From 3938afb51cae8add187fa26c575b1b7193881a17 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 30 Mar 2023 13:26:57 -0400
Subject: [PATCH 1/3] Add github actions

---
 .github/workflows/delete-preview.yml |  27 +++
 .github/workflows/pull_request.yml   | 336 +++++++++++++++++++++++++++
 .github/workflows/render-site.yml    |  68 ++++++
 3 files changed, 431 insertions(+)
 create mode 100644 .github/workflows/delete-preview.yml
 create mode 100644 .github/workflows/pull_request.yml
 create mode 100644 .github/workflows/render-site.yml

diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
new file mode 100644
index 0000000..afd658a
--- /dev/null
+++ b/.github/workflows/delete-preview.yml
@@ -0,0 +1,27 @@
+# Candace Savonen Apr 2021
+
+name: Delete Preview
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  delete-preview:
+    runs-on: ubuntu-latest
+    steps:
+
+      # This is because if a PR is closed before a render finishes it won't find it.
+      - name: Sleep for 5 minutes
+        run: sleep 300s
+        shell: bash
+
+      # Check out current repository
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      # Delete the branch!
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
new file mode 100644
index 0000000..edda242
--- /dev/null
+++ b/.github/workflows/pull_request.yml
@@ -0,0 +1,336 @@
+# Candace Savonen Dec 2021
+
+name: Pull Request
+
+on:
+  pull_request:
+    branches: [ main, staging ]
+
+jobs:
+
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+
+      - name: Make branch if it doesn't exist
+        run: |
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          exists=$(git ls-remote https://${{ secrets.GH_PAT }}@github.com/$GITHUB_REPOSITORY $branch_name | wc -l | xargs)
+          if [[ $exists == 0 ]];then
+            echo branch doesnt exist
+            git checkout -b $branch_name || echo branch exists
+            git push --set-upstream origin $branch_name
+          else
+            echo branch does exist
+          fi
+        shell: bash
+
+      - name: Check if this is a private repository
+        id: public_repository
+        run: |
+          public=$(curl -Is https://github.com/${GITHUB_REPOSITORY} | head -1 | tr -dc '0-9')
+          if [ $public -eq 2200 ];then
+            public='true'
+            echo 'public repository'
+          else
+            public='false'
+            echo 'private repository'
+          fi
+          echo ::set-output name=public::$public
+        shell: bash
+
+    outputs:
+      public_repository: "${{ steps.public_repository.outputs.public }}"
+      toggle_spell_check: "${{ env.SPELL_CHECK }}"
+      toggle_url_check: "${{ env.URL_CHECKER }}"
+      toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+
+  spell-check:
+    name: Check spelling
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
+    container:
+      image: jhudsl/course_template:main
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Configure git
+        run: |
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git fetch --all
+          git checkout $branch_name
+          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
+        shell: bash
+
+      - name: Run spell check
+        id: spell_check_run
+        run: |
+          results=$(Rscript "scripts/spell-check.R")
+          echo "::set-output name=sp_chk_results::$results"
+
+      - name: Commit spell check errors
+        run: |
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git add --force check_reports/spell_check_results.tsv || echo "No changes to commit"
+          git commit -m 'Add spell check file' || echo "No changes to commit"
+          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+          git push --force origin $branch_name || echo "No changes to commit"
+
+      - name: Build components of the spell check comment
+        id: build-components
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          sp_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/spell_check_results.tsv
+          echo ::set-output name=time::$(date +'%Y-%m-%d')
+          echo ::set-output name=commit_id::$GITHUB_SHA
+          echo ::set-output name=sp_error_url::$sp_error_url
+
+      # Handle the commenting
+      - name: Find Comment
+        uses: peter-evans/find-comment@v1
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: spelling errors
+
+      - name: Spelling errors!
