Running stochtree on benchmark datasets #2
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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 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| 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 |