add pkgdwn and update citation

Author: iblacksand

.Rbuildignore

@@ -4,3 +4,6 @@
 ^man\figures\.gitkeep$
 ^studies$
 ^CITATION\.cff$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/check-standard.yaml

@@ -29,15 +29,6 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - name: Install stable toolchain
-        if: ${{startsWith(matrix.config.os, 'windows')}}
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          target: x86_64-pc-windows-msvc
-          profile: minimal
-          default: true
-
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2

.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

.gitignore

@@ -50,3 +50,4 @@ rsconnect/
 
 # Mac Specific Files
 .DS_Store
+docs

CITATION.cff

@@ -50,8 +50,6 @@ preferred-citation:
   doi: 10.1093/nar/gkad871
   journal: "Nucleic Acids Research"
   month: 1
-  start: 1 # First page number
-  end: 9 # Last page number
   title: "ClinicalOmicsDB: exploring molecular associations of oncology drug responses in clinical trials"
   issue: D1
   volume: 52

_pkgdown.yml

@@ -0,0 +1,3 @@
+url: https://bzhanglab.github.io/clinicalomicsdbR/
+template:
+  bootstrap: 5