Update pkgdown GitHub Actions file

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,41 @@
+# 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: master
+  pull_request:
+    branches: 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 }}
+    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: 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

DESCRIPTION

@@ -23,7 +23,7 @@ Description: Defines S4 classes for single-cell genomic data and associated
   and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for
   more details.
 URL: https://mojaveazure.github.io/seurat-object/,
-      https://github.com/mojaveazure/seurat-object
+    https://github.com/mojaveazure/seurat-object
 BugReports:
       https://github.com/mojaveazure/seurat-object/issues
 License: MIT + file LICENSE
@@ -72,3 +72,5 @@ Collate:
     'seurat.R'
     'utils.R'
 LinkingTo: Rcpp, RcppEigen
+Config/Needs/website:
+    pkgdown

_pkgdown.yml

@@ -1,57 +1,54 @@
 url: https://mojaveazure.github.io/seurat-object/
 destination: docs
-
 template:
   params:
     bootswatch: united
-
 development:
   mode: auto
-
 reference:
-  - title: The Seurat Class and Interaction Methods
-    contents:
-      - Seurat-class
-      - Seurat-methods
-      - has_concept("seurat")
-  - title: The Assay Class and Interaction Methods
-    contents:
-      - Assay-class
-      - Assay-methods
-      - has_concept("assay")
-  - title: The DimReduc and JackStrawData Classes and Interaction Methods
-    contents:
-      - DimReduc-class
-      - DimReduc-methods
-      - has_concept("dimreduc")
-      - JackStrawData-class
-      - JackStrawData-methods
-      - has_concept("jackstraw")
-  - title: The SeuratCommand Class and Interaction Methods
-    contents:
-      - SeuratCommand-class
-      - SeuratCommand-methods
-      - has_concept("command")
-  - title: The SpatialImage Class and Interaction Methods
-    contents:
-      - SpatialImage-class
-      - SpatialImage-methods
-      - has_concept("spatialimage")
-  - title: The Graph and Neighbor Classes and Interaction Methods
-    contents:
-      - Graph-class
-      - has_concept("graph")
-      - Neighbor-class
-      - has_concept("neighbor")
-  - title: Accessing and Setting Object Data
-    contents:
-      - has_concept("data-access")
-  - title: Utility Functions
-    contents:
-      - set-if-null
-      - has_concept("utils")
-  - title: Package Information
-    contents:
-      - SeuratObject-package
-      - pbmc_small
-      - reexports
+- title: The Seurat Class and Interaction Methods
+  contents:
+  - Seurat-class
+  - Seurat-methods
+  - has_concept("seurat")
+- title: The Assay Class and Interaction Methods
+  contents:
+  - Assay-class
+  - Assay-methods
+  - has_concept("assay")
+- title: The DimReduc and JackStrawData Classes and Interaction Methods
+  contents:
+  - DimReduc-class
+  - DimReduc-methods
+  - has_concept("dimreduc")
+  - JackStrawData-class
+  - JackStrawData-methods
+  - has_concept("jackstraw")
+- title: The SeuratCommand Class and Interaction Methods
+  contents:
+  - SeuratCommand-class
+  - SeuratCommand-methods
+  - has_concept("command")
+- title: The SpatialImage Class and Interaction Methods
+  contents:
+  - SpatialImage-class
+  - SpatialImage-methods
+  - has_concept("spatialimage")
+- title: The Graph and Neighbor Classes and Interaction Methods
+  contents:
+  - Graph-class
+  - has_concept("graph")
+  - Neighbor-class
+  - has_concept("neighbor")
+- title: Accessing and Setting Object Data
+  contents: has_concept("data-access")
+- title: Utility Functions
+  contents:
+  - set-if-null
+  - has_concept("utils")
+- title: Package Information
+  contents:
+  - SeuratObject-package
+  - pbmc_small
+  - reexports
+