Custom alpha for each fit #42
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| name: Algorithm Analysis | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| - 'analysis/**' | |
| jobs: | |
| algorithms: | |
| runs-on: ubuntu-latest | |
| outputs: # here we use the outputs from steps, and set outputs for the job `configure` | |
| algorithms: ${{ steps.algorithms.outputs.algorithms }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| id: setup_python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: 'pip' | |
| # - name: Cache virtualenv | |
| # uses: actions/cache@v3 | |
| # with: | |
| # key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }} | |
| # path: .venv | |
| - name: Install dependencies | |
| run: | | |
| python -m venv .venv | |
| source .venv/bin/activate | |
| python -m pip install -r requirements.txt | |
| python -m pip install pytest | |
| - name: Read algorithms | |
| id: algorithms | |
| run: | | |
| echo 'algorithms<<EOF' >> $GITHUB_OUTPUT | |
| cat ./tests/IVIMmodels/unit_tests/algorithms.json >> $GITHUB_OUTPUT | |
| echo 'EOF' >> $GITHUB_OUTPUT | |
| - name: Log algorithms | |
| run: | | |
| echo "${{fromJson(steps.algorithms.outputs.algorithms)}}" | |
| echo "${{fromJson(steps.algorithms.outputs.algorithms).algorithms}}" | |
| - name: Log algorithms file | |
| run: cat ./tests/IVIMmodels/unit_tests/algorithms.json | |
| build: | |
| runs-on: ubuntu-latest | |
| needs: algorithms | |
| continue-on-error: false | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| algorithm: ${{fromJson(needs.algorithms.outputs.algorithms).algorithms}} | |
| SNR: [10, 30, 50, 100, 200] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: 'pip' | |
| # - name: Cache virtualenv | |
| # uses: actions/cache@v3 | |
| # with: | |
| # key: venv-${{ runner.os }}-${{ steps.setup_python.outputs.python-version}}-${{ hashFiles('requirements.txt') }} | |
| # path: .venv | |
| - name: Install dependencies | |
| run: | | |
| python -m venv .venv | |
| source .venv/bin/activate | |
| python -m pip install -r requirements.txt | |
| python -m pip install pytest | |
| - name: Generate fitting data | |
| run: | | |
| source .venv/bin/activate | |
| python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv | |
| - name: Upload raw data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Working_Data | |
| retention-days: 1 | |
| path: | | |
| test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv | |
| test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.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: | | |
| head -n 1 $(ls artifacts/Working_Data/test_output_*.csv | head -n 1) > test_output.csv | |
| tail -q -n +2 artifacts/Working_Data/test_output_*.csv >> test_output.csv | |
| - name: Merge timing results | |
| run: | | |
| head -n 1 $(ls artifacts/Working_Data/test_duration_*.csv | head -n 1) > test_duration.csv | |
| tail -q -n +2 artifacts/Working_Data/test_duration_*.csv >> test_duration.csv | |
| - name: Upload merged artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Data | |
| path: | | |
| test_output.csv | |
| test_duration.csv | |
| analyze: | |
| runs-on: ubuntu-latest | |
| needs: merge | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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: 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 | |
| if: always() | |
| with: | |
| name: 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 | |
| compare: | |
| runs-on: ubuntu-latest | |
| needs: merge | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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::tidyverse | |
| any::assertr | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: Data | |
| - name: Test against previous results | |
| run: Rscript --vanilla tests/IVIMmodels/unit_tests/compare.r test_output.csv test_reference.csv tests/IVIMmodels/unit_tests/reference_output.csv test_results.csv | |
| - name: Upload data | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: Comparison | |
| path: | | |
| test_reference.csv | |
| test_results.csv |