register teal.logger handlers (#354)

close insightsengineering/coredev-tasks#502 test with insightsengineering/teal.logger#73 As a bonus, we can safely move `logger` to suggests (it's still used in tests) --------- Signed-off-by: Pawel Rucki <[email protected]> Co-authored-by: Dony Unardi <[email protected]>
insightsengineering · Mar 20, 2024 · 3336364 · 3336364
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commit 3336364
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -24,7 +24,6 @@ repos:
           - forcats
           - bioc::hermes
           - lifecycle
-          - logger
           - bioc::MultiAssayExperiment
           - rtables
           - S4Vectors

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,7 +40,6 @@ Imports:
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
-    logger (>= 0.2.0),
     MultiAssayExperiment,
     rtables (>= 0.5.1),
     S4Vectors,
@@ -50,7 +49,7 @@ Imports:
     stringr,
     SummarizedExperiment,
     teal.data (>= 0.3.0.9018),
-    teal.logger (>= 0.1.1),
+    teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
     tern (>= 0.7.10)
@@ -60,6 +59,7 @@ Suggests:
     dplyr,
     globals,
     knitr,
+    logger (>= 0.2.0),
     matrixStats,
     R6,
     rmarkdown,

diff --git a/R/barplot.R b/R/barplot.R
@@ -35,7 +35,7 @@ tm_g_barplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL) {
-  logger::log_info("Initializing tm_g_barplot")
+  message("Initializing tm_g_barplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)

diff --git a/R/boxplot.R b/R/boxplot.R
@@ -36,7 +36,7 @@ tm_g_boxplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL) {
-  logger::log_info("Initializing tm_g_boxplot")
+  message("Initializing tm_g_boxplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)

diff --git a/R/forestplot.R b/R/forestplot.R
@@ -54,7 +54,7 @@ tm_g_forest_tte <- function(label,
                             post_output = NULL,
                             plot_height = c(600L, 200L, 2000L),
                             plot_width = c(1360L, 500L, 2000L)) {
-  logger::log_info("Initializing tm_g_forest_tte")
+  message("Initializing tm_g_forest_tte")
   assert_string(label)
   assert_string(adtte_name)
   assert_string(mae_name)

diff --git a/R/km.R b/R/km.R
@@ -57,7 +57,7 @@ tm_g_km <- function(label,
                     ),
                     pre_output = NULL,
                     post_output = NULL) {
-  logger::log_info("Initializing tm_g_km")
+  message("Initializing tm_g_km")
   assert_string(label)
   assert_string(adtte_name)
   assert_string(mae_name)

diff --git a/R/pca.R b/R/pca.R
@@ -30,7 +30,7 @@ tm_g_pca <- function(label,
                      exclude_assays = character(),
                      pre_output = NULL,
                      post_output = NULL) {
-  logger::log_info("Initializing tm_g_pca")
+  message("Initializing tm_g_pca")
   assert_string(label)
   assert_string(mae_name)
   assert_tag(pre_output, null.ok = TRUE)

diff --git a/R/scatterplot.R b/R/scatterplot.R
@@ -35,7 +35,7 @@ tm_g_scatterplot <- function(label,
                              ),
                              pre_output = NULL,
                              post_output = NULL) {
-  logger::log_info("Initializing tm_g_scatterplot")
+  message("Initializing tm_g_scatterplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)

diff --git a/R/volcanoplot.R b/R/volcanoplot.R
@@ -30,7 +30,7 @@ tm_g_volcanoplot <- function(label,
                              exclude_assays = character(),
                              pre_output = NULL,
                              post_output = NULL) {
-  logger::log_info("Initializing tm_g_volcanoplot")
+  message("Initializing tm_g_volcanoplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,3 +1,4 @@
 .onLoad <- function(libname, pkgname) { # nolint
   teal.logger::register_logger(namespace = "teal.modules.hermes")
+  teal.logger::register_handlers("teal.modules.hermes")
 }