run build

fixing pkgdown deployment

.Rbuildignore

@@ -4,4 +4,8 @@ debug
 .Rcheck
 ..Rcheck
 ^vignettes/PredomicsPlotting\.Rmd$
-^vignettes/vignette\.Rmd$
+^vignettes/vignette\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/r.yml

@@ -46,15 +46,6 @@ jobs:
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 
-      - name: Build pkgdown site
-        run: Rscript -e 'pkgdown::build_site()'
-
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs
-
       - name: Install Pandoc
         run: brew install pandoc
 

.gitignore

@@ -1,5 +1,3 @@
-man/
-debug/
 .Rproj.user
 .RData
 .Ruserdata
@@ -11,3 +9,6 @@ vignettes/*_cache
 #NAMESPACE
 Profiling_*
 *.yml
+man/
+debug
+pkgdown

DESCRIPTION

@@ -41,3 +41,4 @@ License: GPL-3
 LazyData: TRUE
 RoxygenNote: 7.2.3
 Encoding: UTF-8
+URL: https://predomics.github.io/predomicspkg/