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

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dr. M.S. (Matthijs) Berends
2024-04-23 10:55:48 +02:00
parent 04df6dfcf5
commit 0d8a91db49
10 changed files with 21 additions and 19 deletions
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2
R/aa_globals.R
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@ -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",

2
R/aa_helper_functions.R
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@ -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`

2
R/ab_selectors.R
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@ -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

2
R/eucast_rules.R
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@ -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
}

2
R/guess_ab_col.R
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@ -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`

2
R/mo.R
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@ -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") {