From 0d4d050d0d6d09baf677aa13309938d8cac40e53 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 11:24:50 -0500
Subject: [PATCH 01/14] Attempt at student config

---
 .github/workflows/pull_request.yml |  7 +++++++
 _bookdown.yml                      |  3 +++
 _bookdown_student_guide.yml        | 17 +++++++++++++++++
 config_automation.yml              |  4 ++++
 4 files changed, 31 insertions(+)
 create mode 100644 _bookdown_student_guide.yml

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 60112c66..519f6641 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -55,6 +55,8 @@ jobs:
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       toggle_docker_build: "${{ env.DOCKER_BUILD }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
+      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
+      student_guide_config: "${{ env.STUDENT_GUIDE_CONFIG }}"
       dockerfiles_changed: steps.verify-changed-files.outputs.files_changed
 
   anvil-library-build:
@@ -154,6 +156,11 @@ jobs:
       - name: Run bookdown render
         id: bookdown
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+        
+      - name: Run student guide render
+        if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
+        id: student_guide
+        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config = ${{ needs.yaml-check.outputs.student_guide_config }})"
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
diff --git a/_bookdown.yml b/_bookdown.yml
index 9979919e..d28dbaef 100644
--- a/_bookdown.yml
+++ b/_bookdown.yml
@@ -19,3 +19,6 @@ language:
   ui:
     chapter_name: "Chapter"
 output_dir: "docs"
+output:
+    bookdown::html_book
+      
\ No newline at end of file
diff --git a/_bookdown_student_guide.yml b/_bookdown_student_guide.yml
new file mode 100644
index 00000000..477c03a1
--- /dev/null
+++ b/_bookdown_student_guide.yml
@@ -0,0 +1,17 @@
+book_filename: "Course_Name"
+chapter_name: "Chapter "
+repo: https://github.com/jhudsl/AnVIL_Template/
+rmd_files: ["index.Rmd",
+            "08-student_modules.Rmd",
+            "References.Rmd"]
+new_session: yes
+bibliography: [book.bib]
+delete_merged_file: true
+language:
+  ui:
+    chapter_name: "Chapter"
+output_dir: "docs"
+output:
+    bookdown::word_document2:
+      toc: true
+      
\ No newline at end of file
diff --git a/config_automation.yml b/config_automation.yml
index b907b9b0..7acd1eee 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -19,6 +19,10 @@ render-bookdown: yes
 render-leanpub: no
 render-coursera: no
 
+##### Rendering of student guide (if applicable)
+render-student-guide: yes
+student-guide-config: '_bookdown_student_guide.yml'
+
 # What docker image should be used for rendering?
 # The default is jhudsl/course_template:main
 rendering-docker-image: 'jhudsl/course_template:main'

From 8c9c324923e6f10e7b25977c132d7cf80ad87bdf Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 11:33:00 -0500
Subject: [PATCH 02/14] Add quotations

---
 .github/workflows/pull_request.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 519f6641..5fc03228 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -153,14 +153,14 @@ jobs:
         shell: bash
 
       # Run bookdown rendering
-      - name: Run bookdown render
-        id: bookdown
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-        
+      # - name: Run bookdown render
+      #   id: bookdown
+      #   run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+      #   
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config = ${{ needs.yaml-check.outputs.student_guide_config }})"
+        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config = '${{ needs.yaml-check.outputs.student_guide_config }}')"
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.

From 804106b2676ef3ccdc8630390cdb45053c179d10 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 11:50:05 -0500
Subject: [PATCH 03/14] Fix argument name

---
 .github/workflows/pull_request.yml | 2 +-
 _bookdown_student_guide.yml        | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 5fc03228..ce471a46 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -160,7 +160,7 @@ jobs:
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config = '${{ needs.yaml-check.outputs.student_guide_config }}')"
+        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config_file = '${{ needs.yaml-check.outputs.student_guide_config }}')"
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
diff --git a/_bookdown_student_guide.yml b/_bookdown_student_guide.yml
index 477c03a1..9fb750f1 100644
--- a/_bookdown_student_guide.yml
+++ b/_bookdown_student_guide.yml
@@ -2,7 +2,7 @@ book_filename: "Course_Name"
 chapter_name: "Chapter "
 repo: https://github.com/jhudsl/AnVIL_Template/
 rmd_files: ["index.Rmd",
-            "08-student_modules.Rmd",
+            "01-intro.Rmd",
             "References.Rmd"]
 new_session: yes
 bibliography: [book.bib]
@@ -14,4 +14,3 @@ output_dir: "docs"
 output:
     bookdown::word_document2:
       toc: true
-      
\ No newline at end of file

