Weekly global Tool Linting and Tests #63
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| 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_23.1 | |
| GALAXY_COPERNICUS_CDSAPIRC_KEY: ${{ secrets.GALAXY_COPERNICUS_CDSAPIRC_KEY }} | |
| COPERNICUS_CDSAPIRC_KEY_FILE: ${{ secrets.COPERNICUS_CDSAPIRC_KEY_FILE }} | |
| MAX_CHUNKS: 40 | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| if: ${{ github.repository_owner == 'NordicESMhub' }} | |
| 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: ['3.7'] | |
| steps: | |
| - name: Add reaction | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| uses: peter-evans/create-or-update-comment@v2 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
| comment-id: ${{ github.event.client_payload.github.payload.comment.id }} | |
| reaction-type: hooray | |
| - name: Set galaxy fork and branch | |
| id: get-fork-branch | |
| run: | | |
| TMP="${{ 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@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: 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: ['3.7'] | |
| 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.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 tests,output,inputs,help,general,command,citations,tool_xsd | |
| - uses: actions/upload-artifact@v3 | |
| 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: ['3.7'] | |
| 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.outputs.galaxy-head-sha }} | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v1 | |
| id: cpu-cores | |
| - name: Clean dotnet folder for space | |
| run: rm -Rf /usr/share/dotnet | |
| - name: Create Copernicus Climate Change Config file | |
| uses: jwsi/secret-parser@v1 | |
| with: | |
| filename: tools/essential_climate_variables/cdsapirc.cfg | |
| secret-name: GALAXY_COPERNICUS_CDSAPIRC_KEY | |
| secret-value: ${{ secrets.GALAXY_COPERNICUS_CDSAPIRC_KEY }} | |
| - name: Create Copernicus Atmosphere Monitoring Config file | |
| uses: jwsi/secret-parser@v1 | |
| with: | |
| filename: tools/cads/adsapirc.cfg | |
| secret-name: GALAXY_COPERNICUS_ADSAPIRC_KEY | |
| secret-value: ${{ secrets.GALAXY_COPERNICUS_ADSAPIRC_KEY }} | |
| - name: Get LS8 test files from Zenodo | |
| uses: wei/wget@v1 | |
| with: | |
| args: -O tools/eodie/test-data/LS8.tar https://zenodo.org/record/5796122/files/LC08_L2SP_189017_20190628_20200827_02_T1.tar | |
| - name: Get S2 test files from Zenodo | |
| uses: wei/wget@v1 | |
| with: | |
| args: -O tools/eodie/test-data/S2.tar https://zenodo.org/record/5794508/files/S2B_MSIL2A_20200626T095029_N0214_R079_T34VFN_20200626T123234.SAFE.tar | |
| - 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@v3 | |
| 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: ['3.7'] | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| 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.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@v3 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - 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@v2 | |
| 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 |