Add bio.tools entries to tools #536
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| name: Galaxy Tool Linting and Tests for push and PR | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - 'deprecated/**' | |
| - 'docs/**' | |
| - '*' | |
| push: | |
| branches: | |
| - main | |
| - master | |
| paths-ignore: | |
| - 'deprecated/**' | |
| - 'docs/**' | |
| - '*' | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_24.0 | |
| MAX_CHUNKS: 4 | |
| MAX_FILE_SIZE: 10M | |
| concurrency: | |
| # Group runs by PR, but keep runs on the default branch separate | |
| # because we do not want to cancel ToolShed uploads | |
| group: pr-${{ github.ref == 'refs/heads/main' && github.run_number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| # the setup job does two things: | |
| # 1. cache the pip cache and .planemo | |
| # 2. determine the list of changed repositories | |
| # it produces one artifact which contains | |
| # - a file with the latest SHA from the chosen branch of the Galaxy repo | |
| # - a file containing the list of changed repositories | |
| # which are needed in subsequent steps. | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| 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 }} | |
| commit-range: ${{ steps.discover.outputs.commit-range }} | |
| 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@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_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v4 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ 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 | |
| - name: Install flake8 | |
| run: pip install flake8 flake8-import-order | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - 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: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_BRANCH }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show commit range | |
| run: echo '${{ steps.discover.outputs.commit-range }}' | |
| - name: Show repository list | |
| run: echo '${{ steps.discover.outputs.repository-list }}' | |
| - name: Show tool list | |
| run: echo '${{ steps.discover.outputs.tool-list }}' | |
| - name: Show chunks | |
| run: | | |
| echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' | |
| # Planemo lint the changed repositories | |
| lint: | |
| name: Lint tool-list | |
| 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: Set fail level for pull request | |
| if: ${{ github.event_name == 'pull_request' }} | |
| run: | |
| echo "FAIL_LEVEL=error" >> "$GITHUB_ENV" | |
| - name: Set fail level for merge | |
| if: ${{ github.event_name != 'pull_request' }} | |
| run: | |
| echo "FAIL_LEVEL=error" >> "$GITHUB_ENV" | |
| - name: Planemo lint | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: lint | |
| with: | |
| mode: lint | |
| fail-level: ${{ env.FAIL_LEVEL }} | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| tool-list: ${{ needs.setup.outputs.tool-list }} | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Tool linting output' | |
| path: lint_report.txt | |
| # flake8 of Python scripts in the changed repositories | |
| flake8: | |
| name: Lint Python scripts | |
| needs: setup | |
| if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-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_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install flake8 | |
| run: pip install flake8 flake8-import-order | |
| - name: Flake8 | |
| run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --max-line-length 88 --ignore=I201,W503 --output-file pylint_report.txt --tee | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Python linting output' | |
| path: pylint_report.txt | |
| lintr: | |
| name: Lint R scripts | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04] | |
| r-version: ['release'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: r_cache_${{ matrix.os }}_${{ matrix.r-version }} | |
| - name: Install packages | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: | | |
| any::argparse | |
| any::styler | |
| - name: lintr | |
| run: | | |
| set -eo pipefail | |
| echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off | |
| git status | |
| git diff --exit-code | tee rlint_report.txt | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'R linting output' | |
| path: rlint_report.txt | |
| file_sizes: | |
| name: Check file sizes | |
| needs: setup | |
| if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check file sizes | |
| run: | | |
| touch file_size_report.txt | |
| git diff --diff-filter=d --name-only ${{ needs.setup.outputs.commit-range }} > git.diff | |
| while read line; do | |
| find "$line" -type f -size +${{ env.MAX_FILE_SIZE }} >> file_size_report.txt | |
| done < git.diff | |
| if [[ -s file_size_report.txt ]]; then | |
| echo "Files larger than ${{ env.MAX_FILE_SIZE }} found" | |
| cat file_size_report.txt | |
| exit 1 | |
| fi | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'File size report' | |
| path: file_size_report.txt | |
| # Planemo test the changed repositories, each chunk creates an artifact | |
| # containing HTML and JSON reports for the executed tests | |
| test: | |
| name: Test tools | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| 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: | |
| - 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_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v4 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ 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 | |
| - name: Get test-data for changed repos | |
| run: | | |
| for repo in ${{ needs.setup.outputs.repository-list }}; do | |
| pushd $repo | |
| if [ -f get_test_data.sh ]; then | |
| mkdir -p test-data | |
| chmod u+x get_test_data.sh | |
| ./get_test_data.sh | |
| fi | |
| popd | |
| done | |
| - name: Planemo test | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: test | |
| with: | |
| mode: test | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: ${{ env.GALAXY_FORK }} | |
| galaxy-branch: ${{ env.GALAXY_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: 1800 | |
| - 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] | |
| if: ${{ always() && needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| 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 | |
| markdown-report: true | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check | |
| - name: Check if all test chunks succeeded | |
| run: | | |
| NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l) | |
| if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then | |
| exit 1 | |
| fi | |
| # deploy the tools to the toolsheds (first TTS for testing) | |
| deploy: | |
| name: Deploy | |
| needs: [setup, lint, combine_outputs] | |
| if: ${{ github.ref == 'refs/heads/main' && github.repository_owner == 'ebi-gene-expression-group' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| 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_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Delete large test files | |
| run: | | |
| echo "${{ needs.setup.outputs.repository-list }}" > changed_repositories.list | |
| while read -r DIR; do | |
| if [ -d "$DIR/test-data" ]; then | |
| max_test_file_size=$(du $DIR/test-data/$(ls -S $DIR/test-data | head -n 1) | awk '{print $1}') | |
| if [ $max_test_file_size -gt 1000 ]; then | |
| echo "Deleting test files, found one > 1Mb" 1>&2 | |
| rm -rf $DIR/test-data | |
| fi | |
| fi | |
| done < changed_repositories.list | |
| - name: Deploy on toolshed | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| shed-target: toolshed | |
| shed-key: ${{ secrets.TS_API_KEY }} | |
| deploy-report: | |
| name: Report deploy status | |
| needs: [deploy] | |
| if: ${{ always() && needs.deploy.result != 'success' && github.ref == 'refs/heads/main' && github.repository_owner == 'ebi-gene-expression-group' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| # report to the PR if deployment failed | |
| - name: Get PR object | |
| uses: 8BitJonny/[email protected] | |
| id: getpr | |
| with: | |
| sha: ${{ github.event.after }} | |
| - name: Create comment | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| issue-number: ${{ steps.getpr.outputs.number }} | |
| body: | | |
| Attention: deployment ${{ needs.deploy.result }}! | |
| https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| determine-success: | |
| name: Check workflow success | |
| needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs] | |
| if: ${{ always() && github.ref != 'refs/heads/main' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check tool lint status | |
| if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Indicate Python script lint status | |
| if: ${{ needs.flake8.result != 'success' && needs.flake8.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Indicate R script lint status | |
| if: ${{ needs.lintr.result != 'success' && needs.lintr.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Indicate file size check status | |
| if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }} | |
| run: exit 1 | |
| - name: Check tool test status | |
| if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} | |
| run: exit 1 |