Fix r1.yml CI dependencies and renv fallback #47
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| name: Reproducible R Pipeline | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| permissions: | |
| contents: read | |
| jobs: | |
| pipeline: | |
| name: Run full analysis pipeline | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Debug repository structure and inputs | |
| run: | | |
| echo "Working directory:" | |
| pwd | |
| echo "" | |
| echo "Top level files:" | |
| ls -la | |
| echo "" | |
| echo "Notebooks folder:" | |
| ls -la notebooks || true | |
| echo "" | |
| echo "Analysis R folder:" | |
| ls -la analysis/R || true | |
| echo "" | |
| echo "Data folder (max depth 4):" | |
| find data -maxdepth 4 -type f | sort || true | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.3.2" | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| build-essential \ | |
| gfortran \ | |
| libfontconfig1-dev \ | |
| libfreetype6-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev | |
| - name: Create output directory | |
| run: mkdir -p output | |
| - name: Restore R environment with renv if lockfile exists | |
| run: | | |
| Rscript -e 'cat("R version:\n"); print(R.version.string)' | |
| Rscript -e 'if (!file.exists("renv.lock")) { message("No renv.lock found. Skipping renv restore."); quit(status = 0) }' | |
| Rscript -e 'install.packages("renv", repos = "https://cloud.r-project.org")' | |
| Rscript -e 'renv::restore(prompt = FALSE)' | |
| - name: Install minimal packages if no renv.lock | |
| run: | | |
| Rscript -e 'if (file.exists("renv.lock")) quit(status = 0)' | |
| Rscript -e 'install.packages(c("here","readr","dplyr","tidyr","ggplot2","caret","pROC","randomForest","stringr"), repos = "https://cloud.r-project.org")' | |
| - name: Run full analysis pipeline | |
| run: | | |
| set -e | |
| Rscript --vanilla notebooks/01_load_and_clean.R | |
| Rscript --vanilla notebooks/02_exploration.R | |
| Rscript --vanilla notebooks/03_feature_engineering.R | |
| Rscript --vanilla notebooks/04_model_training.R | |
| Rscript --vanilla notebooks/05_evaluation.R | |
| Rscript --vanilla notebooks/09_tables_confusion_matrices.R | |
| - name: Debug list outputs | |
| if: always() | |
| run: | | |
| echo "Output folder contents:" | |
| find output -type f -maxdepth 5 | sort || true | |
| echo "" | |
| ls -la output || true | |
| - name: Verify outputs (soft fail for now) | |
| if: always() | |
| run: | | |
| echo "Verifying key outputs exist (warnings only)." | |
| missing=0 | |
| check() { | |
| if [ ! -f "$1" ]; then | |
| echo "MISSING: $1" | |
| missing=1 | |
| else | |
| echo "OK: $1" | |
| fi | |
| } | |
| check output/confusion_matrix_logit_oof_youden.csv | |
| check output/confusion_matrix_rf_oof_youden.csv | |
| check output/performance_metrics_oof_youden.csv | |
| check output/Table_5_Logistic_Regression_Confusion_Matrix_OOF_Youden.csv | |
| check output/Table_6_Random_Forest_Confusion_Matrix_OOF_Youden.csv | |
| check output/Table_Confusion_Matrix_Summary_Youden_OOF.csv | |
| if [ $missing -eq 1 ]; then | |
| echo "One or more expected outputs are missing. Check logs above for root cause." | |
| fi | |
| - name: Upload outputs as artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: analysis-outputs | |
| path: output/ | |
| if-no-files-found: warn |