Add handling of .skip_lint file(s)
#222
Workflow file for this run
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| 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: ${{ needs.setup-ci-tools.outputs.tool-list }} | |
| additional-planemo-options: --report_level all | |
| continue-on-error: true | |
| - name: check if all test tools were linted | |
| run: | | |
| set -x | |
| # check if the ToolIDValid linter is called (no of tools - 1 ) times, i.e. is skipped once | |
| if [ "$(grep -c ToolIDValid ToolIDValid) != "2" ]; then | |
| echo "expecting exactly 2 tests for ToolIDValid"; exit 1; | |
| fi | |
| grep tool1 lint_report.txt | |
| grep tool2 lint_report.txt | |
| grep "ERROR: Error 'HTTPConnectionPool" lint_report.txt | |
| grep "Applying linter tests... CHECK" 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 |