From b4fb050457cf91b2846d9f7cd51d57a4023db926 Mon Sep 17 00:00:00 2001
From: Markus <66058642+mhovd@users.noreply.github.com>
Date: Thu, 5 Mar 2026 12:32:40 +0100
Subject: [PATCH 1/2] fix: Use custom CSS globally

---
 Extras/custom.scss | 6 +++---
 NPAG.qmd           | 3 ---
 NPAG_cov.qmd       | 3 ---
 Validate.qmd       | 3 ---
 _quarto.yml        | 1 +
 data.qmd           | 4 ----
 examine.qmd        | 3 ---
 models.qmd         | 4 ----
 objects.qmd        | 3 ---
 overview.qmd       | 3 ---
 plotly.qmd         | 4 ----
 simulation.qmd     | 3 ---
 workflow.qmd       | 3 ---
 13 files changed, 4 insertions(+), 39 deletions(-)

diff --git a/Extras/custom.scss b/Extras/custom.scss
index 6ebc77b..f2408f9 100755
--- a/Extras/custom.scss
+++ b/Extras/custom.scss
@@ -1,13 +1,13 @@
 /*-- scss:defaults --*/
 
+
+/*-- scss:rules --*/
+
 .cell-output {
   background-color: #1e90ff20;
   border-radius: 4px; 
 }
 
-
-/*-- scss:rules --*/
-
 div[data-code-copy="false"] button.code-copy-button {
   display: none;
 }
diff --git a/NPAG.qmd b/NPAG.qmd
index b590e1a..57a2ea3 100755
--- a/NPAG.qmd
+++ b/NPAG.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Fit a model with NPAG"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 
diff --git a/NPAG_cov.qmd b/NPAG_cov.qmd
index bc5ec47..7e440af 100644
--- a/NPAG_cov.qmd
+++ b/NPAG_cov.qmd
@@ -1,8 +1,5 @@
 ---
 title: "More complex models"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 
diff --git a/Validate.qmd b/Validate.qmd
index 0507ac5..2a5c483 100644
--- a/Validate.qmd
+++ b/Validate.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Model Validation"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 
diff --git a/_quarto.yml b/_quarto.yml
index b246ffe..49109ac 100755
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -39,6 +39,7 @@ format:
   html:
     theme: cosmo
     css: Extras/custom.scss
+    include-in-header: Extras/copy-all-code.html
     toc: true
     toc-title: "On this page" 
     link-external-newwindow: true
diff --git a/data.qmd b/data.qmd
index 4f8ea11..436f753 100755
--- a/data.qmd
+++ b/data.qmd
@@ -1,9 +1,5 @@
 ---
 title: "Data"
-format:
-  html:
-    css: Extras/custom.scss
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r}
diff --git a/examine.qmd b/examine.qmd
index bd268ed..9b51c39 100644
--- a/examine.qmd
+++ b/examine.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Examine results"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r, include = FALSE}
diff --git a/models.qmd b/models.qmd
index 8d0dd53..c7cc94f 100755
--- a/models.qmd
+++ b/models.qmd
@@ -1,9 +1,5 @@
 ---
 title: "Models"
-format:
-  html:
-    css: Extras/custom.scss
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r}
diff --git a/objects.qmd b/objects.qmd
index d297604..82e6fa5 100755
--- a/objects.qmd
+++ b/objects.qmd
@@ -1,9 +1,6 @@
 
 ---
 title: "The results"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r, include = FALSE}
diff --git a/overview.qmd b/overview.qmd
index a1560f8..884c7a4 100755
--- a/overview.qmd
+++ b/overview.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Overview"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r, include = FALSE}
diff --git a/plotly.qmd b/plotly.qmd
index 20be8eb..a53ab95 100755
--- a/plotly.qmd
+++ b/plotly.qmd
@@ -1,9 +1,5 @@
 ---
 title: "Plotting Details"
-format:
-  html:
-    css: Extras/custom.scss
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r, include = FALSE}
diff --git a/simulation.qmd b/simulation.qmd
index 37b92d3..add0c1b 100755
--- a/simulation.qmd
+++ b/simulation.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Simulations"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 
diff --git a/workflow.qmd b/workflow.qmd
index f1d5910..a8cce06 100755
--- a/workflow.qmd
+++ b/workflow.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Workflow"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---
 
 ```{r, include = FALSE}

From e9bb86b2a520527f91ba6673dd42d47ca358c242 Mon Sep 17 00:00:00 2001
From: Markus <66058642+mhovd@users.noreply.github.com>
Date: Thu, 5 Mar 2026 12:32:51 +0100
Subject: [PATCH 2/2] Update PTA.qmd

---
 PTA.qmd | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/PTA.qmd b/PTA.qmd
index 7265959..127ad1f 100644
--- a/PTA.qmd
+++ b/PTA.qmd
@@ -1,8 +1,5 @@
 ---
 title: "Probability of Target Attainment (PTA)"
-format:
-  html:
-    include-in-header: Extras/copy-all-code.html
 ---