From 52beb785efa89471814c3ea2d6bbf51d922656c1 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 12:44:10 -0500
Subject: [PATCH 04/14] Rearrange things

---
 09-student_guide.Rmd                                       | 6 ++++++
 config_automation.yml                                      | 1 -
 _bookdown_student_guide.yml => student-guide/_bookdown.yml | 7 ++-----
 student-guide/_output.yml                                  | 2 ++
 4 files changed, 10 insertions(+), 6 deletions(-)
 create mode 100644 09-student_guide.Rmd
 rename _bookdown_student_guide.yml => student-guide/_bookdown.yml (72%)
 create mode 100644 student-guide/_output.yml

diff --git a/09-student_guide.Rmd b/09-student_guide.Rmd
new file mode 100644
index 00000000..58ade0a8
--- /dev/null
+++ b/09-student_guide.Rmd
@@ -0,0 +1,6 @@
+
+# Here's a Student Guide
+
+## A very important section
+
+Lorem Ipsum
\ No newline at end of file
diff --git a/config_automation.yml b/config_automation.yml
index 7acd1eee..f0e50ae4 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -21,7 +21,6 @@ render-coursera: no
 
 ##### Rendering of student guide (if applicable)
 render-student-guide: yes
-student-guide-config: '_bookdown_student_guide.yml'
 
 # What docker image should be used for rendering?
 # The default is jhudsl/course_template:main
diff --git a/_bookdown_student_guide.yml b/student-guide/_bookdown.yml
similarity index 72%
rename from _bookdown_student_guide.yml
rename to student-guide/_bookdown.yml
index 9fb750f1..b5ced82d 100644
--- a/_bookdown_student_guide.yml
+++ b/student-guide/_bookdown.yml
@@ -2,7 +2,7 @@ book_filename: "Course_Name"
 chapter_name: "Chapter "
 repo: https://github.com/jhudsl/AnVIL_Template/
 rmd_files: ["index.Rmd",
-            "01-intro.Rmd",
+            "09-student_guide.Rmd",
             "References.Rmd"]
 new_session: yes
 bibliography: [book.bib]
@@ -10,7 +10,4 @@ delete_merged_file: true
 language:
   ui:
     chapter_name: "Chapter"
-output_dir: "docs"
-output:
-    bookdown::word_document2:
-      toc: true
+output_dir: "student-guide"
diff --git a/student-guide/_output.yml b/student-guide/_output.yml
new file mode 100644
index 00000000..5975d495
--- /dev/null
+++ b/student-guide/_output.yml
@@ -0,0 +1,2 @@
+bookdown::word_document2:
+    toc: true
\ No newline at end of file

From 6155808a7ea04e95b9f4ab2a4210d98f3b7b2730 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:03:25 -0500
Subject: [PATCH 05/14] Add to render-all

---
 .github/workflows/pull_request.yml | 16 +++++++++++-----
 .github/workflows/render-all.yml   | 13 +++++++++++++
 student-guide/_output.yml          |  2 +-
 3 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index ce471a46..05ee86f8 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -56,7 +56,6 @@ jobs:
       toggle_docker_build: "${{ env.DOCKER_BUILD }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
-      student_guide_config: "${{ env.STUDENT_GUIDE_CONFIG }}"
       dockerfiles_changed: steps.verify-changed-files.outputs.files_changed
 
   anvil-library-build:
@@ -160,7 +159,14 @@ jobs:
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all', config_file = '${{ needs.yaml-check.outputs.student_guide_config }}')"
+        run: |
+          mkdir tmp1
+          mv _bookdown.yml _output.yml tmp1
+          mv student-guide/_bookdown.yml student-guide/_output.yml .
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+          mv _bookdown.yml _output.yml student-guide
+          mv tmp1/_bookdown.yml tmp1/_output.yml .
+          rm tmp1
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
@@ -205,10 +211,10 @@ jobs:
           course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
+          student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
           echo ::set-output name=bookdown_link::$bookdown_link
           echo ::set-output name=tocless_link::$tocless_link
-          echo ::set-output name=docx_link::$docx_link
+          echo ::set-output name=student_docx_link::$docx_link
           echo ::set-output name=time::$(date +'%Y-%m-%d')
           echo ::set-output name=commit_id::$GITHUB_SHA
           echo ${{steps.commit.outputs.changes}}
@@ -223,7 +229,7 @@ jobs:
             Re-rendered previews from the latest commit:
             - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
             - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of .docx file](${{ steps.build-components.outputs.docx_link }})
+            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.docx_link }})
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 509474fa..029e7e86 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -31,6 +31,7 @@ jobs:
       toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
 
