Use micromamba with conda/bioconda for all dependencies

Author: yuw444

.github/workflows/pkgdown.yaml

@@ -17,31 +17,20 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libhts-dev libbz2-dev zlib1g-dev libssl-dev libsqlite3-dev
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
+      - name: Install micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+          shell-startup: false
+          isolate: false
 
-      - name: Install R dependencies
+      - name: Build pkgdown site
         run: |
-          Rscript -e 'install.packages(c(
-            "pkgdown", "roxygen2",
-            "Seurat", "monocle3", "glmGamPoi", "dplyr", "ggplot2", "patchwork",
-            "Matrix", "RColorBrewer", "SummarizedExperiment", "fpc", "igraph",
-            "jsonlite", "magrittr", "purrr", "scales", "scam", "tibble"
-          ), repos = "https://cloud.r-project.org")'
-
-      - name: Build site
-        run: Rscript -e 'pkgdown::build_site()'
+          micromamba run -n fastqdesign Rscript -e 'pkgdown::build_site()'
 
       - name: Deploy to GitHub pages
         if: github.event_name != 'pull_request'

environment.yml

@@ -0,0 +1,28 @@
+name: fastqdesign
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - r-base>=4.3
+  - r-pkgdown
+  - r-roxygen2
+  - r-testthat
+  - bioconductor-seurat
+  - bioconductor-monocle3
+  - r-glmgampoi
+  - r-dplyr
+  - r-ggplot2
+  - r-patchwork
+  - r-matrix
+  - r-rcolorbrewer
+  - bioconductor-summarizedexperiment
+  - r-fpc
+  - r-igraph
+  - r-jsonlite
+  - r-magrittr
+  - r-purrr
+  - r-scales
+  - r-scam
+  - r-tibble
+  - htslib
+  - cmake