Decoupler: allow multiple merges on AnnData (#306) #64
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| name: Galaxy Tool Deployment | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_21.01 | |
| MAX_CHUNKS: 4 | |
| jobs: | |
| # This is a setup modified from that at | |
| # https://github.com/galaxyproject/tools-iuc/blob/master/.github/workflows/pr.yaml | |
| # 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 Planemo | |
| runs-on: self-hosted | |
| outputs: | |
| galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }} | |
| 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 }}' | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "::set-output name=galaxy_head_sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" | |
| - 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 Planemo | |
| run: pip install planemo | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Fake a Planemo run to update cache | |
| 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 }} | |
| find_changed: | |
| name: Determine changed repositories | |
| needs: [setup] | |
| runs-on: self-hosted | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8] | |
| outputs: | |
| commit_range: ${{ steps.get-commit-range.outputs.commit_range }} | |
| nchunks: ${{ steps.get-chunks.outputs.nchunks }} | |
| chunk_list: ${{ steps.get-chunks.outputs.chunk_list }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| # The range of commits to check for changes is: | |
| # - for events on the develop branch we compare against the sha before the event | |
| # (note that this does not work for feature branch events since we want all | |
| # commits on the feature branch and not just the commits of the last event) | |
| - name: Set commit range (push to the develop branch, e.g. merge) | |
| run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV | |
| - id: get-commit-range | |
| run: echo "::set-output name=commit_range::$COMMIT_RANGE" | |
| - uses: actions/setup-python@v2 | |
| 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 Planemo | |
| run: pip install planemo | |
| - name: Planemo ci_find_repos | |
| run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --output changed_repositories.list | |
| - name: Show repo list | |
| run: cat changed_repositories.list | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: Workflow artifacts | |
| path: changed_repositories.list | |
| - name: Planemo ci_find_tools for the changed repos | |
| run: | | |
| touch changed_tools.list | |
| if [ -s changed_repositories.list ]; then | |
| planemo ci_find_tools --output changed_tools.list $(cat changed_repositories.list) | |
| fi | |
| - name: Show tool list | |
| run: cat changed_tools.list | |
| - name: Compute chunks | |
| id: get-chunks | |
| run: | | |
| nchunks=$(wc -l < changed_tools.list) | |
| if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then | |
| nchunks=$MAX_CHUNKS | |
| elif [ "$nchunks" -eq 0 ]; then | |
| nchunks=1 | |
| fi | |
| echo "::set-output name=nchunks::$nchunks" | |
| echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]" | |
| - name: Show chunks | |
| run: | | |
| echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})' | |
| # deploy the tools to the toolshed | |
| deploy: | |
| name: Deploy | |
| needs: [setup, find_changed] | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| runs-on: self-hosted | |
| if: github.ref == 'refs/heads/develop' && github.repository_owner == 'ebi-gene-expression-group' | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: Workflow artifacts | |
| path: ../workflow_artifacts/ | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v2 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }} | |
| - name: Install Planemo | |
| run: pip install planemo | |
| - name: Deploy on toolshed | |
| env: | |
| SHED_KEY: ${{ secrets.TS_API_KEY }} | |
| run: | | |
| while read -r DIR; do | |
| if [ -d "$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 10000 ]; then | |
| echo "Deleting test files, found one > 10Mb" 1>&2 | |
| rm -rf $DIR/test-data | |
| fi | |
| fi | |
| planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1; | |
| done < ../workflow_artifacts/changed_repositories.list |