Removed torch and Horovod in Dockerfile #110
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| name: Galaxy Tool Linting and Tests for push and PR | |
| on: [push, pull_request] | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_22.05 | |
| MAX_CHUNKS: 4 | |
| 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 }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| 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: ${{ github.event.after }}' | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v2 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ 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@v2 | |
| 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: ['3.8'] | |
| steps: | |
| # checkout the repository | |
| # and use it as the current working directory | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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 }} | |
| - uses: actions/upload-artifact@v2 | |
| 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: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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 --output-file pylint_report.txt --tee | |
| - uses: actions/upload-artifact@v2 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Python linting output' | |
| path: pylint_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: ['3.8'] | |
| 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@v2 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Cache .planemo | |
| uses: actions/cache@v2 | |
| id: cache-planemo | |
| with: | |
| path: ~/.planemo | |
| key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - 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 }} | |
| - uses: actions/upload-artifact@v2 | |
| 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: ${{ needs.setup.outputs.repository-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ 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@v2 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check | |
| # deploy the tools to the toolsheds (first TTS for testing) | |
| deploy: | |
| name: Deploy | |
| needs: [setup, lint, flake8, combine_outputs] | |
| if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'goeckslab' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Deploy on testtoolshed | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| shed-target: testtoolshed | |
| shed-key: ${{ secrets.TTS_API_KEY }} | |
| continue-on-error: true | |
| - 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 }} | |
| determine-success: | |
| name: Check workflow success | |
| needs: [setup, lint, flake8, combine_outputs] | |
| if: ${{ always() && github.ref != 'refs/heads/master' && 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: Check tool test status | |
| if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }} | |
| run: exit 1 |