   anvil-library-build:
     name: AnVIL Library Build
@@ -73,6 +74,18 @@ jobs:
         run: |
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
           file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
+          
+      - name: Run student guide render
+        if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
+        id: student_guide
+        run: |
+          mkdir tmp1
+          mv _bookdown.yml _output.yml tmp1
+          mv student-guide/_bookdown.yml student-guide/_output.yml .
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+          mv _bookdown.yml _output.yml student-guide
+          mv tmp1/_bookdown.yml tmp1/_output.yml .
+          rm tmp1
 
       # 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
diff --git a/student-guide/_output.yml b/student-guide/_output.yml
index 5975d495..03bf219d 100644
--- a/student-guide/_output.yml
+++ b/student-guide/_output.yml
@@ -1,2 +1,2 @@
 bookdown::word_document2:
-    toc: true
\ No newline at end of file
+  toc: true
\ No newline at end of file

From 79b4a5747a01b09696347ced0cd62234dc310b38 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:08:36 -0500
Subject: [PATCH 06/14] Make recursive

---
 .github/workflows/pull_request.yml | 2 +-
 .github/workflows/render-all.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 05ee86f8..acd6feb9 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -166,7 +166,7 @@ jobs:
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
           mv _bookdown.yml _output.yml student-guide
           mv tmp1/_bookdown.yml tmp1/_output.yml .
-          rm tmp1
+          rm -r tmp1
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 029e7e86..56da16af 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -85,7 +85,7 @@ jobs:
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
           mv _bookdown.yml _output.yml student-guide
           mv tmp1/_bookdown.yml tmp1/_output.yml .
-          rm tmp1
+          rm -r tmp1
 
       # 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

From 2f5458068d2e5ea8ec00d6b9ba2d04c4886aa100 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:09:26 -0500
Subject: [PATCH 07/14] Trivial change

