Merge pull request #42 from NIEHS/staging-internal

July version updates

.github/workflows/test-render.yml → .github/workflows/check-render-bookdown.yml

@@ -2,21 +2,23 @@
 # Need help debugging build failures? 
 # Start at https://github.com/r-lib/actions#where-to-find-help
 ---
-name: Render Bookdown
+name: Check Render Bookdown
 
 on:
-  push:
-    branches: [master, main]
   pull_request:
 
 jobs:
-  test-render-bookdown:
+  check_render_bookdown:
     runs-on: ubuntu-latest
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
@@ -26,11 +28,6 @@ jobs:
           sudo apt-get install -y libudunits2-dev libgdal-dev
           sudo apt-get install libmagick++-dev
 
-      - name: Install pandoc-citeproc
-        run: |
-          sudo apt-get update
-          sudo apt-get install pandoc-citeproc
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           packages: |

.github/workflows/superlint.yml → .github/workflows/check-super-linter.yml

@@ -1,14 +1,13 @@
 ---
-name: Super Linter
+name: Check Super Linter
 
 on:
-  push:
   pull_request:
 
 jobs:
-  super-lint:
-    name: Lint all file types
+  check_super_linter:
     runs-on: ubuntu-latest
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
@@ -23,5 +22,5 @@ jobs:
       - name: Run Super-Linter
         uses: github/super-linter@v4
         env:
-          FILTER_REGEX_EXCLUDE: .*/docs/*
+          FILTER_REGEX_EXCLUDE: .*/docs/.*|.*/.github/workflows/.*
           LINTR_ERROR_ON_LINT: true

.github/workflows/deploy-toolkit.yml

@@ -0,0 +1,82 @@
+# # 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
+# ---
+# name: Deploy Toolkit
+
+# on:
+#   push:
+#     branches: [main, master]
+#   pull_request:
+#     branches: [main, master]
+#   release:
+#     types: [published]
+#   workflow_dispatch:
+
+# jobs:
+#   deploy_toolkit:
+#     runs-on: ubuntu-latest
+
+#     # Only restrict concurrency for non-PR jobs
+#     concurrency:
+#       group: bookdown-${{ 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
+
+#       - name: Install libudunits2 and libmagick
+#         run: |
+#           sudo apt-get install -y libudunits2-dev libgdal-dev
+#           sudo apt-get install libmagick++-dev
+
+#       - name: Build site
+#         run: |
+#           install.packages(c(
+#             "bookdown",
+#             "rmarkdown",
+#             "plotly",
+#             "shiny",
+#             "tidycensus",
+#             "tidyverse",
+#             "viridis",
+#             "ggmap",
+#             "ggplot2",
+#             "maps",
+#             "dplyr",
+#             "knitr",
+#             "latticeExtra",
+#             "pals",
+#             "classInt",
+#             "sf",
+#             "udunits2",
+#             "tmap",
+#             "lubridate",
+#             "gifski",
+#             "magick",
+#             "cowplot",
+#             "BiocManager"
+#             ),
+#             dependencies = TRUE
+#           )
+#           BiocManager::install("Biobase")
+#           bookdown::render_book()
+#         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/protect-main.yml

@@ -0,0 +1,34 @@
+---
+name: Protect Branch `main`
+
+on:
+  pull_request:
+
+jobs:
+  protect_main:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check base branch
+        id: check-base-branch
+        run: |
+          if [[ "${{ github.event.pull_request.base.ref }}" == "main" || "${{ github.event.pull_request.base.ref }}" == "master" ]]; then
+            echo "Protected branch \"main\" detected in pull request."
+            echo "continue=true" >> "$GITHUB_OUTPUT"
+           else
+            echo "Protected branch \"main\" not detected in pull request."
+            echo "continue=false" >> "$GITHUB_OUTPUT"
+          fi
+      
+      - name: Check source branch
+        run: |
+          continue="${{ steps.check-base-branch.outputs.continue }}"
+          if [[ "$continue" == "true" ]]; then
+            source_branch=$(jq -r '.pull_request.head.ref' "$GITHUB_EVENT_PATH")
+            if [[ "$source_branch" != "staging-public" ]]; then
+              echo "Pull requests into \"main\" must come from \"staging-public\"."
+              exit 1
+            fi
+          else
+            echo "Protected branch \"main\" not detected in pull request."
+          fi

