From 0c1a6accb67ca9c0f629166bf0b97228ce0b62d5 Mon Sep 17 00:00:00 2001
From: Kate Isaac <41767733+kweav@users.noreply.github.com>
Date: Thu, 15 Aug 2024 12:36:58 -0400
Subject: [PATCH 1/5] Update customize-docker.Rmd test workflow URL

---
 customize-docker.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/customize-docker.Rmd b/customize-docker.Rmd
index 72b1b79..4599d92 100644
--- a/customize-docker.Rmd
+++ b/customize-docker.Rmd
@@ -205,7 +205,7 @@ For your personalized docker image, you can store the Dockerfile anywhere. In or
 
 It may be easiest to store it in the OTTR-made repository you are working from.
 
-In whichever repository you choose to store your Dockerfile, its recommended you use a GitHub action to automatically test it when you make changes. You can use our Docker handling [GitHub action here as a starting point](https://github.com/jhudsl/OTTR_Template/blob/main/.github/workflows/docker-test.yml).
+In whichever repository you choose to store your Dockerfile, its recommended you use a GitHub action to automatically test it when you make changes. You can use our Docker handling [GitHub action here as a starting point](https://github.com/jhudsl/ottr-docker/blob/main/.github/workflows/docker-test.yml).
 
 You will need to modify this GHA for your own purposes:
 

From 11ef6a8bcdbd113f25387a1a20cf264c2408a01f Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 6 Sep 2024 18:24:09 +0000
Subject: [PATCH 2/5] Render site

---
 docs/customize-docker.html | 2 +-
 docs/customize-style.html  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/customize-docker.html b/docs/customize-docker.html
index 0166238..8151cd0 100644
--- a/docs/customize-docker.html
+++ b/docs/customize-docker.html
@@ -807,7 +807,7 @@ <h4>Github actions for handling your Docker image</h4>
 <p>In whichever repository you choose to store your Dockerfile, its
 recommended you use a GitHub action to automatically test it when you
 make changes. You can use our Docker handling <a
-href="https://github.com/jhudsl/OTTR_Template/blob/main/.github/workflows/docker-test.yml">GitHub
+href="https://github.com/jhudsl/ottr-docker/blob/main/.github/workflows/docker-test.yml">GitHub
 action here as a starting point</a>.</p>
 <p>You will need to modify this GHA for your own purposes:</p>
 <ul>
diff --git a/docs/customize-style.html b/docs/customize-style.html
index 7da889a..22a30d8 100644
--- a/docs/customize-style.html
+++ b/docs/customize-style.html
@@ -614,7 +614,7 @@ <h3>Changing the favicon</h3>
 will be used.</p>
 <pre><code>---
 title: &quot;Course Name &quot;
-date: &quot;July, 2024&quot;
+date: &quot;September, 2024&quot;
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]

From ef65df5f76a25dd062c5edd89df93b6eb0d3bdd3 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Fri, 6 Sep 2024 18:28:35 +0000
Subject: [PATCH 3/5] =?UTF-8?q?=F0=9F=94=84=20Synced=20local=20'.github/wo?=
 =?UTF-8?q?rkflows/'=20with=20remote=20'.github/workflows/'?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

test-run
---
 .github/workflows/delete-preview.yml        |  2 +-
 .github/workflows/docker-test.yml           |  4 +-
 .github/workflows/file-automatic-issues.yml | 43 +++++++++++++++
 .github/workflows/pull_request.yml          | 59 ++++++++++++---------
 .github/workflows/render-site.yml           | 19 +++----
 5 files changed, 91 insertions(+), 36 deletions(-)
 create mode 100644 .github/workflows/file-automatic-issues.yml

diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
index afd658a..faa83cc 100644
--- a/.github/workflows/delete-preview.yml
+++ b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
index 6d786f4..b1cdc47 100644
--- a/.github/workflows/docker-test.yml
+++ b/.github/workflows/docker-test.yml
@@ -33,10 +33,10 @@ jobs:
 
     steps:
       - name: checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Verify Dockerfiles changed?
-        uses: tj-actions/verify-changed-files@v8.8
+        uses: tj-actions/verify-changed-files@v17
         id: verify-changed-files
         with:
           files: |
diff --git a/.github/workflows/file-automatic-issues.yml b/.github/workflows/file-automatic-issues.yml
new file mode 100644
index 0000000..e24658d
--- /dev/null
+++ b/.github/workflows/file-automatic-issues.yml
@@ -0,0 +1,43 @@
+# Code adapted from https://github.com/JetBrains/intellij-platform-plugin-template/blob/deb171483598ee8a5d7621154db880e87b4db4ef/.github/workflows/template-cleanup.yml
+# by Candace Savonen for this repository.
+
+name: Starting a website
+
+on:
+  push:
+    branches: [ main, staging ]
+  workflow_dispatch:
+
+jobs:
+  # Run cleaning process only if workflow is triggered by not being in the Bookdown template anymore
+  template-cleanup:
+    name: Template Cleanup
+    runs-on: ubuntu-latest
+    if: github.event.repository.name != 'OTTR_Template_Website'
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+      
+        # Issue for what repository settings need to be set
+      - name: New Course - Set Repository Settings
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Set Repository Settings
+          content-filepath: .github/automatic-issues/set-repo-settings.md
+          labels: automated training issue
+
+      # Issue for what needs to be edited
+      - name: New Course - Templates to Edit
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Templates to Edit
+          content-filepath: .github/automatic-issues/templates-to-edit.md
+          labels: automated training issue
+
+      # Issue for how to enroll repo for updates
+      - name: New Course - Template Update Enrollment
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: New Course - Template Update Enrollment
+          content-filepath: .github/automatic-issues/update-enrollment.md
+          labels: automated training issue
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 0fa603b..70a1eab 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,5 +1,5 @@
 # Candace Savonen Dec 2021
-# Updated April 2023
+# Updated Aug 2024
 name: Pull Request
 
 on:
@@ -13,9 +13,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -25,17 +26,19 @@ jobs:
 
