Merge branch 'main' into pull_resource

getting html updates from main

.github/workflows/docker-test.yml

@@ -0,0 +1,91 @@
+
+# Candace Savonen Apr 2022
+
+name: Build Docker Image
+
+on:
+  workflow_call:
+    inputs:
+      directory:
+        required: true
+        type: string
+      tag:
+        required: true
+        type: string
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: false
+        default: 'false'
+        type: string
+    secrets:
+      GH_PAT:
+        required: true
+      DOCKERHUB_USERNAME:
+        required: false
+      DOCKERHUB_TOKEN:
+        required: false
+
+jobs:
+
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+
+      - name: Verify Dockerfiles changed?
+        uses: tj-actions/verify-changed-files@v8.8
+        id: verify-changed-files
+        with:
+          files: |
+             ${{ inputs.directory }}/Dockerfile
+             ${{ inputs.directory }}/github_package_list.tsv
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --local --add safe.directory "$GITHUB_WORKSPACE"
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Set up Docker Build
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v4
+        with:
+          push: false
+          load: true
+          context: ${{ inputs.directory }}
+          file: ${{ inputs.directory }}/Dockerfile
+          tags: ${{ inputs.tag }}
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        run: docker push ${{ inputs.tag }}

.github/workflows/manual_dispatch.yml

@@ -0,0 +1,32 @@
+# Candace Savonen May 2022
+
+name: Manual build of docker image
+
+on:
+  workflow_dispatch:
+    inputs:
+      directory:
+        required: true
+        type: string
+      tag:
+        required: true
+        type: string
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: false
+        default: 'false'
+        type: string
+
+jobs:
+
+  build-it:
+    name: Build docker image on command
+    uses: ./.github/workflows/docker-test.yml
+    with:
+      directory: ${{github.event.inputs.directory}}
+      tag: ${{github.event.inputs.tag}}
+      dockerhubpush: ${{github.event.inputs.dockerhubpush}}
+    secrets:
+      GH_PAT: ${{ secrets.GH_PAT }}
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/pull_request.yml

@@ -269,7 +269,7 @@ jobs:
     needs: yaml-check
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/intro_to_r:1.0
+      image: jhudsl/intro_to_r:1.1
     if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
 
     steps:
@@ -279,10 +279,14 @@ jobs:
           repo_name='${{ github.event.repository.name }}'
           git config --global --add safe.directory /__w/$repo_name/$repo_name
 
-      - name: Checkout files
+      # # Checks-out your repository with the token so your job can access it
+      - name: checkout
         uses: actions/checkout@v3
         with:
+          # get the full repo
           fetch-depth: 0
+          # use github PAT
+          token: ${{ secrets.GH_PAT }}
 
       # Set up git checkout
       - name: Set up git checkout
@@ -295,15 +299,22 @@ jobs:
           git checkout $branch_name
           git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
         shell: bash
+
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/changed-files@v37
+      # NOTE: `since_last_remote_commit: true` is implied by default and falls back to the previous local commit.
+
+      - name: List all changed files
+        run: |
+          for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
+            echo "$file was changed"
+          done
 
       # We want a fresh run of the renders each time - so first delete old html files
       - name: Delete old *.html
         run: Rscript -e "rmarkdown::clean_site(preview = FALSE)"
 
-      # TODO: add this to docker
-      - name: Install config package
-        run: Rscript -e "install.packages('config')"
-
        # Now we want to render all the html files from the Rmd files
       - name: Run render html for the main site
         id: site
@@ -315,15 +326,33 @@ jobs:
 
        # Render all module files
       - name: Render html of modules
-        run: Rscript "scripts/render_modules.R"
-
+        run: |
+          Rscript --vanilla "scripts/render_modules.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
+          
        # Render the cheatsheets
       - name: Render Cheatsheet pdfs
-        run: Rscript "scripts/render_cheatsheets.R"
-
+        run: |
+          Rscript --vanilla "scripts/render_cheatsheets.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
+        
        # Render resource pdfs
       - name: Render Resource pdfs
-        run: Rscript "scripts/render_resources.R"
+        run: |
+          Rscript --vanilla "scripts/render_resources.R" --files "${{ steps.changed-files.outputs.all_changed_files }}"
+        
+       # Generate list of files that need pdfs
+      - name: Get list of html to pdfs
+        run: |
+          Rscript --vanilla "scripts/render_html_list.R"
+          echo "$(cat files.txt)"
+        
+      - name: Read html and pdf files
+        id: getfiles
+        run: |
+          echo "files=$(cat files.txt)" >> $GITHUB_OUTPUT 
+          rm files.txt
+          rm cheatsheet_files.csv
+          rm lab_files.csv
+          rm lecture_files.csv
 
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
@@ -342,7 +371,7 @@ jobs:
           echo "changes=$changes" >> $GITHUB_OUTPUT
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"
         shell: bash
 
@@ -387,35 +416,30 @@ jobs:
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
+
+    # Save files for conversion to pdf      
+    outputs:
+      pdffiles: "${{ steps.getfiles.outputs.files }}"
+
 
   render-pdf-lectures:
     name: Render pdf lecture slides
     needs: render-preview
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/course_template:main
+      image: jhudsl/intro_to_r:1.1
     if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
     strategy:
       matrix:
-        modulenames: 
-          - Intro
-          - RStudio
-          - Reproducibility
-          - Basic_R
-          - Data_Input
-          - Subsetting_Data_in_R
-          - Data_Summarization
-          - Data_Classes
-          - Data_Cleaning
-          - Manipulating_Data_in_R
-          - Esquisse_Data_Visualization
-          - Data_Visualization
-          - Factors
-          - Statistics
-          - Data_Output
-          - Functions
+        modulenames: ${{fromJson(needs.render-preview.outputs.pdffiles)}}
 
     steps:
+      # Give permission to access the repo
+      - name: safelist repository
+        run: |
+          repo_name='${{ github.event.repository.name }}'
+          git config --global --add safe.directory /__w/$repo_name/$repo_name
+          
       - name: Checkout files
         uses: actions/checkout@v3
         with: