Add pkgdown configuration and update GitHub Actions for deployment

Author: stemangiola

.Rbuildignore

@@ -26,3 +26,6 @@ model_glm_dirichlet_multinomial_imputation.rds
 ^Meta$
 sccomp_draws_files
 
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/workflow_with_cmdstanr.yml

@@ -125,26 +125,15 @@ jobs:
       - name: Build pkgdown site
         shell: Rscript {0}
         run: |
-          pkgdown::build_site()
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request' || github.head_ref == 'fix-github-pages'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
-          path: ./docs
-
-  # Deploy job
-  deploy:
-    needs: build
-    permissions:
-      pages: write
-      id-token: write
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4
+          clean: false
+          branch: gh-pages
+          folder: docs
+

.gitignore

@@ -45,3 +45,4 @@ Rplot.pdf
 /Meta/
 sccomp_draws_files
 .DS_Store
+docs

DESCRIPTION

@@ -55,7 +55,7 @@ SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan), C++1
 biocViews: Bayesian, Regression, DifferentialExpression, SingleCell, Metagenomics, FlowCytometry, Spatial
 LazyData: true
 VignetteBuilder: knitr
-URL: https://github.com/MangiolaLaboratory/sccomp
+URL: https://github.com/MangiolaLaboratory/sccomp, https://mangiolalaboratory.github.io/sccomp/
 BugReports: https://github.com/MangiolaLaboratory/sccomp/issues
 Config/testthat/edition: 3
 Config/testthat/parallel: true

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://mangiolalaboratory.github.io/sccomp/
+template:
+  bootstrap: 5
+