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Add pkgdown configuration and update GitHub Actions for deployment #224

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3 changes: 3 additions & 0 deletions .Rbuildignore
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Expand Up @@ -26,3 +26,6 @@ model_glm_dirichlet_multinomial_imputation.rds
^Meta$
sccomp_draws_files

^_pkgdown\.yml$
^docs$
^pkgdown$
27 changes: 8 additions & 19 deletions .github/workflows/workflow_with_cmdstanr.yml
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Expand Up @@ -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
Comment on lines +133 to +138
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Copilot AI Jul 20, 2025

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The hardcoded branch name 'fix-github-pages' in the conditional makes the workflow fragile. Consider using a more generic approach or removing this specific branch exception to avoid maintenance issues when branch names change.

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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -45,3 +45,4 @@ Rplot.pdf
/Meta/
sccomp_draws_files
.DS_Store
docs
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -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
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4 changes: 4 additions & 0 deletions _pkgdown.yml
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@@ -0,0 +1,4 @@
url: https://mangiolalaboratory.github.io/sccomp/
template:
bootstrap: 5

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