Bump Python from 3.8 to 3.11 #111
Workflow file for this run
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| name: Regression tests | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: ['develop'] | |
| paths: | |
| - .github/workflows/regressiontests.yml | |
| - superdsm/** | |
| - examples/** | |
| - superdsm.yml | |
| - tests/regression | |
| - requirements.txt | |
| jobs: | |
| regression_tests: | |
| name: "Test: ${{ matrix.taskdir }}" | |
| if: ${{ github.event.action != 'synchronize' || github.event.pull_request.draft == false }} | |
| timeout-minutes: 1440 | |
| runs-on: gpuagrohr-01 | |
| container: | |
| image: ubuntu:22.04 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| taskdir: | |
| - U2OS | |
| - NIH3T3 | |
| - GOWT1-1 | |
| - GOWT1-2 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Clear cache # otherwise corrupted packages can be reported sometimes | |
| run: rm -rf /github/home/conda_pkgs_dir | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: 'latest' | |
| channels: conda-forge, bioconda, defaults | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: superdsm | |
| environment-file: superdsm.yml | |
| - name: Download image data | |
| run: | | |
| cd examples | |
| python load_data.py | |
| - name: Run SuperDSM | |
| run: | | |
| python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}" | |
| python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}" --run | |
| env: | |
| SUPERDSM_INTERMEDIATE_OUTPUT: false | |
| SUPERDSM_NUM_CPUS: 20 | |
| - name: Validate results | |
| id: validation | |
| run: | | |
| mkdir "actual_csv" | |
| sh "tests/regression/validate-${{ matrix.taskdir }}.sh" "actual_csv" | |
| - name: Upload artifact | |
| if: failure() && steps.validation.outcome != 'success' | |
| uses: actions/upload-artifact@v3 ## v4 requires GLIBC_2.28 which is not found on host | |
| with: | |
| name: Results ${{ matrix.taskdir }} | |
| path: actual_csv/${{ matrix.taskdir }} |