Update generate.yml

Author: guydavenport

.github/workflows/generate.yml

@@ -35,84 +35,73 @@ jobs:
             echo "skip_commit=true" >> "$GITHUB_OUTPUT"
             echo "Normal branch - Will NOT commit of generated files"
           fi
-  generate:
+  build:
     runs-on: ubuntu-latest
     needs: check
     if: needs.check.outputs.skip_job != 'true'
     steps:
-      - name: debug
-        run: |
-          echo ${{ needs.check.outputs.skip_job }} 
-          echo ${{ needs.check.outputs.skip_commit }} 
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
           ssh-key: ${{ secrets.DEPLOY_KEY }}
           path: main
+
       - name: Checkout BrAPI repo to temp directory
         uses: actions/checkout@v4
         with:
           repository: plantbreeding/BrAPI
           path: BrAPI
+
       - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '21'
+
       - name: Change wrapper permissions
         working-directory: ./main/generator
         run: chmod +x ./gradlew
+
       - name: Generate R Code
         working-directory: ./main/generator
         run: ./gradlew generateR
+
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
+
       - name: Install devtools
         working-directory: main/pkg
         run: Rscript -e "install.packages('devtools')"
+
       - name: Document R package
         working-directory: main/pkg
         run: Rscript -e "devtools::document()"
-      - if: needs.check.outputs.skip_commit == 'false'
-        uses: stefanzweifel/git-auto-commit-action@v5
-        with:
-          repository: main
-          commit_message: Apply automatic changes
-          file_pattern: main/**
-  pkgdown:
-    runs-on: ubuntu-latest
-    needs: generate
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
-    steps:
-      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
-          working-directory: pkg
+          working-directory: main/pkg
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
-        working-directory: pkg
-
+        working-directory: main/pkg
+      - if: needs.check.outputs.skip_commit == 'false'
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          repository: main
+          commit_message: Apply automatic changes
+          file_pattern: main/**
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
         uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
           folder: pkg/docs
+
+