Speed up the algorithm analysis workflow #70
Workflow file for this run
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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@v4 | ||
| - name: Cache dependencies | ||
| uses: actions/[email protected] | ||
| id: cache | ||
| with: | ||
| path: ${{ runner.tool_cache }}/Python/3.11 | ||
| key: ${{ runner.tool_cache }}/Python/$3.11/${{ runner.arch }}-${{ hashFiles('requirements.txt') }} | ||
| - name: Set up Python | ||
| id: setup_python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install dependencies | ||
| run: | | ||
| pip install -r requirements.txt | ||
| - 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@v4 | ||
| - name: Restore python cache | ||
| uses: actions/[email protected] | ||
| id: restore_cache | ||
| with: | ||
| path: ${{ runner.tool_cache }}/Python/3.11 | ||
| key: ${{ runner.tool_cache }}/Python/$3.11/${{ runner.arch }}-${{ hashFiles('requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.tool_cache }}/Python/$3.11/${{ runner.arch }}- | ||
| - name: Generate fitting data | ||
| run: | | ||
| 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@v4 | ||
| - 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@v4 | ||
| - 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 | ||