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            :warning: There are spelling errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Spell-check).
+            [Download the errors here.](${{ steps.build-components.outputs.sp_error_url }})
+            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+      - name: Check spell check results - fail if too many errors
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
+        run: exit 1
+
+      - name: No spelling errors
+        if: ${{ steps.spell_check_run.outputs.sp_chk_results < 3 }}
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            No spelling errors! :tada:
+            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+  url-check:
+    name: Check URLs
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
+    container:
+      image: jhudsl/course_template:main
+
+    steps:
+    - name: checkout repo
+      uses: actions/checkout@v3
+
+    - name: Configure git
+      run: |
+        git config --local user.email "itcrtrainingnetwork@gmail.com"
+        git config --local user.name "jhudsl-robot"
+
+        branch_name='preview-${{ github.event.pull_request.number }}'
+        git fetch --all
+        git checkout $branch_name
+        git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
+      shell: bash
+
+    - name: URLs checker
+      id: url_errors
+      run: |
+        chk_results=$(Rscript scripts/url-check.R)
+        echo $chk_results
+
+        echo "::set-output name=url_results::$chk_results"
+
+    - name: Commit URL check
+      run: |
+        branch_name='preview-${{ github.event.pull_request.number }}'
+        git add --force check_reports/url_checks.tsv || echo "No changes to commit"
+        git commit -m 'Add URL check file' || echo "No changes to commit"
+        git fetch
+        git merge -s recursive --strategy-option=ours origin/${{ github.head_ref }} --allow-unrelated-histories
+        git push --force origin $branch_name || echo "No changes to commit"
+
+    - name: Build components of the spell check comment
+      id: build-components
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        branch_name='preview-${{ github.event.pull_request.number }}'
+        url_errors=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/url_checks.tsv
+        echo ::set-output name=time::$(date +'%Y-%m-%d')
+        echo ::set-output name=commit_id::$GITHUB_SHA
+        echo ::set-output name=url_errors::$url_errors
+
+    # Handle the commenting
+    - name: Find Comment
+      uses: peter-evans/find-comment@v1
+      id: fc
+      with:
+        issue-number: ${{ github.event.pull_request.number }}
+        comment-author: 'github-actions[bot]'
+        body-includes: broken URLs
+
+    - name: URL errors!
+      if: ${{ steps.url_errors.outputs.url_results > 0 }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        comment-id: ${{ steps.fc.outputs.comment-id }}
+        issue-number: ${{ github.event.pull_request.number }}
+        body: |
+          :warning: There are broken URLs that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#check-for-broken-urls).
+          [Download the errors here.](${{ steps.build-components.outputs.url_errors }})
+          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+        edit-mode: replace
+
+    - name: Check URL results - fail if too many errors
+      if: ${{ steps.url_errors.outputs.url_results > 0 }}
+      run: exit 1
+
+    - name: No URL errors
+      if: ${{ steps.url_errors.outputs.url_results == 0 }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        comment-id: ${{ steps.fc.outputs.comment-id }}
+        issue-number: ${{ github.event.pull_request.number }}
+        body: |
+          No broken URLs detected! :tada:
+          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+        edit-mode: replace
+
+  render-preview:
+    name: Render preview
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/course_template:main
+    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      # Set up git checkout
+      - name: Set up git checkout
+        run: |
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git fetch --all
+          git checkout $branch_name
+          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
+        shell: bash
+
+      # 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)"
+
+       # Now we want to render all the html files from the Rmd files
