Add regression tests #20
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| name: Regression tests | |
| on: | |
| pull_request: | |
| branches: ['develop'] | |
| jobs: | |
| compute_seg_masks: | |
| name: Compute results | |
| runs-on: self-hosted | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| # - uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: '3.8.5' | |
| # | |
| # - name: Install dependencies | |
| # run: pip install -r requirements.txt | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: 'latest' | |
| channels: conda-forge, bioconda | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: superdsm | |
| environment-file: superdsm.yml | |
| - name: Download image data | |
| run: | | |
| conda info | |
| python --version | |
| cd examples | |
| python load_data.py | |
| - name: Run SuperDSM | |
| run: python -m "superdsm.batch" examples --task-dir "U2OS" --task-dir "NIH3T3" --task-dir "BBBC039" --task-dir "GOWT1-1" --task-dir "GOWT1-2" --run | |
| - name: Aggregate results | |
| run: | | |
| rm -rf examples/fibroblast | |
| for taskdir in $(cd examples && find . -name 'seg') | |
| do | |
| mkdir -p "results/$taskdir" | |
| mv examples/$taskdir/*.png "results/$taskdir/" | |
| done | |
| - name: Upload results artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: seg_masks | |
| path: results | |
| validate_results: | |
| name: Validate results | |
| runs-on: ubuntu-latest | |
| needs: ['compute_seg_masks'] | |
| strategy: | |
| matrix: | |
| taskdir: | |
| - U2OS/default | |
| - U2OS/default/adapted | |
| - U2OS/default/adapted/isbi24 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.8.5' | |
| - name: Install dependencies | |
| run: pip install -r tests/regression/requirements.txt | |
| - name: Download results artifact | |
| uses: actions/download-artifact@v3 | |
| - name: Run tests | |
| run: | | |
| mkdir actual_csv | |
| python tests/regression/test.py results/${{ matrix.taskdir }}/seg actual_csv tests/regression/expected/${{ matrix.taskdir }} |