mirror of
https://github.com/msberends/AMR.git
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dr. M.S. (Matthijs) Berends
9e609dae83
Package: - stop_() called cli::ansi_has_hyperlink_support() before checking that cli is available, so without cli every error became "there is no package called 'cli'" - interpretive_rules() failed on R 3.0 for guidelines without AmpC rules (assignment to zero rows) - Guard the ggplot2 example of wisca_plot() CI: - check-old: R 3.0 could not install tinytest over HTTPS, so no unit tests ran; install it with curl, and fail when tinytest is missing or any test fails - tinytest shim: record expectations in the test file environment, support skips and errors per test_that() block, add missing testthat equivalents, source helper files - Add R 4.0 (oldrel-6) to check-old, and oldrel-5 to check-recent
115 lines
5.4 KiB
Plaintext
115 lines
5.4 KiB
Plaintext
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in the Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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# we use {tinytest} for older R versions to allow unit testing in R >= 3.0.0.
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# test only on GitHub Actions - not on CRAN as tests are lengthy
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if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
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# env var 'R_LIBS_USER' gets overwritten during 'R CMD check' in GitHub Actions, so:
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.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
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if (!AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
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stop("R_RUN_TINYTEST is 'true', but the tinytest package could not be loaded, so no unit tests were run")
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} else {
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# load the package
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library(AMR)
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# testthat equivalents; tinytest only records expectations that are called from the environment
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# of a test file, so these call the expectations found there (via `env`) instead of tinytest::
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test_that <- function(desc, code) {
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env <- parent.frame()
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tryCatch(code,
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skip_test = function(s) invisible(NULL),
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error = function(e) get("expect_true", envir = env)(FALSE, info = paste0("Error in '", desc, "': ", conditionMessage(e)))
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)
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}
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skip_if <- function(condition, message = "") {
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if (isTRUE(condition)) stop(structure(class = c("skip_test", "condition"), list(message = message, call = NULL)))
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}
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skip_on_cran <- function() invisible(NULL)
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expect_output <- function(...) get("expect_stdout", envir = parent.frame())(...)
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expect_named <- function(object, expected, ...) get("expect_identical", envir = parent.frame())(names(object), expected, ...)
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expect_setequal <- function(object, expected, ...) get("expect_true", envir = parent.frame())(setequal(object, expected), ...)
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expect_lte <- function(object, expected, ...) get("expect_true", envir = parent.frame())(isTRUE(all(object <= expected)), ...)
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# set language
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set_AMR_locale("English")
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# set some functions for older R versions
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if (getRversion() < "3.2.0") {
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anyNA <- AMR:::anyNA
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dir.exists <- AMR:::dir.exists
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file.size <- AMR:::file.size
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file.mtime <- AMR:::file.mtime
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isNamespaceLoaded <- AMR:::isNamespaceLoaded
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lengths <- AMR:::lengths
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}
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if (getRversion() < "3.3.0") {
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strrep <- AMR:::strrep
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}
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if (getRversion() < "3.5.0") {
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isFALSE <- AMR:::isFALSE
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}
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if (getRversion() < "3.6.0") {
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str2lang <- AMR:::str2lang
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# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
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trimws <- AMR:::trimws
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}
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if (getRversion() < "4.0.0") {
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deparse1 <- AMR:::deparse1
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}
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if (getRversion() < "4.4.0") {
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`%||%` <- AMR:::`%||%`
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}
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testdir <- ifelse(dir.exists("inst/testthat"), "inst/testthat", "testthat")
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# helper files are sourced by testthat, but not by tinytest; helper-functions.R only contains expect_inherits(), which tinytest has itself
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helpers <- list.files(system.file(testdir, package = "AMR"), pattern = "^helper.*[.]R$", full.names = TRUE)
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for (helper in helpers[basename(helpers) != "helper-functions.R"]) {
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source(helper)
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}
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suppressMessages(
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out <- test_package("AMR",
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testdir = testdir,
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verbose = FALSE,
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color = FALSE
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)
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)
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cat("\n\nSUMMARY:\n")
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print(summary(out))
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if (!all_pass(out)) {
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cat("\n\nFAILURES:\n")
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print(out, passes = FALSE, limit = 100)
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stop("Unit tests failed, see above")
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}
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}
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}
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