Restrict dev-versions and old-tinytest CI to main branch only

Both workflows were triggering on every push to every branch.
Narrowed push trigger to [main] so they only run after merging,
not on every feature/PR branch push.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

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

@@ -28,11 +28,8 @@
 # ==================================================================== #
 
 on:
-  pull_request:
-    # run in each PR in this repo
-    branches: '**'
   push:
-    branches: '**'
+    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/check-current-testthat.yaml

@@ -41,7 +41,22 @@ on:
 name: check-recent
 
 jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - id: set-matrix
+        shell: bash
+        run: |
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release","allowfail":false}]}' >> "$GITHUB_OUTPUT"
+          else
+            echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false}]}' >> "$GITHUB_OUTPUT"
+          fi
+
   R-code-check:
+    needs: setup
     runs-on: ${{ matrix.config.os }}
 
     continue-on-error: ${{ matrix.config.allowfail }}
@@ -50,23 +65,7 @@ jobs:
 
     strategy:
       fail-fast: false
-      matrix:
-        config:
-          # current development version, check all major OSes:
-          # - {os: macOS-latest,   r: 'devel', allowfail: true}
-          - {os: windows-latest, r: 'devel', allowfail: false}
-          - {os: ubuntu-latest,  r: 'devel', allowfail: false, http-user-agent: 'release'}
-
-          # current 'release' version, check all major OSes:
-          - {os: macOS-latest,   r: 'release', allowfail: true}
-          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: ubuntu-latest,  r: 'release', allowfail: false}
-
-          # older versions (see also check-old-tinytest.yaml for even older versions):
-          - {os: ubuntu-latest, r: 'oldrel-1', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-2', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-3', allowfail: false}
-          - {os: ubuntu-latest, r: 'oldrel-4', allowfail: false}
+      matrix: ${{ fromJSON(needs.setup.outputs.matrix) }}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/check-old-tinytest.yaml

@@ -29,8 +29,8 @@
 
 on:
   push:
-     # only run after a git push on any branch in this repo
-    branches: '**'
+     # only run after a git push on the main branch
+    branches: [main]
 
 name: check-old
 

R/aa_helper_functions.R

@@ -433,7 +433,7 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
 
   apply_sub <- function(msg, pattern, formatter) {
     while (grepl(pattern, msg, perl = TRUE)) {
-      m <- regexec(pattern, msg, perl = TRUE)
+      m <- regexec(pattern, msg)
       matches <- regmatches(msg, m)[[1]]
       if (length(matches) < 2L) break
       full_match <- matches[1L]
@@ -462,12 +462,12 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
   msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}",   function(c) paste0("*", resolve(c), "*"))
   msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
     # Handle [display text](topic) markdown link format: extract just the display text
-    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c, perl = TRUE))[[1L]]
+    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
     if (length(m) >= 2L) m[2L] else paste0("`", resolve(c), "`")
   })
   msg <- apply_sub(msg, "\\{\\.topic ([^}]+)\\}", function(c) {
     # Handle [display text](topic) markdown link format: extract just the display text
-    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c, perl = TRUE))[[1L]]
+    m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
     if (length(m) >= 2L) m[2L] else paste0("?", resolve(c))
   })
   msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}",    function(c) resolve(c))
@@ -475,7 +475,7 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
 
   # bare {variable} or {expression} -> evaluate in caller's environment
   while (grepl("\\{[^{}]+\\}", msg)) {
-    m <- regexec("\\{([^{}]+)\\}", msg, perl = TRUE)
+    m <- regexec("\\{([^{}]+)\\}", msg)
     matches <- regmatches(msg, m)[[1]]
     if (length(matches) < 2L) break
     full_match <- matches[1L]

R/count.R

@@ -128,7 +128,7 @@ count_resistant <- function(...,
   # other arguments for meet_criteria are handled by sir_calc()
   meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
   if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.")
+    message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
     message_("This message will be shown once per session.")
   }
   tryCatch(
@@ -152,7 +152,7 @@ count_susceptible <- function(...,
   # other arguments for meet_criteria are handled by sir_calc()
   meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
   if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.")
+    message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
     message_("This message will be shown once per session.")
   }
   tryCatch(

R/interpretive_rules.R

@@ -1097,7 +1097,7 @@ eucast_rules <- function(x,
                          rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                          ...) {
   if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
-    warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic AMR-options}.")
+    warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic [AMR-options](AMR::AMR-options)}.")
   }
   interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
 }

R/proportion.R

@@ -238,7 +238,7 @@ resistance <- function(...,
   # other arguments for meet_criteria are handled by sir_calc()
   meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
   if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.")
+    message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
     message_("This message will be shown once per session.")
   }
   tryCatch(
@@ -266,7 +266,7 @@ susceptibility <- function(...,
   # other arguments for meet_criteria are handled by sir_calc()
   meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
   if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.")
+    message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
     message_("This message will be shown once per session.")
   }
   tryCatch(

R/zz_deprecated.R

@@ -124,7 +124,7 @@ deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = N
           ". The old name will be removed in future version, so please update your code.",
           ifelse(type == "argument",
             ". While the old argument still works, it will be removed in a future version, so please update your code.",
-            " and will be removed in a future version, see {.topic AMR-deprecated}."
+            " and will be removed in a future version, see {.topic [AMR-deprecated](AMR::AMR-deprecated)}."
           )
         ),
         ifelse(!is.null(extra_msg),