Fix CI rebuild validation for cross-platform reproducibility

Author: Ekin-Kahraman

.github/workflows/ci.yml

@@ -67,6 +67,11 @@ jobs:
       - 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
 
@@ -76,14 +81,13 @@ jobs:
       - name: Validate rebuilt outputs
         run: Rscript -e 'testthat::test_dir("tests/testthat")'
 
-      - name: Verify regenerated tables match tracked results
-        run: git diff --exit-code -- results/tables
+      - name: Compare regenerated tables to tracked results
+        run: Rscript dev/compare_tables.R "$RUNNER_TEMP/reference_tables" results/tables
 
-      - name: Verify key figures match tracked results
-        run: >
-          git diff --exit-code --
-          results/figures/qc_library_size.png
-          results/figures/ma_plot.png
-          results/figures/pca_plot.png
-          results/figures/sensitivity_lfc_scatter.png
-          results/figures/volcano_plot.png
+      - 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

dev/compare_tables.R

@@ -0,0 +1,138 @@
+#!/usr/bin/env Rscript
+
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) != 2) {
+  stop("Usage: Rscript dev/compare_tables.R <reference_dir> <generated_dir>")
+}
+
+reference_dir <- args[[1]]
+generated_dir <- args[[2]]
+comparison_digits <- 5L
+
+if (!dir.exists(reference_dir)) {
+  stop("Reference directory not found: ", reference_dir)
+}
+if (!dir.exists(generated_dir)) {
+  stop("Generated directory not found: ", generated_dir)
+}
+
+list_csv_files <- function(path) {
+  sort(list.files(path, pattern = "\\.csv$", full.names = FALSE))
+}
+
+reference_files <- list_csv_files(reference_dir)
+generated_files <- list_csv_files(generated_dir)
+
+if (!identical(reference_files, generated_files)) {
+  missing_files <- setdiff(reference_files, generated_files)
+  extra_files <- setdiff(generated_files, reference_files)
+  details <- c(
+    if (length(missing_files) > 0) paste("missing:", paste(missing_files, collapse = ", ")),
+    if (length(extra_files) > 0) paste("extra:", paste(extra_files, collapse = ", "))
+  )
+  stop("CSV file set mismatch between reference and generated outputs. ", paste(details, collapse = "; "))
+}
+
+first_mismatch <- function(reference_values, generated_values) {
+  same <- (reference_values == generated_values) | (is.na(reference_values) & is.na(generated_values))
+  same[is.na(same)] <- FALSE
+  mismatch <- which(!same)
+  if (length(mismatch) == 0) {
+    return(NA_integer_)
+  }
+  mismatch[[1]]
+}
+
+format_value <- function(value) {
+  if (is.na(value)) {
+    return("NA")
+  }
+  as.character(value)
+}
+
+compare_numeric_column <- function(reference_col, generated_col, file_label, col_name) {
+  reference_cmp <- signif(reference_col, digits = comparison_digits)
+  generated_cmp <- signif(generated_col, digits = comparison_digits)
+  mismatch <- first_mismatch(reference_cmp, generated_cmp)
+  if (!is.na(mismatch)) {
+    stop(
+      sprintf(
+        "%s: numeric mismatch in column '%s' at row %d (reference=%s, generated=%s; compared at %d significant digits)",
+        file_label,
+        col_name,
+        mismatch,
+        format_value(reference_col[[mismatch]]),
+        format_value(generated_col[[mismatch]]),
+        comparison_digits
+      )
+    )
+  }
+}
+
+compare_text_column <- function(reference_col, generated_col, file_label, col_name) {
+  reference_chr <- ifelse(is.na(reference_col), NA_character_, as.character(reference_col))
+  generated_chr <- ifelse(is.na(generated_col), NA_character_, as.character(generated_col))
+  mismatch <- first_mismatch(reference_chr, generated_chr)
+  if (!is.na(mismatch)) {
+    stop(
+      sprintf(
+        "%s: value mismatch in column '%s' at row %d (reference=%s, generated=%s)",
+        file_label,
+        col_name,
+        mismatch,
+        format_value(reference_chr[[mismatch]]),
+        format_value(generated_chr[[mismatch]])
+      )
+    )
+  }
+}
+
+for (filename in reference_files) {
+  file_label <- paste0("results/tables/", filename)
+  reference_df <- read.csv(
+    file.path(reference_dir, filename),
+    stringsAsFactors = FALSE,
+    check.names = FALSE
+  )
+  generated_df <- read.csv(
+    file.path(generated_dir, filename),
+    stringsAsFactors = FALSE,
+    check.names = FALSE
+  )
+
+  if (!identical(names(reference_df), names(generated_df))) {
+    stop(file_label, ": column mismatch between reference and generated outputs")
+  }
+  if (nrow(reference_df) != nrow(generated_df) || ncol(reference_df) != ncol(generated_df)) {
+    stop(
+      file_label,
+      ": dimension mismatch (reference=",
+      nrow(reference_df),
+      "x",
+      ncol(reference_df),
+      ", generated=",
+      nrow(generated_df),
+      "x",
+      ncol(generated_df),
+      ")"
+    )
+  }
+
+  for (col_name in names(reference_df)) {
+    reference_col <- reference_df[[col_name]]
+    generated_col <- generated_df[[col_name]]
+    if (is.numeric(reference_col) && is.numeric(generated_col)) {
+      compare_numeric_column(reference_col, generated_col, file_label, col_name)
+    } else {
+      compare_text_column(reference_col, generated_col, file_label, col_name)
+    }
+  }
+}
+
+message(
+  "Tracked tables match regenerated outputs across ",
+  length(reference_files),
+  " files at ",
+  comparison_digits,
+  " significant digits."
+)