Add *.Rproj to gitignore #59
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| r-checks: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libglpk40 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.5.2" | |
| use-public-rspm: true | |
| - name: Restore renv packages | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Restore pinned dependencies | |
| run: Rscript 000_install_dependencies.R | |
| - name: Verify renv.lock unchanged | |
| run: git diff --exit-code renv.lock | |
| - name: Check renv status | |
| run: > | |
| Rscript -e 's <- renv::status(); | |
| if (is.list(s) && !isTRUE(s$synchronized)) quit(status = 1)' | |
| - name: Lint | |
| run: Rscript dev/lint.R | |
| - name: Tests | |
| run: Rscript -e 'testthat::test_dir("tests/testthat")' | |
| pipeline-rebuild: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libglpk40 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.5.2" | |
| use-public-rspm: true | |
| - name: Restore renv packages | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Install pinned dependencies | |
| run: Rscript 000_install_dependencies.R | |
| - name: Save tracked tables for comparison | |
| run: | | |
| mkdir -p "$RUNNER_TEMP/reference_tables" | |
| cp results/tables/*.csv "$RUNNER_TEMP/reference_tables"/ | |
| - name: Remove committed analysis outputs before rebuild | |
| run: rm -f results/figures/*.png results/tables/*.csv | |
| - name: Rebuild analysis outputs | |
| run: Rscript run_all.R | |
| - name: Validate rebuilt outputs | |
| run: Rscript -e 'testthat::test_dir("tests/testthat")' | |
| - name: Compare regenerated tables to tracked results | |
| run: Rscript dev/compare_tables.R "$RUNNER_TEMP/reference_tables" results/tables | |
| - name: Verify key figures were regenerated | |
| run: | | |
| test -f results/figures/qc_library_size.png | |
| test -f results/figures/ma_plot.png | |
| test -f results/figures/pca_plot.png | |
| test -f results/figures/sensitivity_lfc_scatter.png | |
| test -f results/figures/volcano_plot.png |