release: finalize CancerPPIr v1.2.0 and strengthen end-to-end validation

.github/workflows/r-tests.yml

@@ -66,9 +66,28 @@ jobs:
       - name: Install Linux runtime libraries
         if: runner.os == 'Linux'
         shell: bash
+        timeout-minutes: 10
         run: |
-          sudo apt-get update
-          sudo apt-get install -y --no-install-recommends libglpk40
+          for attempt in 1 2 3; do
+            echo "apt-get update attempt ${attempt}/3"
+            if sudo timeout --kill-after=10s 90s apt-get \
+              -o Acquire::Retries=2 \
+              -o Acquire::http::Timeout=20 \
+              -o Acquire::https::Timeout=20 update; then
+              break
+            fi
+            if [ "$attempt" -eq 3 ]; then
+              echo "::error::apt-get update failed or timed out after 3 attempts"
+              exit 1
+            fi
+            sleep 5
+          done
+
+          sudo timeout --kill-after=10s 180s apt-get \
+            -o Acquire::Retries=2 \
+            -o Acquire::http::Timeout=20 \
+            -o Acquire::https::Timeout=20 \
+            install -y --no-install-recommends libglpk40
 
       - name: Restore renv environment
         uses: r-lib/actions/setup-renv@d3c5be51b12e724e68f33216ca3c148b66d5f0b6 # v2

R/analytical_workbook.R

@@ -1544,7 +1544,8 @@ build_executive_summary <- function(
   score_threshold,
   string_version,
   louvain_seed,
-  fdr_threshold
+  fdr_threshold,
+  run_enrichment = TRUE
 ) {
   module_class <- analytical_vector_text(
     module_annotations$interpretation_class,
@@ -1657,7 +1658,9 @@ build_executive_summary <- function(
       string_version,
       "; score_threshold=",
       score_threshold,
-      "; offline_enrichment=TRUE; FDR<=",
+      "; offline_enrichment=",
+      as.character(isTRUE(run_enrichment)),
+      "; FDR<=",
       fdr_threshold,
       "; Louvain_seed=",
       louvain_seed
@@ -2202,7 +2205,8 @@ build_analytical_workbook <- function(
   biological_evidence,
   string_version = "12.0",
   louvain_seed = CANCERPPIR_LOUVAIN_SEED,
-  fdr_threshold = 0.05
+  fdr_threshold = 0.05,
+  run_enrichment = TRUE
 ) {
   required_evidence_objects <- c(
     "module_annotations",
@@ -2273,7 +2277,8 @@ build_analytical_workbook <- function(
     score_threshold = score_threshold,
     string_version = string_version,
     louvain_seed = louvain_seed,
-    fdr_threshold = fdr_threshold
+    fdr_threshold = fdr_threshold,
+    run_enrichment = run_enrichment
   )
 
   network_overview <- build_network_overview(

R/pipeline.R

@@ -1007,7 +1007,8 @@ run_cancerppir <- function(
     biological_evidence = biological_evidence,
     string_version = "12.0",
     louvain_seed = CANCERPPIR_LOUVAIN_SEED,
-    fdr_threshold = 0.05
+    fdr_threshold = 0.05,
+    run_enrichment = run_enrichment
   )
 
   analytical_sheets <- analytical_report$sheets

scripts/README.md

@@ -28,14 +28,25 @@ still does not run the seven-case production regression.
 Individual commands remain available for focused diagnosis:
 
 - `run_unit_tests.R` — complete unit and CLI test suite.
-- `run_smoke_test.R` — single-case smoke validation.
+- `run_smoke_test.R` — bundled synthetic end-to-end smoke validation.
 - `validate_documentation_contract.R` — documentation contract.
 - `validate_reproducibility_contract.R` — pinned software-environment contract.
 - `validate_release_contract.R` — static release contract.
 - `validate_publication_readiness.R` — publication metadata and public-contract
   audit.
 - `validate_repository_quality.R` — repository and CI hygiene gate.
 
+Run one complete non-clinical analysis against an existing STRING v12 cache:
+
+```bash
+Rscript scripts/run_smoke_test.R STRING_CACHE OUTPUT_ROOT
+```
+
+Both paths must be outside the repository, and all required STRING resources
+must already exist. The command validates all six outputs, workbook schemas,
+GraphML, versioned provenance, checksums, and mapping metadata without running
+any of the seven clinical release cases.
+
 ## Release qualification
 
 - `run_release_qualification.R` — final seven-case release gate.