add _pkgdown.yml and GHA deployment

Author: LiNk-NY

.github/workflows/pr_check.yml

@@ -0,0 +1,94 @@
+name: PR CMD check & build site
+
+on:
+  push:
+    paths:
+      - 'DESCRIPTION'
+      - '**.yml'
+    branches:
+      - RELEASE_3_21
+      - pkgdown
+
+env:
+  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  CRAN: https://p3m.dev/cran/__linux__/noble/latest
+  BIOC_RELEASE: RELEASE_3_21
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:RELEASE_3_21
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ env.BIOC_RELEASE }}
+
+      - name: Copy .github and _pkgdown.yml
+        run: |
+          git fetch origin pkgdown
+          git checkout origin/pkgdown -- .github
+          git checkout origin/pkgdown -- _pkgdown.yml
+
+      - name: Query dependencies
+        run: |
+          BiocManager::install(c("covr", "BiocCheck"))
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v4
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ runner.os }}-r-${{ env.BIOC_RELEASE }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ env.BIOC_RELEASE }}-
+
+      - name: Install GPG
+        if: ${{ github.ref == 'refs/heads/devel' && github.event_name != 'pull_request' }}
+        run: sudo apt-get update && sudo apt-get install -y gpg
+
+      - name: Install Dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install(c("rcmdcheck", "BiocCheck"), ask = FALSE, update = TRUE)
+        shell: Rscript {0}
+
+      - name: Check Package
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        id: bioccheck
+        run: |
+          BiocCheck::BiocCheck(
+            dir('check', 'tar.gz$', full.names = TRUE),
+            `quit-with-status` = TRUE, `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}
+
+      - name: Build pkgdown
+        run: |
+           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()'
+
+      - name: Upload pkgdown artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs
+
+  deploy:
+    needs: check
+    permissions:
+      contents: write
+      pages: write
+      id-token: write
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+

_pkgdown.yml

@@ -0,0 +1,7 @@
+title: AnnotationHub
+url: https://waldronlab.github.io/AnnotationHub
+
+template:
+  bootstrap: 5
+  params:
+    bootswatch: flatly