       # Delete the branch if this has been run before
       - name: Delete branch locally and remotely
-        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+        run: git push --force origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
 
       # Make the branch fresh
       - name: Make the branch fresh
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name
+          git push --force --set-upstream origin $branch_name
         shell: bash
 
     outputs:
@@ -71,21 +74,21 @@ jobs:
     needs: yaml-check
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/course_template:main
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
     if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         run: |
-          git config --system --add safe.directory $GITHUB_WORKSPACE
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
@@ -110,21 +113,24 @@ jobs:
           echo site status ${{steps.site.outcome}}
           exit 1
 
-      # Commit the rendered website files
-      - name: Commit rendered website files to preview branch
+      - name: Website preview for download
+        run: zip website-preview.zip docs/* -r
+
+      # Commit the website files
+      - name: Commit rendered website files
         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 diff origin/main -- docs >/dev/null && changes=true || changes=false
+          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
 
       - name: Find Comment
-        uses: peter-evans/find-comment@v1
+        uses: peter-evans/find-comment@v3
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -136,26 +142,31 @@ jobs:
         run: |
           course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
           website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
-          echo ::set-output name=website_link::$website_link
-          echo ::set-output name=time::$(date +'%Y-%m-%d')
-          echo ::set-output name=commit_id::$GITHUB_SHA
+          docs_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          echo "zip_link=$docs_link" >> $GITHUB_OUTPUT
+          echo "website_link=$website_link" >> $GITHUB_OUTPUT
+          echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+          echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
 
       - name: Create or update comment
         if: steps.commit.outputs.changes == 'true'
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v3
         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 }})
+            :eyes: Quick [preview of website here](${{ steps.build-components.outputs.website_link }}) \*
+            :microscope: Comprehensive [download of the website here](${{ steps.build-components.outputs.zip_link }})
 
-            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+            \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ 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
+        uses: peter-evans/create-or-update-comment@v3
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
diff --git a/.github/workflows/render-site.yml b/.github/workflows/render-site.yml
index 508c0b1..d5d6415 100644
--- a/.github/workflows/render-site.yml
+++ b/.github/workflows/render-site.yml
@@ -15,10 +15,8 @@ on:
       - '**.Rmd'
       - styles.css
       - _site.yml
-      - subdir_html/*.Rmd
       - resources/images/*.png
       - resources/images/favicon.ico
-      - site_libs/*
 
 jobs:
   yaml-check:
@@ -26,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -43,11 +41,11 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
+      
+    steps:    
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # get the full repo
           fetch-depth: 0
@@ -72,11 +70,14 @@ jobs:
           exit 1
 
 # Commit the rendered site files - html files and site_libs files
+# The git reset step will remove any other files created in this workflow, such as API keys
       - name: Commit rendered site files
         run: |
-          git config --system --add safe.directory $GITHUB_WORKSPACE
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
           git add --force docs/*
           git commit -m 'Render site' || echo "No changes to commit"
+          git reset --hard HEAD
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
           git push origin main || echo "No changes to push"

From c329e0e0640fdf726daf7648c1395ee65dd06b1f Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Fri, 6 Sep 2024 18:28:36 +0000
Subject: [PATCH 4/5] =?UTF-8?q?=F0=9F=94=84=20Synced=20local=20'config=5Fa?=
 =?UTF-8?q?utomation.yml'=20with=20remote=20'config=5Fautomation.yml'?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

test-run
---
 config_automation.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/config_automation.yml b/config_automation.yml
index 12d9dd0..1a1a577 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -12,6 +12,8 @@ spell-check: yes
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
@@ -19,6 +21,10 @@ render-bookdown: yes
 render-leanpub: yes
 render-coursera: no
 
+## Automate the creation of Book.txt file? TRUE/FALSE?
+## This is only relevant if render-leanpub is yes, otherwise it will be ignored
+make-book-txt: TRUE
+
 # What docker image should be used for rendering?
 # The default is jhudsl/base_ottr:main
 rendering-docker-image: 'jhudsl/base_ottr:main'

From ca7b9769f9b821134d9d6140fe857895eebe18c2 Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:46:52 -0400
Subject: [PATCH 5/5] Update .github/workflows/file-automatic-issues.yml

---
 .github/workflows/file-automatic-issues.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/file-automatic-issues.yml b/.github/workflows/file-automatic-issues.yml
index e24658d..55f5baa 100644
--- a/.github/workflows/file-automatic-issues.yml
+++ b/.github/workflows/file-automatic-issues.yml
@@ -1,7 +1,7 @@
 # Code adapted from https://github.com/JetBrains/intellij-platform-plugin-template/blob/deb171483598ee8a5d7621154db880e87b4db4ef/.github/workflows/template-cleanup.yml
 # by Candace Savonen for this repository.
 
-name: Starting a website
+name: Starting a Website
 
 on:
   push: