Reformat json read #22
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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: | | |
| echo "algorithms<<EOF" >> $GITHUB_OUTPUT | |
| cat tests/IVIMmodels/unit_tests/algorithms.json >> $GITHUB_OUTPUT | |
| echo "EOF" >> $GITHUB_OUTPUT | |
| 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 |