stochtree/.github/workflows/regression-test.yml at main · StochasticTree/stochtree · GitHub

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on:
  workflow_dispatch:

name: Running stochtree on benchmark datasets

jobs:
  stochtree_r:
    name: stochtree-r-bart-regression-test
    runs-on: ubuntu-latest

    steps:
      - name: Checkout stochtree repo
        uses: actions/checkout@v4
        with:
          submodules: 'recursive'

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Create a properly formatted version of the stochtree R package in a subfolder
        run: |
          Rscript cran-bootstrap.R 0 0 1

      - name: Setup R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::testthat, any::decor, local::stochtree_cran

      - name: Create output directory for R regression test results
        run: |
          mkdir -p tools/regression/bart/stochtree_bart_r_results
          mkdir -p tools/regression/bcf/stochtree_bcf_r_results

      - name: Run the R regression test benchmark suite
        run: |
          Rscript tools/regression/bart/regression_test_dispatch_bart.R
          Rscript tools/regression/bcf/regression_test_dispatch_bcf.R

      - name: Collate and analyze R regression test results
        run: |
          Rscript tools/regression/bart/regression_test_analysis_bart.R
          Rscript tools/regression/bcf/regression_test_analysis_bcf.R

      - name: Setup Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"

      - name: Install Package with Relevant Dependencies
        run: |
          pip install --upgrade pip
          pip install -r requirements.txt
          pip install .

      - name: Create output directory for python regression test results
        run: |
          mkdir -p tools/regression/bart/stochtree_bart_python_results
          mkdir -p tools/regression/bcf/stochtree_bcf_python_results

      - name: Run the python regression test benchmark suite
        run: |
          python tools/regression/bart/regression_test_dispatch_bart.py
          python tools/regression/bcf/regression_test_dispatch_bcf.py

      - name: Collate and analyze python regression test results
        run: |
          python tools/regression/bart/regression_test_analysis_bart.py
          python tools/regression/bcf/regression_test_analysis_bcf.py

      - name: Store R BART benchmark test results as an artifact of the run
        uses: actions/upload-artifact@v4
        with:
          name: stochtree-r-bart-summary
          path: tools/regression/bart/stochtree_bart_r_results/stochtree_bart_r_summary.csv

      - name: Store R BCF benchmark test results as an artifact of the run
        uses: actions/upload-artifact@v4
        with:
          name: stochtree-r-bcf-summary
          path: tools/regression/bcf/stochtree_bcf_r_results/stochtree_bcf_r_summary.csv

      - name: Store python BART benchmark test results as an artifact of the run
        uses: actions/upload-artifact@v4
        with:
          name: stochtree-python-bart-summary
          path: tools/regression/bart/stochtree_bart_python_results/stochtree_bart_python_summary.csv

      - name: Store python BCF benchmark test results as an artifact of the run
        uses: actions/upload-artifact@v4
        with:
          name: stochtree-python-bcf-summary
          path: tools/regression/bcf/stochtree_bcf_python_results/stochtree_bcf_python_summary.csv