+      - name: Run render html
+        id: site
+        run: Rscript -e "rmarkdown::render_site()"
+
+      # We may have html files that we want to render to add as links on the pages -these will be stored in a dir called subdir_html
+      - name: Render subdir_html
+        id: subdir_html
+        run: Rscript -e "for (i in list.files(path = './subdir_html', pattern = 'Rmd$', recursive = TRUE, full.names = TRUE)){rmarkdown::render(i)}"
+
+      # 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
+      - name: Check on render steps
+        if: steps.site.outcome != 'success'
+        run: |
+          echo site status ${{steps.site.outcome}}
+          exit 1
+
+      # Commit the rendered website files
+      - name: Commit rendered website files to preview branch
+        id: commit
+        run: |
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git diff origin/main -- '*.html' >/dev/null && changes=true || changes=false
+          echo ::set-output name=changes::$changes
+          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 push --force || echo "No changes to commit"
+        shell: bash
+
+      - name: Find Comment
+        uses: peter-evans/find-comment@v1
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: latest commit
+
+      - name: Build components of the comment
+        id: build-components
+        run: |
+          course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
+          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/index.html")
+          echo ::set-output name=website_link::$website_link
+          echo ::set-output name=time::$(date +'%Y-%m-%d')
+          echo ::set-output name=commit_id::$GITHUB_SHA
+          echo ${{steps.commit.outputs.changes}}
+
+      - name: Create or update comment
+        if: steps.commit.outputs.changes == 'true'
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            Re-rendered previews from the latest commit: See [preview of website here](${{ steps.build-components.outputs.website_link }})
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+      - name: No comment if no changes
+        if: steps.commit.outputs.changes == 'false'
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            The latest commit did not produce rendering changes.
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
diff --git a/.github/workflows/render-site.yml b/.github/workflows/render-site.yml
new file mode 100644
index 0000000..1d2a1bf
--- /dev/null
+++ b/.github/workflows/render-site.yml
@@ -0,0 +1,68 @@
+
+# It was adapted by Candace Savonen for the OTTR_template https://github.com/jhudsl/OTTR_Template.
+
+# This code was adapted by Carrie Wright to enable automated rendering of the site associated with this repository
+
+name: Render html
+
+# Controls when the action will run. Triggers the workflow on push
+# events only for the master branch
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths:
+      - '**.Rmd'
+      - styles.css
+      - _site.yml
+      - subdir_html/*.Rmd
+      - resources/images/*.png
+      - resources/images/favicon.ico
+      - site_libs/*
+
+jobs:
+  # This workflow contains a single job called "build-all"
+  render-main:
+    runs-on: ubuntu-latest
+          # install.packages("remotes") # in case we decide not to go with the container...
+          # remotes::install_cran("rmarkdown")
+          # remotes::install_deps(dependencies = TRUE)
+    container:
+      image: jhudsl/course_template
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, 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 }}
+
+      # 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)"
+
+       # Now we want to render all the html files from the Rmd files
+      - name: Run render html
+        id: site
+        run: Rscript -e "rmarkdown::render_site()"
+
+      # 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
+      - name: Check on render steps
+        if: steps.site.outcome != 'success'
+        run: |
+          echo site status ${{steps.site.outcome}}
+          exit 1
+
+# Commit the rendered site files - html files and site_libs files
+      - name: Commit rendered site files
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add --force *.html
+          git add --force site_libs/*
+          git commit -m 'Render site' || echo "No changes to commit"
+          git push origin main || echo "No changes to push"

