the number of chunks is three, i.e. the number of tools | |
| run: if [ "${{ steps.discover.outputs.chunk-count }}" != "3" ]; then exit 1; fi | |
| lint: | |
| name: Test linting of tools | |
| needs: [setup-ci-tools] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }} | |
| - name: Install wheel | |
| run: pip install wheel | |
| - name: Planemo lint tools | |
| uses: ./ | |
| with: | |
| mode: lint | |
| report-level: all | |
| fail-level: warn | |
| repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }} | |
| tool-list: ${{ needs.setup-ci-tools.outputs.tool-list }} | |
| additional-planemo-options: --report_level all | |
| continue-on-error: true | |
| - name: check if all test tools were linted | |
| run: | | |
| grep tool1 lint_report.txt | |
| grep tool2 lint_report.txt | |
| grep "ERROR: Error 'HTTPConnectionPool" lint_report.txt | |
| grep "TestsNoValid" lint_report.txt | |
| test-tools: | |
| name: Test testing of tools | |
| needs: [setup-ci-tools] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk: ${{ fromJson(needs.setup-ci-tools.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@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }} | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v1 | |
| id: cpu-cores | |
| - name: Planemo test tools | |
| uses: ./ | |
| id: test-tools | |
| with: | |
| mode: test | |
| repository-list: ${{ needs.setup-ci-tools.outputs.repository-list }} | |
| galaxy-fork: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | |
| chunk: ${{ matrix.chunk }} | |
| chunk-count: ${{ needs.setup-ci-tools.outputs.chunk-count }} | |
| additional-planemo-options: --simultaneous_uploads --check_uploads_ok | |
| galaxy-slots: ${{ steps.cpu-cores.outputs.count }} | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'Tool test output ${{ matrix.chunk }}' | |
| path: upload | |
| combine_outputs: | |
| name: Test combining 'chunked' test results | |
| needs: [setup-ci-tools, test-tools] | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }} | |
| - name: Combine outputs | |
| uses: ./ | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| - name: Check statistics | |
| run: if ! grep -q "3\s\+success" <<<$(echo ${{ steps.combine.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - name: Check outputs | |
| uses: ./ | |
| id: check | |
| with: | |
| mode: check |