From ad1df5e109566bdc59a27cb61db3ed7f3e316027 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 9 Apr 2026 10:30:01 -0400
Subject: [PATCH 1/3] fix(pkgdown): Fix url to the MSstatsPTM github page

---
 .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++++++++++
 _pkgdown.yml                   |  3 +++
 2 files changed, 51 insertions(+)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..cc5dbdd
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [devel]
+  pull_request:
+    branches: [devel]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    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@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e69de29..05a6726 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -0,0 +1,3 @@
+url: https://vitek-lab.github.io/MSstatsPTM/
+template:
+  bootstrap: 5
\ No newline at end of file

From 3039e413a3f574928da4cc69576280e12c165540 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 9 Apr 2026 10:42:18 -0400
Subject: [PATCH 2/3] new line to pkgdown

---
 _pkgdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 05a6726..87868c1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,3 +1,3 @@
 url: https://vitek-lab.github.io/MSstatsPTM/
 template:
-  bootstrap: 5
\ No newline at end of file
+  bootstrap: 5

From 5ce542759563ca034c25bcb694518a39688a2a9d Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 9 Apr 2026 10:59:14 -0400
Subject: [PATCH 3/3] update files

---
 .Rbuildignore | 1 +
 .gitignore    | 1 +
 DESCRIPTION   | 1 +
 3 files changed, 3 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index ad47a5c..4e6d71e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$
diff --git a/.gitignore b/.gitignore
index 2949e12..835f4c1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ inst/doc
 doc
 Meta
 docs
+*.html
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index cc41024..43c5cb9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -41,6 +41,7 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE
            OneChannel, TwoChannel, Normalization, QualityControl
 BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues
 Encoding: UTF-8
+URL: https://vitek-lab.github.io/MSstatsPTM/
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Config/testthat/edition: 3