From 1fe421c723b29ae82ae0cb77a78fe47a04c13d6e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 30 Mar 2023 14:00:43 -0400
Subject: [PATCH 2/3] Update github actions

---
 .github/workflows/pull_request.yml | 177 +++--------------------------
 .github/workflows/render-site.yml  |  28 ++++-
 2 files changed, 37 insertions(+), 168 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index edda242..af50f0a 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -58,180 +58,29 @@ jobs:
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
+########################## Make the error reports ##############################
   spell-check:
     name: Check spelling
     needs: yaml-check
-    runs-on: ubuntu-latest
     if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
-    container:
-      image: jhudsl/course_template:main
-
-    steps:
-      - name: Checkout files
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: Configure git
-        run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
-
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git fetch --all
-          git checkout $branch_name
-          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-        shell: bash
-
-      - name: Run spell check
-        id: spell_check_run
-        run: |
-          results=$(Rscript "scripts/spell-check.R")
-          echo "::set-output name=sp_chk_results::$results"
-
-      - name: Commit spell check errors
-        run: |
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git add --force check_reports/spell_check_results.tsv || echo "No changes to commit"
-          git commit -m 'Add spell check file' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
-          git push --force origin $branch_name || echo "No changes to commit"
-
-      - name: Build components of the spell check comment
-        id: build-components
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-        run: |
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          sp_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/spell_check_results.tsv
-          echo ::set-output name=time::$(date +'%Y-%m-%d')
-          echo ::set-output name=commit_id::$GITHUB_SHA
-          echo ::set-output name=sp_error_url::$sp_error_url
-
-      # Handle the commenting
-      - name: Find Comment
-        uses: peter-evans/find-comment@v1
-        id: fc
-        with:
-          issue-number: ${{ github.event.pull_request.number }}
-          comment-author: 'github-actions[bot]'
-          body-includes: spelling errors
-
-      - name: Spelling errors!
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
-        uses: peter-evans/create-or-update-comment@v1
-        with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            :warning: There are spelling errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Spell-check).
-            [Download the errors here.](${{ steps.build-components.outputs.sp_error_url }})
-            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
-
-      - name: Check spell check results - fail if too many errors
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }}
-        run: exit 1
-
-      - name: No spelling errors
-        if: ${{ steps.spell_check_run.outputs.sp_chk_results < 3 }}
-        uses: peter-evans/create-or-update-comment@v1
-        with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            No spelling errors! :tada:
-            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: spelling
+      error_min: 3
+      gh_pat: secrets.GH_PAT
 
   url-check:
     name: Check URLs
     needs: yaml-check
-    runs-on: ubuntu-latest
     if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
-    container:
-      image: jhudsl/course_template:main
-
-    steps:
-    - name: checkout repo
-      uses: actions/checkout@v3
-
-    - name: Configure git
-      run: |
-        git config --local user.email "itcrtrainingnetwork@gmail.com"
-        git config --local user.name "jhudsl-robot"
-
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        git fetch --all
-        git checkout $branch_name
-        git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-      shell: bash
-
-    - name: URLs checker
-      id: url_errors
-      run: |
-        chk_results=$(Rscript scripts/url-check.R)
-        echo $chk_results
-
-        echo "::set-output name=url_results::$chk_results"
-
-    - name: Commit URL check
-      run: |
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        git add --force check_reports/url_checks.tsv || echo "No changes to commit"
-        git commit -m 'Add URL check file' || echo "No changes to commit"
-        git fetch
-        git merge -s recursive --strategy-option=ours origin/${{ github.head_ref }} --allow-unrelated-histories
-        git push --force origin $branch_name || echo "No changes to commit"
-
-    - name: Build components of the spell check comment
-      id: build-components
-      env:
-        GH_PAT: ${{ secrets.GH_PAT }}
-      run: |
-        branch_name='preview-${{ github.event.pull_request.number }}'
-        url_errors=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/url_checks.tsv
-        echo ::set-output name=time::$(date +'%Y-%m-%d')
-        echo ::set-output name=commit_id::$GITHUB_SHA
-        echo ::set-output name=url_errors::$url_errors
-
-    # Handle the commenting
-    - name: Find Comment
-      uses: peter-evans/find-comment@v1
-      id: fc
-      with:
-        issue-number: ${{ github.event.pull_request.number }}
-        comment-author: 'github-actions[bot]'
-        body-includes: broken URLs
-
-    - name: URL errors!
-      if: ${{ steps.url_errors.outputs.url_results > 0 }}
-      uses: peter-evans/create-or-update-comment@v1
-      with:
-        comment-id: ${{ steps.fc.outputs.comment-id }}
-        issue-number: ${{ github.event.pull_request.number }}
-        body: |
-          :warning: There are broken URLs that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#check-for-broken-urls).
-          [Download the errors here.](${{ steps.build-components.outputs.url_errors }})
-          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-        edit-mode: replace
-
-    - name: Check URL results - fail if too many errors
-      if: ${{ steps.url_errors.outputs.url_results > 0 }}
-      run: exit 1
-
-    - name: No URL errors
-      if: ${{ steps.url_errors.outputs.url_results == 0 }}
-      uses: peter-evans/create-or-update-comment@v1
-      with:
-        comment-id: ${{ steps.fc.outputs.comment-id }}
-        issue-number: ${{ github.event.pull_request.number }}
-        body: |
-          No broken URLs detected! :tada:
-          _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-        edit-mode: replace
-
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT
+      
   render-preview:
     name: Render preview
     needs: yaml-check
diff --git a/.github/workflows/render-site.yml b/.github/workflows/render-site.yml
index 1d2a1bf..1e87727 100644
--- a/.github/workflows/render-site.yml
+++ b/.github/workflows/render-site.yml
@@ -21,14 +21,28 @@ on:
       - site_libs/*
 