---
 .github/workflows/pull_request.yml | 1 +
 index.Rmd                          | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index acd6feb9..f75df350 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -156,6 +156,7 @@ jobs:
       #   id: bookdown
       #   run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
       #   
+      
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
diff --git a/index.Rmd b/index.Rmd
index f579d8fb..d6e92dcd 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -53,3 +53,6 @@ exclude = c(
 # Create table for AnVIL repos detected through the API
 knitr::kable(make_anvil_repo_table(exclude), format = "html")
 ```
+
+
+change

From 5cdbd1412067f1add9c9d633f31bd143a478ae60 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:17:06 -0500
Subject: [PATCH 08/14] Turn off bookdown check for now

---
 .github/workflows/pull_request.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index f75df350..5e6ad7a5 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -178,12 +178,12 @@ jobs:
 
       # 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.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
-        run: |
-          echo Bookdown status ${{steps.bookdown.outcome}}
-          echo Toc-less status ${{steps.tocless.outcome}}
-          exit 1
+      # - name: Check on render steps
+      #   if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
+      #   run: |
+      #     echo Bookdown status ${{steps.bookdown.outcome}}
+      #     echo Toc-less status ${{steps.tocless.outcome}}
+      #     exit 1
 
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files to preview branch

From 3ab255c52f7955754271f488b0d06ec814a27d3a Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:24:02 -0500
Subject: [PATCH 09/14] fix link

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

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 5e6ad7a5..b0203d26 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -230,7 +230,7 @@ jobs:
             Re-rendered previews from the latest commit:
             - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
             - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.docx_link }})
+            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace

From aa383bb682b3a4ffb9f9e2fd1cb3913b863accde Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:35:12 -0500
Subject: [PATCH 10/14] missed one more link

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index b0203d26..f633dcbd 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -209,13 +209,13 @@ jobs:
       - name: Build components of the comment
         id: build-components
         run: |
-          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
+          course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
           student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
           echo ::set-output name=bookdown_link::$bookdown_link
           echo ::set-output name=tocless_link::$tocless_link
-          echo ::set-output name=student_docx_link::$docx_link
+          echo ::set-output name=student_docx_link::$student_docx_link
           echo ::set-output name=time::$(date +'%Y-%m-%d')
           echo ::set-output name=commit_id::$GITHUB_SHA
           echo ${{steps.commit.outputs.changes}}

From c6ef359f58c75468cfbd0da64537f3b0a54dbb8c Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:42:27 -0500
Subject: [PATCH 11/14] Uncomment relevant info

---
 .github/workflows/pull_request.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index f633dcbd..7614c458 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -152,10 +152,10 @@ jobs:
         shell: bash
 
       # Run bookdown rendering
-      # - name: Run bookdown render
-      #   id: bookdown
-      #   run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-      #   
+      - name: Run bookdown render
+        id: bookdown
+        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+
       
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
@@ -178,12 +178,12 @@ jobs:
 
       # 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.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
-      #   run: |
-      #     echo Bookdown status ${{steps.bookdown.outcome}}
-      #     echo Toc-less status ${{steps.tocless.outcome}}
-      #     exit 1
+      - name: Check on render steps
+        if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
+        run: |
+          echo Bookdown status ${{steps.bookdown.outcome}}
+          echo Toc-less status ${{steps.tocless.outcome}}
+          exit 1
 
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files to preview branch

From 66bf7b4c7129156f6d0c3ee5a3f6762b76d65033 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Mon, 5 Dec 2022 13:46:04 -0500
Subject: [PATCH 12/14] Bit better text examples

---
 .github/workflows/pull_request.yml |  4 +++-
 .github/workflows/render-all.yml   |  5 ++++-
 09-student_guide.Rmd               | 10 +++++++---
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 7614c458..1c1f8f8b 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -156,7 +156,9 @@ jobs:
         id: bookdown
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
-      
+      # Render a student guide if specified. This is a bit clunky because 
+      # Bookdown does not work well if the files aren't named as such in the 
+      # root directory
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 56da16af..36e2628b 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -74,7 +74,10 @@ jobs:
         run: |
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
           file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
-          
+      
+      # Render a student guide if specified. This is a bit clunky because 
+      # Bookdown does not work well if the files aren't named as such in the 
+      # root directory
       - name: Run student guide render
         if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
         id: student_guide
diff --git a/09-student_guide.Rmd b/09-student_guide.Rmd
index 58ade0a8..18488f7f 100644
--- a/09-student_guide.Rmd
+++ b/09-student_guide.Rmd
@@ -1,6 +1,10 @@
 
-# Here's a Student Guide
+# Student Guide
 
-## A very important section
+## Activity One
 
-Lorem Ipsum
\ No newline at end of file
+You might want to create a student guide that renders to a word document or other format. You can specify the output and Rmd files that will be used for the student guide in the student-guide directory.
+
+## Activity Two
+
+Steps of the guide could go here.
\ No newline at end of file

From 35036bb3f8b9e0bebb7262ea74c25817c2caf543 Mon Sep 17 00:00:00 2001
From: AM Hoffman <avamariehoffman@gmail.com>
Date: Tue, 6 Dec 2022 09:34:16 -0500
Subject: [PATCH 13/14] Add Katie's suggestion

Co-authored-by: KatherineCox <katherinecox@jhu.edu>
---
 09-student_guide.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/09-student_guide.Rmd b/09-student_guide.Rmd
index 18488f7f..d6fff4a9 100644
--- a/09-student_guide.Rmd
+++ b/09-student_guide.Rmd
@@ -3,7 +3,7 @@
 
 ## Activity One
 
-You might want to create a student guide that renders to a word document or other format. You can specify the output and Rmd files that will be used for the student guide in the student-guide directory.
+You might want to create a student guide that contains a different subset of Rmd files from your book, or renders to a different output format (e.g. word document). You can specify the output and Rmd files that will be used for the student guide using the `_output.yml` and `_bookdown.yml` files in the student-guide directory.
 
 ## Activity Two
 

From ad30bcdaacbc072eef24560cd4286ed6daa51d9a Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Tue, 6 Dec 2022 09:58:56 -0500
Subject: [PATCH 14/14] Whoops- remove that trivial change

---
 index.Rmd | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/index.Rmd b/index.Rmd
index d6e92dcd..f579d8fb 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -53,6 +53,3 @@ exclude = c(
 # Create table for AnVIL repos detected through the API
 knitr::kable(make_anvil_repo_table(exclude), format = "html")
 ```
-
-
-change