From 2e1ec0cedb08ffe7c8ab56e0217b95b02dfc3083 Mon Sep 17 00:00:00 2001
From: "Eric R. Scott" <scottericr@gmail.com>
Date: Thu, 13 Jul 2023 11:46:51 -0400
Subject: [PATCH] use_pkgdown_github_pages()

---
 .Rbuildignore                  |  3 +++
 .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++++++++++
 .gitignore                     |  1 +
 DESCRIPTION                    |  1 +
 _pkgdown.yml                   |  4 +++
 man/volcalc-package.Rd         |  7 +++++
 6 files changed, 64 insertions(+)
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 7dffdb3..30e1802 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -7,3 +7,6 @@ README.Rmd
 ^CITATION\.cff$
 ^CODE_OF_CONDUCT\.md$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
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 9658ca0..bd6655b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@
 inst/doc
 /doc/
 /Meta/
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index cbd967f..d29f45b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,3 +32,4 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+URL: https://meredith-lab.github.io/volcalc/
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..79b2ab3
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://meredith-lab.github.io/volcalc/
+template:
+  bootstrap: 5
+
diff --git a/man/volcalc-package.Rd b/man/volcalc-package.Rd
index 7f8ea20..d8ce42c 100644
--- a/man/volcalc-package.Rd
+++ b/man/volcalc-package.Rd
@@ -7,6 +7,13 @@
 \title{volcalc: Calculate Volatility of Chemical Compounds}
 \description{
 Use this package to calculate estimated volatility values for individual compounds of interest or for all compounds in a pathway. Calculation uses the SIMPOL method (Prankow and Asher, 2008), and is only currently applicable to compounds and pathways in KEGG.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://meredith-lab.github.io/volcalc/}
+}
+
 }
 \author{
 \strong{Maintainer}: Kristina Riemer \email{kristinariemer@arizona.edu} (\href{https://orcid.org/0000-0003-3802-3331}{ORCID}) [copyright holder]