Split analysis into matrix jobs #18
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| name: Algorithm Analysis | ||
| on: | ||
| push: | ||
| branches: | ||
| - 'main' | ||
| - 'analysis/**' | ||
| jobs: | ||
| read_algorithms: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Read algorithms | ||
| id: read_algorithms | ||
| run: | | ||
| algorithms=$(cat tests/IVIMmodels/unit_tests/algorithms.json) | ||
| echo "::set-output name=algorithms::$algorithms" | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| needs: read_algorithms | ||
| continue-on-error: false | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| algorithm: ${{ fromJson(needs.read_algorithms.outputs.algorithms).algorithms }} | ||
| SNR: [10 30 50 100 200] | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -r requirements.txt | ||
| - name: Generate fitting data | ||
| run: | | ||
| pip install pytest | ||
| python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration.csv | ||
| - name: Upload raw data | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: RawData/raw_data_${{ matrix.algorithm }}_${{ matrix.SNR }} | ||
| path: | | ||
| test_output.csv | ||
| test_duration.csv | ||
| merge: | ||
| runs-on: ubuntu-latest | ||
| needs: build | ||
| steps: | ||
| - name: Download artifacts | ||
| uses: actions/download-artifact@v3 | ||
| with: | ||
| path: artifacts | ||
| - name: Merge fitting results | ||
| run: | | ||
| cat artifacts/raw_data_*/test_output.csv > test_output.csv | ||
| - name: Merge timing results | ||
| run: | | ||
| cat artifacts/raw_data_*/test_duration.csv > test_duration.csv | ||
| - name: Upload merged artifacts | ||
| uses: actions/upload-artifacts@v3 | ||
| with: | ||
| name: Raw Data | ||
| path: | | ||
| test_output.csv | ||
| test_duration.csv | ||
| analyze: | ||
| runs-on: ubuntu-latest | ||
| needs: merge | ||
| steps: | ||
| - name: Set up R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
| - name: Install R dependencies | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| packages: | | ||
| any::plyr | ||
| any::dplyr | ||
| any::tidyverse | ||
| any::data.table | ||
| any::ggplot2 | ||
| - name: Download artifacts | ||
| uses: actions/download-artifact@v3 | ||
| with: | ||
| name: Raw Data | ||
| - name: Generate figures | ||
| run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv | ||
| - name: Upload figures | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: Fit Figures | ||
| path: | | ||
| D.pdf | ||
| f.pdf | ||
| Dp.pdf | ||
| D_limited.pdf | ||
| f_limited.pdf | ||
| Dp_limited.pdf | ||
| durations.pdf | ||
| curve_plot.pdf | ||
| fitted_curves.pdf | ||
