updated python container #115
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| name: Pytest-workflow | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| name: ${{ matrix.profile }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| profile: ["docker"] | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - uses: actions/[email protected] | |
| - name: Set up Python | |
| uses: actions/[email protected] | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/[email protected] | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow | |
| - uses: actions/[email protected] | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| # Test the pipeline | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest -vvv --symlink --kwdof --git-aware --color=yes | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt-get update > /dev/null | |
| sudo apt-get install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/[email protected] | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /home/runner/pytest_workflow_*/*/.nextflow.log | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/work | |
| /home/runner/pytest_workflow_*/*/results |