Update r1.yml

Author: julian-borges-md

.github/workflows/r1.yml

@@ -19,6 +19,18 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Debug repo contents
+        run: |
+          pwd
+          echo "=== top level ==="
+          ls -la
+          echo "=== notebooks ==="
+          ls -la notebooks || true
+          echo "=== analysis/R ==="
+          ls -la analysis/R || true
+          echo "=== data files ==="
+          find data -maxdepth 4 -type f || true
+
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
@@ -28,62 +40,38 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+          sudo apt-get install -y \
+            libcurl4-openssl-dev libssl-dev libxml2-dev \
+            build-essential gfortran \
+            libfontconfig1-dev libfreetype6-dev \
+            libharfbuzz-dev libfribidi-dev
 
       - name: Restore R environment with renv
         run: |
           Rscript -e 'install.packages("renv", repos = "https://cloud.r-project.org")'
           Rscript -e 'renv::restore(prompt = FALSE)'
 
-      - name: Run full analysis pipeline
-        run: |
-          Rscript notebooks/01_load_and_clean.R
-          Rscript notebooks/02_exploration.R
-          Rscript notebooks/03_feature_engineering.R
-          Rscript notebooks/04_model_training.R
-          Rscript notebooks/05_evaluation.R
-          Rscript notebooks/09_tables_confusion_matrices.R
+      - name: Create output directory
+        run: mkdir -p output
 
-      - name: List output directory
+      - name: Run full analysis pipeline
         run: |
-          ls -la output || true
-
-      - name: Verify outputs
+          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: |
-          # Figures 1–4 from EDA
-          test -f output/Figure_1_Correlation_Matrix_Diabetes.png
-          test -f output/Figure_2_Correlation_Matrix_Heart_Failure.png
-          test -f output/Figure_3_Age_Distribution_Diabetes.png
-          test -f output/Figure_4_Age_Distribution_Heart_Failure.png
-
-          # Models saved to output (ensure 04_model_training.R saves here)
-          test -f output/logistic_model.rds
-          test -f output/random_forest_model.rds
-
-          # Pooled OOF evaluation artifacts
-          test -f output/oof_predictions_logit.csv
-          test -f output/oof_predictions_rf.csv
-          test -f output/chosen_thresholds_youden.csv
-          test -f output/confusion_matrix_logit_oof_youden.csv
-          test -f output/confusion_matrix_rf_oof_youden.csv
-          test -f output/performance_metrics_oof_youden.csv
-
-          # Full caret printed confusion reports
-          test -f output/logistic_regression_confusion_report_oof_youden.txt
-          test -f output/random_forest_confusion_report_oof_youden.txt
-
-          # ROC plots
-          test -f output/roc_logit_oof.png
-          test -f output/roc_rf_oof.png
-
-          # Journal-style confusion matrix tables (Tables 5–6)
-          test -f output/Table_5_Logistic_Regression_Confusion_Matrix_OOF_Youden.csv
-          test -f output/Table_6_Random_Forest_Confusion_Matrix_OOF_Youden.csv
-          test -f output/Table_5_Logistic_Regression_Confusion_Matrix_OOF_Youden.txt
-          test -f output/Table_6_Random_Forest_Confusion_Matrix_OOF_Youden.txt
-          test -f output/Table_Confusion_Matrix_Summary_Youden_OOF.csv
+          echo "=== output files ==="
+          find output -maxdepth 5 -type f | sort || true
 
       - name: Upload outputs as artifacts
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: analysis-outputs