analysis.yml

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: Set up Python
        id: setup_python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Cache pip
        uses: actions/cache@v3
        id: pip-cache
        with:
          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
          path: ${{ env.pythonLocation }}
        if: steps.pip-cache.outputs.cache-hit != 'true'

      - 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: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
        if: steps.pip-cache.outputs.cache-hit != 'true'
      - name: Restore cache
        id: python-cache
        uses: actions/cache@v3
        with:
          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
          path: ${{ env.pythonLocation }}

      - 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