rename pre-commit hook to pre-commit checks (no-check)

.github/prehooks/commit-msg

@@ -29,22 +29,24 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#!/bin/bash
+########################################
+# This script runs before every commit #
+########################################
 
-echo "Running commit-msg hook..."
+# check the commit message
-
-# check if the commit message contains '(no-check)' or '(no-verify)'
 COMMIT_MSG=$(cat "$1")
-if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-verify\) ]]; then
+if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
-  echo "Commit check bypassed by commit message."
+  echo "Not running pre-commit checks; commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
   exit 0
 fi
 
 
+echo "Running pre-commit checks..."
+
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 if command -v Rscript > /dev/null; then
   if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
-    Rscript -e "source('data-raw/_pre_commit_hook.R')"
+    Rscript -e "source('data-raw/_pre_commit_checks.R')"
     currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
     echo "- Adding changed files in ./data-raw and ./man to this commit"
     git add data-raw/*

.github/workflows/check-recent.yaml

@@ -58,9 +58,9 @@ jobs:
           - {os: ubuntu-latest,  r: 'devel', allowfail: false}
 
           # current 'release' version, check all major OSes:
-          - {os: macOS-latest,   r: '4.3', allowfail: false}
+          - {os: macOS-latest,   r: 'release', allowfail: false}
-          - {os: windows-latest, r: '4.3', allowfail: false}
+          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: ubuntu-latest,  r: '4.3', allowfail: false}
+          - {os: ubuntu-latest,  r: 'release', allowfail: false}
 
           # older versions (see also check-old.yaml for even older versions):
           - {os: ubuntu-latest, r: '4.2', allowfail: false}

R/aa_globals.R

@@ -28,7 +28,7 @@
 # ==================================================================== #
 
 # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
-# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
+# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
 EUCAST_VERSION_BREAKPOINTS <- list(
   # "13.0" = list(
   #   version_txt = "v13.0",

R/aa_helper_functions.R

@@ -689,7 +689,7 @@ create_eucast_ab_documentation <- function() {
   ab <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AMR_env$AB_lookup$ab) {
       # separate drugs, such as `AMX`

R/ab_selectors.R

@@ -611,7 +611,7 @@ ab_select_exec <- function(function_name,
     } else if (isTRUE(function_name == "antimycobacterials")) {
       abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
     } else {
-      # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_hook.R
+      # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_checks.R
       # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
       abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
       # manually added codes from add_custom_antimicrobials() must also be supported

R/eucast_rules.R

@@ -590,7 +590,7 @@ eucast_rules <- function(x,
     # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
     eucast_rules_df <- list(...)$eucast_rules_df
   } else {
-    # otherwise internal data file, created in data-raw/_pre_commit_hook.R
+    # otherwise internal data file, created in data-raw/_pre_commit_checks.R
     eucast_rules_df <- EUCAST_RULES_DF
   }
 

R/guess_ab_col.R

@@ -335,7 +335,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
   x_new <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `AB_CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `AB_CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AMR_env$AB_lookup$ab) {
       # separate drugs, such as `AMX`

R/mo.R

@@ -460,7 +460,7 @@ as.mo <- function(x,
       }
     }
     
-    # 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_hook.R
+    # 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_checks.R
     out[out %in% MO_CONS] <- "B_STPHY_CONS"
     out[out %in% MO_COPS] <- "B_STPHY_COPS"
     if (Becker == "all") {

data-raw/_pre_commit_checks.R

@@ -28,7 +28,7 @@
 # ==================================================================== #
 
 # Run this file to update the package using:
-# source("data-raw/_pre_commit_hook.R")
+# source("data-raw/_pre_commit_checks.R")
 
 library(dplyr, warn.conflicts = FALSE)
 try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like

data-raw/reproduction_of_microorganisms.R

@@ -251,7 +251,7 @@ taxonomy_gbif <- taxonomy_gbif.bak %>%
     kingdom %in% c("Archaea", "Bacteria", "Protozoa") |
       # include all of these fungal orders
       order %in% include_fungal_orders |
-      # and all of these important genera (see "data-raw/_pre_commit_hook.R")
+      # and all of these important genera (see "data-raw/_pre_commit_checks.R")
       # (they also contain bacteria and protozoa, but these will get prevalence = 2 later on)
       genus %in% AMR:::MO_PREVALENT_GENERA
   ) %>%
@@ -1671,7 +1671,7 @@ if (!identical(example_isolates$mo, as.mo(example_isolates$mo, language = NULL))
 
 # load new data sets again
 devtools::load_all(".")
-source("data-raw/_pre_commit_hook.R")
+source("data-raw/_pre_commit_checks.R")
 devtools::load_all(".")
 
 if (!identical(intrinsic_resistant$mo, as.mo(intrinsic_resistant$mo, language = NULL))) {