mirror of
https://github.com/msberends/AMR.git
synced 2026-05-14 01:10:45 +02:00
23beebc6c3
* Migrate parallel computing in as.sir() from parallel:: to future/future.apply Replace parallel::mclapply() and parallel::parLapply() with future.apply::future_lapply(), enabling transparent support for any future backend (multisession, multicore, mirai_multisession, cluster) on all platforms including Windows. When parallel = TRUE the function now: (1) respects an active future::plan() set by the user without overriding it on exit, or (2) sets a temporary multisession plan with parallelly::availableCores() and tears it down on exit. The max_cores argument controls worker count only when no user plan is active. future and future.apply are added to Suggests in DESCRIPTION. https://claude.ai/code/session_01M1Jvf2Miu6JL4TQrEh1wS8 * Require user plan() for parallel=TRUE; fix as_wt_nwt false-positive warnings - parallel = TRUE now errors with a cli-styled message if no non-sequential future::plan() is active; users must call e.g. future::plan(future::multisession) before using parallel = TRUE (breaking change) - Removed auto-setup/teardown of multisession plan inside as.sir(), which was slow and caused version-mismatch issues with load_all() workflows - Added as_wt_nwt to the exclusion list in as_sir_method() to suppress false-positive "no longer used" warnings during parallel runs - Fixed pieces_per_col row-batch calculation to use n_workers (total available workers from the active plan) instead of n_cores (workers clipped to n_cols), so row-batch mode activates correctly when n_cols < n_workers - Updated @param parallel and @param max_cores roxygen docs; regenerated man/as.sir.Rd - Updated sequential-mode hint to instruct users to set plan() first https://claude.ai/code/session_01M1Jvf2Miu6JL4TQrEh1wS8 * fix parallel * fix parallel * unit tests * unit tedts --------- Co-authored-by: Claude <noreply@anthropic.com>
223 lines
8.0 KiB
R
223 lines
8.0 KiB
R
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
|
|
# Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://amr-for-r.org #
|
|
# ==================================================================== #
|
|
|
|
test_that("test-zzz.R", {
|
|
skip_on_cran()
|
|
|
|
# Check if these functions still exist in their package (all are in Suggests field)
|
|
# Since GitHub Actions runs every night, we will get emailed when a dependency fails based on this unit test
|
|
|
|
# functions used by import_fn()
|
|
import_functions <- c(
|
|
"%chin%" = "data.table",
|
|
"ansi_has_hyperlink_support" = "cli",
|
|
"anti_join" = "dplyr",
|
|
"as.data.table" = "data.table",
|
|
"as_tibble" = "tibble",
|
|
"chmatch" = "data.table",
|
|
"cli_abort" = "cli",
|
|
"cur_column" = "dplyr",
|
|
"cur_group" = "dplyr",
|
|
"document_position" = "rstudioapi",
|
|
"document_range" = "rstudioapi",
|
|
"full_join" = "dplyr",
|
|
"getActiveDocumentContext" = "rstudioapi",
|
|
"has_color" = "crayon",
|
|
"has_internet" = "curl",
|
|
"html_attr" = "rvest",
|
|
"html_children" = "rvest",
|
|
"html_node" = "rvest",
|
|
"html_nodes" = "rvest",
|
|
"html_table" = "rvest",
|
|
"html_text" = "rvest",
|
|
"inner_join" = "dplyr",
|
|
"insertText" = "rstudioapi",
|
|
"left_join" = "dplyr",
|
|
"modifyRange" = "rstudioapi",
|
|
"new_pillar_shaft_simple" = "pillar",
|
|
"progress_bar" = "progress",
|
|
"read_html" = "xml2",
|
|
"right_join" = "dplyr",
|
|
"select" = "dplyr",
|
|
"semi_join" = "dplyr",
|
|
"showQuestion" = "rstudioapi",
|
|
"symbol" = "cli",
|
|
"tibble" = "tibble",
|
|
"where" = "tidyselect",
|
|
"write.xlsx" = "openxlsx"
|
|
)
|
|
|
|
# functions that are called directly with ::
|
|
call_functions <- c(
|
|
# cleaner
|
|
"freq" = "cleaner",
|
|
"freq.default" = "cleaner",
|
|
"percentage" = "cleaner",
|
|
# cli
|
|
"ansi_has_hyperlink_support" = "cli",
|
|
"cli_abort" = "cli",
|
|
"cli_inform" = "cli",
|
|
"cli_warn" = "cli",
|
|
"code_highlight" = "cli",
|
|
"format_inline" = "cli",
|
|
"symbol" = "cli",
|
|
# curl
|
|
"has_internet" = "curl",
|
|
# future
|
|
"plan" = "future",
|
|
"nbrOfWorkers" = "future",
|
|
# future.apply
|
|
"future_lapply" = "future.apply",
