From c179b8d44aecadb208c598a4ddf5021499337334 Mon Sep 17 00:00:00 2001
From: Simon Scholler <schollers@rki.de>
Date: Mon, 27 Oct 2025 13:54:23 +0100
Subject: [PATCH 1/2] readme: added r as language to code blocks for syntax
 highlighting

---
 Readme.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/Readme.md b/Readme.md
index 68b2ad1..36e8558 100644
--- a/Readme.md
+++ b/Readme.md
@@ -3,6 +3,7 @@
 
 
 Documentation  
+
 # excode: Excess Count Detection in Epidemiological Time Series
 
 <br> 
@@ -57,7 +58,7 @@ surveillance.
 This is an R package. You can use `install_github()` from devtools to
 install this package.
 
-``` commandline
+```r
 library(devtools)
 install_github("robert-koch-institut/excode",subdir = "software")
 ```
@@ -103,7 +104,7 @@ The following code example illustrates how to fit a three-state model with
 sine/cosine functions ('Harmonic') to model seasonal and a natural cubic 
 spline with two knots to caputre long-term trends ('Spline2').
 
-``` commandline
+```r
 library(excode)
 data(mort_df_germany)
 sum_har_nb <- run_excode(surv_ts = mort_df_germany,
@@ -118,7 +119,7 @@ sum_har_nb <- run_excode(surv_ts = mort_df_germany,
 Results can be extracted using the `summary()` and plotted with the 
 `plot_excode_summary()` functions:
 
-``` commandline
+```r
 sum_har_nb <- summary(res_har_nb)
 plot_excode_summary(sum_har_nb)
 ```

From 24b5d0079776f75499a51ba4819c8c24dc287b37 Mon Sep 17 00:00:00 2001
From: tinneuro <tin.vietor@t-online.de>
Date: Thu, 6 Nov 2025 16:04:02 +0100
Subject: [PATCH 2/2] moved the pkgdown.yml to the workflows on the upper
 levels to get the action for gh-pages running again and changed inside the
 yaml that pkgdown needs to go to the subfolder software to find excode

---
 {software/.github => .github}/workflows/pkgdown.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)
 rename {software/.github => .github}/workflows/pkgdown.yaml (84%)

diff --git a/software/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
similarity index 84%
rename from software/.github/workflows/pkgdown.yaml
rename to .github/workflows/pkgdown.yaml
index bfc9f4d..e647dde 100644
--- a/software/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -16,6 +16,10 @@ jobs:
   pkgdown:
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
+    defaults:
+      run:
+        working-directory: software
+        # specification that the job is run inside the software folder where the excode package lives
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
@@ -33,6 +37,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          working-directory: software
           extra-packages: any::pkgdown, local::.
           needs: website
 
@@ -46,4 +51,4 @@ jobs:
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: software/docs