move inline opts into app template; silent logger; ignore lintr (#210)

- closes #191 using temp solution of `"FATAL"` log threshold - move `message` option specified individually for each app chunk to the `app` template to keep it DRY - replace `# nolint` with empty string to prevent it from being rendered out --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Feb 14, 2024 · 1c9f1a0 · 1c9f1a0
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diff --git a/book/_quarto.yml b/book/_quarto.yml
@@ -42,7 +42,7 @@ execute:
 knitr:
   opts_chunk:
     echo: true
-    fig.width: 15
+    tidy: function(code, ...) gsub(pattern = "#\\s?nolint.*|#\\s?styler:.*", replacement = "", code)
 
 editor: visual
 highlight-style: github

diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd
@@ -189,7 +189,7 @@ height <- 5
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
@@ -170,7 +170,7 @@ plot_v3.width <- 8
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd
@@ -113,7 +113,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/other/brg01.qmd b/book/graphs/other/brg01.qmd
@@ -298,7 +298,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/other/bwg01.qmd b/book/graphs/other/bwg01.qmd
@@ -336,7 +336,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.general)
 
 ## Data reproducible code

diff --git a/book/graphs/other/cig01.qmd b/book/graphs/other/cig01.qmd
@@ -163,7 +163,7 @@ table
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd
@@ -87,7 +87,7 @@ plots
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/other/kmg01.qmd b/book/graphs/other/kmg01.qmd
@@ -122,7 +122,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/other/ltg01.qmd b/book/graphs/other/ltg01.qmd
@@ -217,7 +217,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd
@@ -145,7 +145,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/graphs/pharmacokinetic/pkcg01.qmd b/book/graphs/pharmacokinetic/pkcg01.qmd
@@ -91,7 +91,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/pharmacokinetic/pkcg02.qmd b/book/graphs/pharmacokinetic/pkcg02.qmd
@@ -92,7 +92,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd
@@ -104,7 +104,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd
@@ -139,7 +139,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/pharmacokinetic/pkpg02.qmd b/book/graphs/pharmacokinetic/pkpg02.qmd
@@ -144,7 +144,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/graphs/pharmacokinetic/pkpg06.qmd b/book/graphs/pharmacokinetic/pkpg06.qmd
@@ -180,7 +180,7 @@ plot
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ADA/adat01.qmd b/book/tables/ADA/adat01.qmd
@@ -220,7 +220,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ADA/adat02.qmd b/book/tables/ADA/adat02.qmd
@@ -141,7 +141,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ADA/adat03.qmd b/book/tables/ADA/adat03.qmd
@@ -121,7 +121,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ADA/adat04a.qmd b/book/tables/ADA/adat04a.qmd
@@ -230,7 +230,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ADA/adat04b.qmd b/book/tables/ADA/adat04b.qmd
@@ -213,7 +213,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd
@@ -83,7 +83,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd
@@ -79,7 +79,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd
@@ -142,7 +142,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/ECG/egt04.qmd b/book/tables/ECG/egt04.qmd
@@ -89,7 +89,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 #| code-fold: show
 
 # In progress

diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd
@@ -107,7 +107,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd
@@ -338,7 +338,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd
@@ -493,7 +493,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd
@@ -640,7 +640,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd
@@ -173,7 +173,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd
@@ -106,7 +106,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd
@@ -561,7 +561,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet04_pi.qmd b/book/tables/adverse-events/aet04_pi.qmd
@@ -372,7 +372,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet05.qmd b/book/tables/adverse-events/aet05.qmd
@@ -72,7 +72,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet05_all.qmd b/book/tables/adverse-events/aet05_all.qmd
@@ -73,7 +73,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet06.qmd b/book/tables/adverse-events/aet06.qmd
@@ -365,7 +365,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet06_smq.qmd b/book/tables/adverse-events/aet06_smq.qmd
@@ -239,7 +239,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet07.qmd b/book/tables/adverse-events/aet07.qmd
@@ -109,7 +109,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet09.qmd b/book/tables/adverse-events/aet09.qmd
@@ -173,7 +173,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet09_smq.qmd b/book/tables/adverse-events/aet09_smq.qmd
@@ -181,7 +181,7 @@ Note that filtering AEs for relatedness to study drug is not a necessary data pr
 It can be achieved using the `teal` module filter panel.
 The example here pre-sets the filters using `AEREL = "Y"` in `adae`.
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/adverse-events/aet10.qmd b/book/tables/adverse-events/aet10.qmd
@@ -104,7 +104,7 @@ result
 The desired frequency is specified in `prune_freq`.
 For illustration, frequency is set to $\geq$ 35%.
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/concomitant-medications/cmt01.qmd b/book/tables/concomitant-medications/cmt01.qmd
@@ -231,7 +231,7 @@ result
 
 Here, `adcm` is processed to keep only one path per treatment.
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 ## Data reproducible code

diff --git a/book/tables/concomitant-medications/cmt01a.qmd b/book/tables/concomitant-medications/cmt01a.qmd
@@ -226,7 +226,7 @@ result
 
 ## `teal` App
 
-```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')}
+```{r teal, opts.label=c('skip_if_testing', 'app')}
 library(teal.modules.clinical)
 
 adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")