|
|
# ggplot2
|
|
"aes" = "ggplot2",
|
|
"arrow" = "ggplot2",
|
|
"autoplot" = "ggplot2",
|
|
"element_blank" = "ggplot2",
|
|
"element_line" = "ggplot2",
|
|
"element_text" = "ggplot2",
|
|
"expand_limits" = "ggplot2",
|
|
"facet_wrap" = "ggplot2",
|
|
"fortify" = "ggplot2",
|
|
"geom_col" = "ggplot2",
|
|
"geom_errorbar" = "ggplot2",
|
|
"geom_path" = "ggplot2",
|
|
"geom_point" = "ggplot2",
|
|
"geom_ribbon" = "ggplot2",
|
|
"geom_segment" = "ggplot2",
|
|
"geom_text" = "ggplot2",
|
|
"ggplot" = "ggplot2",
|
|
"labs" = "ggplot2",
|
|
"position_dodge2" = "ggplot2",
|
|
"position_fill" = "ggplot2",
|
|
"scale_colour_discrete" = "ggplot2",
|
|
"scale_discrete_manual" = "ggplot2",
|
|
"scale_fill_discrete" = "ggplot2",
|
|
"scale_fill_manual" = "ggplot2",
|
|
"scale_x_discrete" = "ggplot2",
|
|
"scale_y_continuous" = "ggplot2",
|
|
"scale_y_discrete" = "ggplot2",
|
|
"theme" = "ggplot2",
|
|
"theme_minimal" = "ggplot2",
|
|
"unit" = "ggplot2",
|
|
"xlab" = "ggplot2",
|
|
"ylab" = "ggplot2",
|
|
# knitr
|
|
"asis_output" = "knitr",
|
|
"kable" = "knitr",
|
|
"knit_print" = "knitr",
|
|
"opts_chunk" = "knitr",
|
|
# pillar
|
|
"pillar_shaft" = "pillar",
|
|
"style_na" = "pillar",
|
|
"style_subtle" = "pillar",
|
|
"tbl_format_footer" = "pillar",
|
|
"tbl_sum" = "pillar",
|
|
"type_sum" = "pillar",
|
|
# readxl
|
|
"read_excel" = "readxl",
|
|
# recipes
|
|
"add_step" = "recipes",
|
|
"bake" = "recipes",
|
|
"check_new_data" = "recipes",
|
|
"check_type" = "recipes",
|
|
"has_role" = "recipes",
|
|
"is_trained" = "recipes",
|
|
"prep" = "recipes",
|
|
"print_step" = "recipes",
|
|
"rand_id" = "recipes",
|
|
"recipe" = "recipes",
|
|
"recipes_eval_select" = "recipes",
|
|
"sel2char" = "recipes",
|
|
"step" = "recipes",
|
|
"step_center" = "recipes",
|
|
"tidy" = "recipes",
|
|
# rlang
|
|
"enquos" = "rlang",
|
|
# rmarkdown
|
|
"html_vignette" = "rmarkdown",
|
|
# skimr
|
|
"get_skimmers" = "skimr",
|
|
"inline_hist" = "skimr",
|
|
"sfl" = "skimr",
|
|
# tibble
|
|
"tibble" = "tibble",
|
|
# vctrs
|
|
"vec_arith" = "vctrs",
|
|
"vec_cast" = "vctrs",
|
|
"vec_math" = "vctrs",
|
|
"vec_ptype2" = "vctrs",
|
|
"vec_ptype_abbr" = "vctrs",
|
|
"vec_ptype_full" = "vctrs",
|
|
# usethis
|
|
"use_course" = "usethis"
|
|
)
|
|
|
|
import_functions <- c(import_functions, call_functions)
|
|
|
|
suggests <- strsplit(utils::packageDescription("AMR")$Suggests, "[,\n ]+")[[1]]
|
|
for (i in seq_len(length(import_functions))) {
|
|
fn <- names(import_functions)[i]
|
|
pkg <- unname(import_functions[i])
|
|
expect_true(pkg %in% suggests,
|
|
info = paste0("package `", pkg, "` is not in Suggests")
|
|
)
|
|
# function should exist in foreign pkg namespace
|
|
if (AMR:::pkg_is_available(pkg,
|
|
also_load = FALSE,
|
|
min_version = if (pkg == "dplyr") "1.0.0" else NULL
|
|
)) {
|
|
if (pkg == "rstudioapi") {
|
|
expect_true(is.function(tryCatch(get(fn, envir = asNamespace(pkg)), error = function(e) NULL)),
|
|
info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
|
|
)
|
|
} else {
|
|
expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
|
|
info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
|
|
)
|
|
}
|
|
} else if (pkg != "rstudioapi") {
|
|
warning("Package '", pkg, "' not available")
|
|
}
|
|
}
|
|
|
|
if (AMR:::pkg_is_available("cli")) {
|
|
expect_true(!is.null(cli::symbol$bullet) && is.character(cli::symbol$bullet) && length(cli::symbol$bullet) == 1)
|
|
expect_true(!is.null(cli::symbol$ellipsis) && is.character(cli::symbol$ellipsis) && length(cli::symbol$ellipsis) == 1)
|
|
expect_true(!is.null(cli::symbol$info) && is.character(cli::symbol$info) && length(cli::symbol$info) == 1)
|
|
expect_true(!is.null(cli::symbol$sup_1) && is.character(cli::symbol$sup_1) && length(cli::symbol$sup_1) == 1)
|
|
}
|
|
if (AMR:::pkg_is_available("ggplot2")) {
|
|
# the scale_*_mic() functions rely on these
|
|
expect_true(is.function(ggplot2::scale_x_discrete()$transform))
|
|
expect_true(is.function(ggplot2::scale_y_discrete()$transform))
|
|
expect_true(is.function(ggplot2::scale_colour_discrete()$transform))
|
|
expect_true(is.function(ggplot2::scale_fill_discrete()$transform))
|
|
}
|
|
})
|