Limit push trigger to main in code-coverage workflow

Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

.github/workflows/check-current-testthat.yaml

@@ -29,10 +29,11 @@
 
 on:
   pull_request:
-    # run in each PR in this repo
+    # run in each PR in this repo (1 worker, see matrix logic below)
     branches: '**'
   push:
-    branches: '**'
+    # only on main; pushing to a PR branch is already covered by pull_request above
+    branches: [main]
   schedule:
     # also run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)

.github/workflows/codecovr.yaml

@@ -28,10 +28,12 @@
 # ==================================================================== #
 
 on:
-  push:
-    branches: '**'
   pull_request:
+    # run on every PR update (once per push)
     branches: '**'
+  push:
+    # only on main; PR pushes are already covered by pull_request above
+    branches: [main]
 
 name: code-coverage
 

R/sir.R

@@ -835,8 +835,7 @@ as.sir.data.frame <- function(x,
         message_(
           "Assuming value", plural[1], " ",
           vector_and(col_values, quotes = TRUE),
-          " in column '", font_bold(col_specimen),
+          " in column ", paste0("{.field ", col_specimen, "}"), " reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
-          "' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
           ".\n  Use `as.sir(uti = FALSE)` to prevent this."
         )
       }
@@ -975,7 +974,7 @@ as.sir.data.frame <- function(x,
       if (!all(x[, ab, drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Cleaning values in column '", font_bold(ab), "' (",
+          message_("Cleaning values in column ", paste0("{.field ", ab, "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
             appendLF = FALSE,
@@ -985,7 +984,7 @@ as.sir.data.frame <- function(x,
       } else if (!is.sir(x.bak[, ab, drop = TRUE])) {
         show_message <- TRUE
         if (isTRUE(info)) {
-          message_("Assigning class {.cls sir} to already clean column '", font_bold(ab), "' (",
+          message_("Assigning class {.cls sir} to already clean column ", paste0("{.field ", ab, "}"), " (",
             ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
             ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
             appendLF = FALSE,
@@ -2227,10 +2226,13 @@ check_reference_data <- function(reference_data, .call_depth) {
     class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
     class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
     if (!all(names(class_sir) == names(class_ref))) {
-      stop_("{.arg reference_data} must have the same column names as the {.code clinical_breakpoints} data set.", call = .call_depth)
+      stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
     }
     if (!all(class_sir == class_ref)) {
-      stop_("{.arg reference_data} must be the same structure as the {.code clinical_breakpoints} data set. Column '", names(class_ref[class_sir != class_ref][1]), "' is of class ", class_ref[class_sir != class_ref][1], ", but should be of class ", class_sir[class_sir != class_ref][1], ".", call = .call_depth)
+      bad_col <- names(class_ref[class_sir != class_ref][1])
+      bad_cls <- gsub("<|>", "", class_ref[class_sir != class_ref][1])
+      exp_cls <- gsub("<|>", "", class_sir[class_sir != class_ref][1])
+      stop_("{.arg reference_data} must be the same structure as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", bad_col, "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
     }
   }
 }