 jobs:
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+
+    outputs:
+      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
+
   # This workflow contains a single job called "build-all"
   render-main:
+    needs: yaml-check
     runs-on: ubuntu-latest
-          # install.packages("remotes") # in case we decide not to go with the container...
-          # remotes::install_cran("rmarkdown")
-          # remotes::install_deps(dependencies = TRUE)
     container:
-      image: jhudsl/course_template
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -49,6 +63,11 @@ jobs:
         id: site
         run: Rscript -e "rmarkdown::render_site()"
 
+      # We may have html files that we want to render to add as links on the pages -these will be stored in a dir called subdir_html
+      - name: Render subdir_html
+        id: subdir_html
+        run: Rscript -e "for (i in list.files(path = './subdir_html', pattern = 'Rmd$', recursive = TRUE, full.names = TRUE)){rmarkdown::render(i)}"
+
       # 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
       - name: Check on render steps
@@ -63,6 +82,7 @@ jobs:
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
           git add --force *.html
+          git add --force subdir_html/*.html
           git add --force site_libs/*
           git commit -m 'Render site' || echo "No changes to commit"
           git push origin main || echo "No changes to push"

From 9ece92cfd551c03e1eb8ac931ca4edc1e1efa53a Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 30 Mar 2023 14:04:01 -0400
Subject: [PATCH 3/3] Update github actions

---
 .github/workflows/pull_request.yml | 38 ++++--------------------------
 1 file changed, 4 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index af50f0a..bc1c850 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -8,8 +8,8 @@ on:
 
 jobs:
 
-  yaml-check:
-    name: Load user automation choices
+  create-branch:
+    name: Create Branch
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -17,12 +17,6 @@ jobs:
         with:
           fetch-depth: 0
 
-        # Use the yaml-env-action action.
-      - name: Load environment from YAML
-        uses: doughepi/yaml-env-action@v1.0.0
-        with:
-            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
-
       - name: Make branch if it doesn't exist
         run: |
           git config --local user.email "itcrtrainingnetwork@gmail.com"
@@ -39,32 +33,10 @@ jobs:
           fi
         shell: bash
 
-      - name: Check if this is a private repository
-        id: public_repository
-        run: |
-          public=$(curl -Is https://github.com/${GITHUB_REPOSITORY} | head -1 | tr -dc '0-9')
-          if [ $public -eq 2200 ];then
-            public='true'
-            echo 'public repository'
-          else
-            public='false'
-            echo 'private repository'
-          fi
-          echo ::set-output name=public::$public
-        shell: bash
-
-    outputs:
-      public_repository: "${{ steps.public_repository.outputs.public }}"
-      toggle_spell_check: "${{ env.SPELL_CHECK }}"
-      toggle_url_check: "${{ env.URL_CHECKER }}"
-      toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
-      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-
 ########################## Make the error reports ##############################
   spell-check:
     name: Check spelling
     needs: yaml-check
-    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
     uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
     with:
       check_type: spelling
@@ -74,20 +46,18 @@ jobs:
   url-check:
     name: Check URLs
     needs: yaml-check
-    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
     uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
     with:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
-      
+
   render-preview:
     name: Render preview
     needs: yaml-check
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/course_template:main
-    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
+      image: jhudsl/base_ottr:main
 
     steps:
       - name: Checkout files