From 564186e54620f5cf88d0f05a4c3e17e7081add11 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 15 Jan 2026 19:50:24 +0000
Subject: [PATCH 1/3] Initial plan


From 37597c5297e8691217dd750d4076fe711ad68c98 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 15 Jan 2026 19:57:47 +0000
Subject: [PATCH 2/3] Disable tutorial exercise checker in R Markdown templates

Co-authored-by: dputhier <1831198+dputhier@users.noreply.github.com>
---
 inst/rmarkdown/index.Rmd  | 5 +++++
 inst/rmarkdown/module.Rmd | 4 ++++
 2 files changed, 9 insertions(+)

diff --git a/inst/rmarkdown/index.Rmd b/inst/rmarkdown/index.Rmd
index f4e42ac..abdaf4a 100644
--- a/inst/rmarkdown/index.Rmd
+++ b/inst/rmarkdown/index.Rmd
@@ -27,6 +27,11 @@ params:
 library(knitr)
 options(width=400)
 scigenex::set_verbosity(0)
+
+# Disable tutorial exercise checking to prevent chunks ending in
+# '-check' from being interpreted as learnr exercise check chunks
+options(tutorial.exercise.checker = NULL)
+
 knitr::opts_chunk$set(
   fig.path="all_",
   fig.align = "center", 
diff --git a/inst/rmarkdown/module.Rmd b/inst/rmarkdown/module.Rmd
index 0bf914c..5ff2242 100644
--- a/inst/rmarkdown/module.Rmd
+++ b/inst/rmarkdown/module.Rmd
@@ -23,6 +23,10 @@ scigenex::set_verbosity(0)
 library(knitr)
 options(width=400)
 
+# Disable tutorial exercise checking to prevent chunks ending in
+# '-check' from being interpreted as learnr exercise check chunks
+options(tutorial.exercise.checker = NULL)
+
 knitr::opts_chunk$set(
   fig.path="FIG_PATH",
   fig.align = "center", 

From d44c88ab99f2de59a5603fafb6bb347c7450fc23 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 15 Jan 2026 19:59:56 +0000
Subject: [PATCH 3/3] Add exercise checker disable to all vignettes

Co-authored-by: dputhier <1831198+dputhier@users.noreply.github.com>
---
 vignettes/report.Rmd  | 6 ++++++
 vignettes/spatial.Rmd | 7 +++++++
 vignettes/usage.Rmd   | 7 +++++++
 3 files changed, 20 insertions(+)

diff --git a/vignettes/report.Rmd b/vignettes/report.Rmd
index aa5b042..3048866 100644
--- a/vignettes/report.Rmd
+++ b/vignettes/report.Rmd
@@ -9,6 +9,12 @@ vignette: >
   %\usepackage[UTF-8]{inputenc}
 ---
 
+```{r setup, include=FALSE}
+# Disable tutorial exercise checking to prevent any chunks ending in
+# '-check' from being interpreted as learnr exercise check chunks
+options(tutorial.exercise.checker = NULL)
+knitr::opts_chunk$set(echo = TRUE)
+```
 
 ## Introduction
 
diff --git a/vignettes/spatial.Rmd b/vignettes/spatial.Rmd
index a955e81..9d2b7c0 100644
--- a/vignettes/spatial.Rmd
+++ b/vignettes/spatial.Rmd
@@ -9,6 +9,13 @@ vignette: >
   %\usepackage[UTF-8]{inputenc}
 ---
 
+```{r setup, include=FALSE}
+# Disable tutorial exercise checking to prevent any chunks ending in
+# '-check' from being interpreted as learnr exercise check chunks
+options(tutorial.exercise.checker = NULL)
+knitr::opts_chunk$set(echo = TRUE)
+```
+
 ## Working with spatial transcriptomics datasets
 
 The scigenex package offers a certain number of functions dedicated to spatial transcriptomic data analysis. At the moment these functions have been mainly developed to analyse VISIUM technology (10X Genomics).
diff --git a/vignettes/usage.Rmd b/vignettes/usage.Rmd
index 2a81c90..21ac6b8 100644
--- a/vignettes/usage.Rmd
+++ b/vignettes/usage.Rmd
@@ -9,6 +9,13 @@ vignette: >
   %\usepackage[UTF-8]{inputenc}
 ---
 
+```{r setup, include=FALSE}
+# Disable tutorial exercise checking to prevent any chunks ending in
+# '-check' from being interpreted as learnr exercise check chunks
+options(tutorial.exercise.checker = NULL)
+knitr::opts_chunk$set(echo = TRUE)
+```
+
 # Guided tutorial
 
 The easiest way to use scigenex is to perform the following steps using the Seurat R package: