Merge pull request #173 from MangiolaLaboratory/github-pages-for-cmdstanr

Create pkgdown.yaml

Author: stemangiola

.github/workflows/pkgdown.yaml

@@ -0,0 +1,57 @@
+# 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
+    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
+
+      - name: Repos
+        run: |
+          cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::., any::cmdstanr
+          needs: website
+          cache-version: 2
+
+      - name: Install CmdStan
+        shell: Rscript {0}
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan()
+
+      - 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

.github/workflows/rworkflows.yml

@@ -46,7 +46,7 @@ jobs:
         run_vignettes: ${{ true }}
         has_testthat: ${{ true }}
         run_covr: ${{ true }}
-        run_pkgdown: ${{ true }}
+        run_pkgdown: ${{ false }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sccomp
 Title: Tests differences in cell-type proportion for single-cell data, robust to outliers
-Version: 1.99.13
+Version: 1.99.14
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre"))
                   )