.github/workflows/protect-staging-public.yml

@@ -0,0 +1,34 @@
+---
+name: Protect Branch `staging-public`
+
+on:
+  pull_request:
+
+jobs:
+  protect_staging_public:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check base branch
+        id: check-base-branch
+        run: |
+          if [[ "${{ github.event.pull_request.base.ref }}" == "staging-public" ]]; then
+            echo "Protected branch \"staging-public\" detected in pull request."
+            echo "continue=true" >> "$GITHUB_OUTPUT"
+           else
+            echo "Protected branch \"staging-public\" not detected in pull request."
+            echo "continue=false" >> "$GITHUB_OUTPUT"
+          fi
+      
+      - name: Check source branch
+        run: |
+          continue="${{ steps.check-base-branch.outputs.continue }}"
+          if [[ "$continue" == "true" ]]; then
+            source_branch=$(jq -r '.pull_request.head.ref' "$GITHUB_EVENT_PATH")
+            if [[ "$source_branch" != "staging-internal" ]]; then
+              echo "Pull requests into \"staging-public\" must come from \"staging-internal\"."
+              exit 1
+            fi
+          else
+            echo "Protected branch \"staging-public\" not detected in pull request."
+          fi

.github/workflows/update-staging-external.yml

@@ -0,0 +1,49 @@
+# workflow to update external repository hosting staging webpage
+---
+name: Update external repository `PCOR_bookdown_staging`
+
+on:
+  push:
+    branches: [staging-internal]
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout `PCOR_public` repository
+        uses: actions/checkout@v3
+        with:
+          ref: staging-internal
+
+      - name: Set up Git
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Clone the staging repository
+        run: |
+          cd ../
+          git clone https://${{ secrets.PCOR_bookdown_staging_actions_06262024 }}@github.com/NIEHS/PCOR_bookdown_staging.git
+          cd PCOR_bookdown_staging
+          git checkout main
+          cd ../
+
+      - name: Check directory debug
+        run: |
+          cd ../
+          pwd
+          ls -l
+
+      - name: Sync files
+        run: |
+          cd ../
+          rsync -av --checksum --ignore-missing-args --exclude='.git' --exclude='.github' --exclude='.gitignore' --exclude='README.md' --delete ./PCOR_bookdown_tools/ ./PCOR_bookdown_staging/ || true
+          cd PCOR_bookdown_staging
+          git add .
+          git status
+          git commit -m "Sync PCOR_public staging-internal branch" || echo "No changes to commit"
+          git push https://${{ secrets.PCOR_bookdown_staging_actions_06262024 }}@github.com/NIEHS/PCOR_bookdown_staging.git main
+
+    env:
+      GITHUB_PAT: ${{ secrets.PCOR_bookdown_staging_actions_06262024 }}

.github/workflows/update-staging-internal.yml

@@ -0,0 +1,22 @@
+# ---
+# name: Update Branch `staging-internal`
+
+# on:
+#   push:
+#     branches: [staging-public]
+
+# jobs:
+#   update_staging_internal:
+#     runs-on: ubuntu-latest
+
+#     if: github.event_name == 'push' && contains(github.event.head_commit.message, 'Merge pull request')
+
+#     steps:
+#       - name: Checkout code
+#         uses: actions/checkout@v2
+
+#       - name: Delete old branch
+#         run: |
+#           git push origin --delete staging-internal || true
+#           git checkout -b staging-internal
+#           git push origin staging-internal

.github/workflows/update-staging-public.yml

@@ -0,0 +1,22 @@
+# ---
+# name: Update Branch `staging-public`
+
+# on:
+#   push:
+#     branches: [main, master]
+
+# jobs:
+#   update_staging_public:
+#     runs-on: ubuntu-latest
+
+#     if: github.event_name == 'push' && contains(github.event.head_commit.message, 'Merge pull request')
+
+#     steps:
+#       - name: Checkout code
+#         uses: actions/checkout@v2
+
+#       - name: Delete old branch
+#         run: |
+#           git push origin --delete staging-public || true
+#           git checkout -b staging-public
+#           git push origin staging-public

.gitignore

@@ -9,3 +9,4 @@ _book/
 _bookdown_files/
 _main_files
 .DS_Store
+docs/