From dbd6ccd6f5b186bbf7c73be3f82d03a49f4c1785 Mon Sep 17 00:00:00 2001
From: Nick <nickrrrr@gmail.com>
Date: Tue, 2 Jul 2024 15:52:19 +1000
Subject: [PATCH] Set up pkgdown

---
 .Rbuildignore                  |  1 +
 .github/.gitignore             |  1 +
 .github/workflows/pkgdown.yaml | 50 ++++++++++++++++++++++++++++++++++
 .gitignore                     |  1 +
 DESCRIPTION                    |  2 +-
 _pkgdown.yml                   |  9 ++++++
 6 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.Rbuildignore b/.Rbuildignore
index 33cc41e..91fb891 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -3,3 +3,4 @@
 ^_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
new file mode 100644
index 0000000..c9f0165
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,50 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  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/.gitignore b/.gitignore
index 9e9e119..f97e24b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@
 *.DS_Store
 StabMap.BiocCheck
 .Rproj.user
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index ad0e11c..763ec19 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,7 @@ Description: StabMap performs single cell mosaic data integration by first
     given reference and query cell lists.
 License: GPL-2
 Encoding: UTF-8
-URL: https://sydneybiox.github.io/StabMap
+URL: https://sydneybiox.github.io/StabMap, https://sydneybiox.github.io/StabMap/
 BugReports: https://github.com/sydneybiox/StabMap/issues
 biocViews: SingleCell, DimensionReduction, Software
 Depends: R (>= 4.4.0),
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e69de29..152384a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -0,0 +1,9 @@
+url: https://sydneybiox.github.io/StabMap/
+template:
+  bootstrap: 5
+  bootswatch: cosmo
+toc:
+  depth: 3
+navbar:
+  title: ~
+  bg: dark