P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 13:41:42 +02:00
Code Releases Activity

Move parallel gate to top of antibiogram.default() like sir.R

Browse Source 
The gate was inside the wisca==TRUE block, so parallel=TRUE with a
sequential plan was silently ignored for non-WISCA antibiograms.
Now the gate runs unconditionally at the top of the function,
identical to the as.sir() pattern: error on explicit parallel=TRUE
with sequential plan, auto-upgrade when a non-sequential plan is
already active.

https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF
This commit is contained in:
Claude
2026-04-30 15:31:37 +00:00
parent 8fb640256a
commit 48af4b7cdc
1 changed files with 28 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
R/antibiogram.R
View File

@@ -483,6 +483,34 @@ antibiogram.default <- function(x,
meet_criteria(info, allow_class = "logical", has_length = 1) meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(parallel, allow_class = "logical", has_length = 1) meet_criteria(parallel, allow_class = "logical", has_length = 1)
# parallel gate - identical pattern to as.sir()
if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
if (isFALSE(parallel)) {
message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")
}
parallel <- TRUE
}
if (isTRUE(parallel)) {
stop_ifnot(
requireNamespace("future.apply", quietly = TRUE),
"Setting {.code parallel = TRUE} requires the {.pkg future.apply} package.\n",
"Install it with {.code install.packages(\"future.apply\")}."
)
stop_if(inherits(future::plan(), "sequential"),
"Setting {.code parallel = TRUE} requires a non-sequential {.help [{.fun future::plan}](future::plan)} to be active.\n",
"For your system, you could first run: {.code library(future); ",
ifelse(.Platform$OS.type == "windows" || in_rstudio(),
"plan(multisession)",
"plan(multicore)"
),
"}",
call = FALSE
)
n_workers <- future::nbrOfWorkers()
} else {
n_workers <- 1L
}
# try to find columns based on type # try to find columns based on type
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info) col_mo <- search_type_in_df(x = x, type = "mo", info = info)
@@ -720,34 +748,6 @@ antibiogram.default <- function(x,
unique_groups <- unique(wisca_parameters$group) unique_groups <- unique(wisca_parameters$group)
# parallel gate for WISCA - identical pattern to as.sir()
if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
if (isFALSE(parallel)) {
message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")
}
parallel <- TRUE
}
if (isTRUE(parallel)) {
stop_ifnot(
requireNamespace("future.apply", quietly = TRUE),
"Setting {.code parallel = TRUE} requires the {.pkg future.apply} package.\n",
"Install it with {.code install.packages(\"future.apply\")}."
)
stop_if(inherits(future::plan(), "sequential"),
"Setting {.code parallel = TRUE} requires a non-sequential {.help [{.fun future::plan}](future::plan)} to be active.\n",
"For your system, you could first run: {.code library(future); ",
ifelse(.Platform$OS.type == "windows" || in_rstudio(),
"plan(multisession)",
"plan(multicore)"
),
"}",
call = FALSE
)
n_workers <- future::nbrOfWorkers()
} else {
n_workers <- 1L
}
use_parallel_wisca <- isTRUE(parallel) && n_workers > 1L && length(unique_groups) > 0L use_parallel_wisca <- isTRUE(parallel) && n_workers > 1L && length(unique_groups) > 0L
if (use_parallel_wisca) { if (use_parallel_wisca) {