options for strict tests; few enhancements

DESCRIPTION

@@ -45,7 +45,8 @@ Suggests:
     nestcolor (>= 0.1.0),
     rmarkdown,
     teal.data (>= 0.3.0.9018),
-    testthat (>= 3.1.5)
+    testthat (>= 3.1.5),
+    withr (>= 2.0.0)
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US

R/teal.osprey.R

@@ -3,7 +3,5 @@
 #' The \code{teal.osprey} R package contains interactive \code{\link{teal}} modules for the outputs
 #'
 #' @import dplyr osprey shiny teal formatters teal.transform
-#' @name teal.osprey
 #' @keywords internal
-#'
 "_PACKAGE"

R/tm_g_ae_sub.R

@@ -33,11 +33,11 @@
 #'     tm_g_ae_sub(
 #'       label = "AE by Subgroup",
 #'       dataname = "ADAE",
-#'       arm_var = teal.transform::choices_selected(
+#'       arm_var = choices_selected(
 #'         selected = "ACTARMCD",
 #'         choices = c("ACTARM", "ACTARMCD")
 #'       ),
-#'       group_var = teal.transform::choices_selected(
+#'       group_var = choices_selected(
 #'         selected = c("SEX", "REGION1", "RACE"),
 #'         choices = c("SEX", "REGION1", "RACE")
 #'       ),

R/tm_g_heat_bygrade.R

@@ -400,6 +400,7 @@ srv_g_heatmap_bygrade <- function(id,
         ADSL <- data()[[sl_dataname]] # nolint
         ADEX <- data()[[ex_dataname]] # nolint
         ADAE <- data()[[ae_dataname]] # nolint
+        ADCM <- data()[[cm_dataname]] # nolint
 
         teal::validate_has_data(ADSL, min_nrow = 1, msg = sprintf("%s contains no data", sl_dataname))
         teal::validate_inputs(iv(), iv_cm())

R/tm_g_swimlane.R

@@ -36,53 +36,52 @@
 #'
 #' @examples
 #' # Example using stream (ADaM) dataset
-#' data <- teal.data::cdisc_data() |>
+#' data <- cdisc_data() |>
 #'   within(library(dplyr)) |>
 #'   within(library(nestcolor)) |>
-#'   within(ADSL <- osprey::rADSL %>%
-#'     dplyr::mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
-#'     dplyr::filter(STRATA1 == "A" & ARMCD == "ARM A")) |>
-#'   within(ADRS <- osprey::rADRS) |>
-#'   within(ADRS <- ADRS %>%
-#'     dplyr::filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
+#'   within(ADSL <- rADSL %>%
+#'     mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
+#'     filter(STRATA1 == "A" & ARMCD == "ARM A")) |>
+#'   within(ADRS <- rADRS %>%
+#'     filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
 #'     mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
-#'     base::rbind(ADRS %>% dplyr::filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
+#'     rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
 #'     arrange(USUBJID))
 #'
-#' teal.data::datanames(data) <- c("ADSL", "ADRS")
-#' teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[teal.data::datanames(data)]
+#' datanames(data) <- c("ADSL", "ADRS")
+#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
 #'
 #' ADSL <- data[["ADSL"]]
 #' ADRS <- data[["ADRS"]]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
+#'   modules = modules(
 #'     tm_g_swimlane(
 #'       label = "Swimlane Plot",
 #'       dataname = "ADRS",
-#'       bar_var = teal.transform::choices_selected(
+#'       bar_var = choices_selected(
 #'         selected = "TRTDURD",
 #'         choices = c("TRTDURD", "EOSDY")
 #'       ),
-#'       bar_color_var = teal.transform::choices_selected(
+#'       bar_color_var = choices_selected(
 #'         selected = "EOSSTT",
 #'         choices = c("EOSSTT", "ARM", "ARMCD", "ACTARM", "ACTARMCD", "SEX")
 #'       ),
-#'       sort_var = teal.transform::choices_selected(
+#'       sort_var = choices_selected(
 #'         selected = "ACTARMCD",
 #'         choices = c("USUBJID", "SITEID", "ACTARMCD", "TRTDURD")
 #'       ),
-#'       marker_pos_var = teal.transform::choices_selected(
+#'       marker_pos_var = choices_selected(
 #'         selected = "ADY",
 #'         choices = c("ADY")
 #'       ),
-#'       marker_shape_var = teal.transform::choices_selected(
+#'       marker_shape_var = choices_selected(
 #'         selected = "AVALC",
 #'         c("AVALC", "AVISIT")
 #'       ),
 #'       marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
-#'       marker_color_var = teal.transform::choices_selected(
+#'       marker_color_var = choices_selected(
 #'         selected = "AVALC",
 #'         choices = c("AVALC", "AVISIT")
 #'       ),
@@ -91,7 +90,7 @@
 #'         "PD" = "red", "Death" = "black"
 #'       ),
 #'       vref_line = c(30, 60),
-#'       anno_txt_var = teal.transform::choices_selected(
+#'       anno_txt_var = choices_selected(
 #'         selected = c("ACTARM", "SEX"),
 #'         choices = c(
 #'           "ARM", "ARMCD", "ACTARM", "ACTARMCD", "AGEGR1",

tests/testthat/setup-logger.R

@@ -0,0 +1 @@
+logger::log_appender(function(...) NULL, namespace = "teal.osprey")

tests/testthat/setup-options.R

@@ -0,0 +1,20 @@
+# `opts_partial_match_old` is left for exclusions due to partial matching in dependent packages (i.e. not fixable here)
+# it might happen that it is not used right now, but it is left for possible future use
+# use with: `withr::with_options(opts_partial_match_old, { ... })` inside the test
+opts_partial_match_old <- list(
+  warnPartialMatchDollar = getOption("warnPartialMatchDollar"),
+  warnPartialMatchArgs = getOption("warnPartialMatchArgs"),
+  warnPartialMatchAttr = getOption("warnPartialMatchAttr")
+)
+opts_partial_match_new <- list(
+  warnPartialMatchDollar = TRUE,
+  warnPartialMatchArgs = TRUE,
+  warnPartialMatchAttr = TRUE
+)
+
+if (isFALSE(getFromNamespace("on_cran", "testthat")()) && requireNamespace("withr", quietly = TRUE)) {
+  withr::local_options(
+    opts_partial_match_new,
+    .local_envir = testthat::teardown_env()
+  )
+}