From 48929b3f0be7455b30f295ba82fa5af12f6ca143 Mon Sep 17 00:00:00 2001
From: lwaldron <lwaldron.research@gmail.com>
Date: Tue, 9 May 2023 12:36:02 -0400
Subject: [PATCH] Add pkgdown pages site with GHA

---
 .Rbuildignore                  |  4 +++
 .github/.gitignore             |  1 +
 .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++++++++++
 .gitignore                     |  1 +
 DESCRIPTION                    |  1 +
 _pkgdown.yml                   |  4 +++
 6 files changed, 59 insertions(+)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 8eef8c1..fc6a617 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^html_docs$
+^_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..ed7650c
--- /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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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@v3
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.gitignore b/.gitignore
index d5937e3..071d37d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 *_cache*
 .Rproj.user
 .Rhistory
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 367e54b..e523a76 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,3 +45,4 @@ Collate:
     'get_edgeR_results.R'
     'loadQiimeData.R'
     'prettytable_functions.R'
+URL: http://waldronlab.io/nychanesmicrobiome/
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..0b805d9
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: http://waldronlab.io/nychanesmicrobiome/
+template:
+  bootstrap: 5
+