Adds namer for naming code chunks

.github/workflows/bookdown.yml

@@ -1,5 +1,4 @@
 name: Build Bookdown
-
 on:
   push:
     branches:
@@ -14,15 +13,14 @@ permissions:
 jobs:
   build:
     runs-on: macos-latest
-
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
 
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "4.4.0"
+          r-version: "4.5.0"
 
       - name: Install system dependencies
         run: |
@@ -31,17 +29,19 @@ jobs:
 
       - name: Install CRAN & Bioconductor packages
         run: |
-          # Install remotes if missing
           Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")'
 
-          # Install CRAN dependencies from DESCRIPTION
-          Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
-
-          # Install BiocManager if missing
+          # Install BiocManager and Bioconductor packages FIRST
+          # so remotes::install_deps() doesn't warn about missing deps
           Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
+
+          Rscript -e 'BiocManager::install(c("EnhancedVolcano","DESeq2","edgeR","RUVSeq","piano","pcaMethods","impute","imputeLCMD","GEOquery"), ask = FALSE)'
+
+          # Pin factoextra
+          Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
 
-          # Install Bioconductor packages
-          Rscript -e 'BiocManager::install(c("EnhancedVolcano","DESeq2","edgeR","RUVSeq","piano","pcaMethods","impute", "imputeLCMD"), ask = FALSE)'
+          # Now install remaining CRAN deps from DESCRIPTION
+          Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
 
       - name: Build bookdown
         run: |
@@ -61,4 +61,4 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./book
-          force_orphan: true
+          force_orphan: true

.github/workflows/test_bookdown.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: "4.4.0"
+          r-version: "4.5.0"
 
       - name: Install system dependencies
         run: |
@@ -36,17 +36,19 @@ jobs:
 
       - name: Install CRAN & Bioconductor packages
         run: |
-          # Install remotes if missing
           Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")'
 
-          # Install CRAN dependencies from DESCRIPTION
-          Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
-
-          # Install BiocManager if missing
+          # Install BiocManager and Bioconductor packages FIRST
+          # so remotes::install_deps() doesn't warn about missing deps
           Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
 
-          # Install Bioconductor packages
-          Rscript -e 'BiocManager::install(c("EnhancedVolcano","DESeq2","edgeR","RUVSeq","piano","pcaMethods","impute", "imputeLCMD"), ask = FALSE)'
+          Rscript -e 'BiocManager::install(c("EnhancedVolcano","DESeq2","edgeR","RUVSeq","piano","pcaMethods","impute","imputeLCMD","GEOquery"), ask = FALSE)'
+
+          # Pin factoextra
+          Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
+
+          # Now install remaining CRAN deps from DESCRIPTION
+          Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
 
       - name: Build bookdown
         run: |

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+  - repo: local
+    hooks:
+      - id: namer
+        name: Name Rmd chunks with namer
+        language: system
+        entry: Rscript -e 'files <- list.files(".", pattern="[.][Rr]md$", recursive=TRUE, full.names=TRUE); files <- files[!grepl("(^|/)book/|(^|/)_book/", files)]; for (f in files) namer::name_chunks(f); cat("Processed", length(files), "Rmd files\n")'
+        pass_filenames: false
+        always_run: true