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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 06:21:56 +02:00

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

This commit is contained in:
2024-04-23 10:55:48 +02:00
parent 04df6dfcf5
commit 0d8a91db49
10 changed files with 21 additions and 19 deletions

View File

@ -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

View File

@ -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))) {