Implement fragments aggregation into instances: modified main.py and map.py #136
Workflow file for this run
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| name: Pytest-workflow | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - 'irescue/**' | |
| - 'tests/**' | |
| - '.github/workflows/pytest-workflow.yml' | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-24.04 | |
| name: test | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] | |
| steps: | |
| - name: Install Ubuntu dependencies | |
| run: sudo apt-get update && sudo apt-get install -y liblzma-dev | |
| - name: Checkout | |
| uses: actions/checkout@v3.3.0 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: tests/config/environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| condarc-file: tests/config/condarc.yml | |
| auto-update-conda: true | |
| - name: Install Python dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest-workflow | |
| python -m pip install . | |
| - name: Run pytest-workflow | |
| shell: bash -el {0} | |
| run: TMPDIR=~ pytest --symlink --kwdof --git-aware --color=yes | |
| - name: Output dependency tree | |
| if: success() | |
| shell: bash -el {0} | |
| run: | | |
| pip install --no-cache-dir pipdeptree | |
| pipdeptree | |
| - name: Output log on failure | |
| if: failure() | |
| shell: bash -el {0} | |
| run: | | |
| echo "=== Environment Variables ===" | |
| env | tee /home/runner/pytest_workflow_env.log | |
| echo "=== Logs ===" | |
| cat /home/runner/pytest_workflow_*/*/log.{out,err} | tee /home/runner/pytest_workflow_combined.log | |
| echo "=== Tool Versions ===" | |
| if command -v bedtools; then bedtools --version; else echo "bedtools not found"; fi | |
| if command -v samtools; then samtools --version; else echo "samtools not found"; fi | |
| if command -v python; then python --version; else echo "python not found"; fi | |
| conda list -n test | tee /home/runner/pytest_workflow_conda_list.log | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v4.6.0 | |
| with: | |
| name: pytest_logs_py${{matrix.python-version}}_${{ github.run_id }} | |
| path: | | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/IRescue_out | |
| /home/runner/pytest_workflow_*/*/IRescue_tmp | |
| /home/runner/pytest_workflow_env.log | |
| /home/runner/pytest_workflow_combined.log | |
| /home/runner/pytest_workflow_conda_list.log | |
| include-hidden-files: true |