analysis.yml

name: Algorithm Analysis

on:
  push:
    branches:
      - 'main'
      - 'analysis/**'

jobs:
  build:

    runs-on: ubuntu-latest
    continue-on-error: false
    strategy:
      fail-fast: false
    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: 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: Generate fitting data
        run: |
          pip install pytest
          python -m pytest -m slow --saveFileName test_output.csv --SNR 10 30 50 100 200 --fitCount 300 --saveDurationFileName test_duration.csv
      - name: Generate figures
        run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv
      - name: Upload raw data
        uses: actions/upload-artifact@v3
        with:
            name: Raw data
            path: |
              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