From da3bfd2c7a6767589a2244093c8a2a5d0c859ce3 Mon Sep 17 00:00:00 2001
From: Matt Secrest <secrestm@gene.com>
Date: Fri, 27 Oct 2023 07:32:37 -0700
Subject: [PATCH 1/3] pkgdown

---
 .Rbuildignore | 3 +++
 .gitignore    | 1 +
 _pkgdown.yml  | 4 ++++
 3 files changed, 8 insertions(+)
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 5163d0b..afa5e21 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1 +1,4 @@
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
diff --git a/.gitignore b/.gitignore
index e75435c..1e236e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,3 +47,4 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+docs
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..41b29a6
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: mattsecrest.github.io/TreatmentSequence
+template:
+  bootstrap: 5
+

From 1926be7fd31ce296bb508eb5bc086bf7148707b1 Mon Sep 17 00:00:00 2001
From: Matt Secrest <secrestm@gene.com>
Date: Fri, 27 Oct 2023 09:02:39 -0700
Subject: [PATCH 2/3] pkgdown template

---
 .Rbuildignore                  |  1 +
 .github/.gitignore             |  1 +
 .github/workflows/pkgdown.yaml | 10 ++++++----
 DESCRIPTION                    |  1 +
 _pkgdown.yml                   |  2 +-
 5 files changed, 10 insertions(+), 5 deletions(-)
 create mode 100644 .github/.gitignore

diff --git a/.Rbuildignore b/.Rbuildignore
index afa5e21..7c6667d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 6c19fc5..ed7650c 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -13,14 +13,16 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -34,7 +36,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = TRUE, install = TRUE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
@@ -43,4 +45,4 @@ jobs:
         with:
           clean: false
           branch: gh-pages
-          folder: docs
\ No newline at end of file
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
index b8260ab..0542d89 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,3 +12,4 @@ RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+URL: https://mattsecrest.github.io/TreatmentSequence/
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 41b29a6..a32c594 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: mattsecrest.github.io/TreatmentSequence
+url: https://mattsecrest.github.io/TreatmentSequence/
 template:
   bootstrap: 5
 

From 087f62f27ef04a5cac19fd1a55527520ed0c538b Mon Sep 17 00:00:00 2001
From: Matt Secrest <secrestm@gene.com>
Date: Mon, 30 Oct 2023 08:05:07 -0700
Subject: [PATCH 3/3] pkgdowntest

---
 .github/workflows/pkgdown.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index ed7650c..d15e912 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -13,7 +13,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -36,7 +36,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = TRUE, install = TRUE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