Merge pull request #33 from fhdsl/repo-sync/AnVIL_Template/default

🔄 Synced file(s) with jhudsl/AnVIL_Template
fhdsl · Aug 23, 2024 · 4649774 · 4649774
2 parents b8336bc + 3cced84
commit 4649774
Show file tree

Hide file tree

Showing 4 changed files with 33 additions and 13 deletions.
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -48,7 +48,9 @@ jobs:
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
 ########################## Make the error reports ##############################
@@ -142,7 +144,11 @@ jobs:
       # Make sure the link for AnVIL feedback is prepopulated for the specific course
       - name: Set up feedback link
         id: feedback
-        run: bash scripts/AnVIL_Feedback_Script.sh
+        if: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}}
+        run: |
+          bash scripts/AnVIL_Feedback_Script.sh
+          git add _output.yml
+          git commit -m 'Set up feedback link' || echo "No changes to commit"
 
       # Run bookdown rendering
       - name: Run bookdown render
@@ -153,7 +159,7 @@ jobs:
       # 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'}}
+        if: ${{needs.yaml-check.outputs.toggle_student_guide == 'yes'}}
         id: student_guide
         run: |
           mkdir tmp1
@@ -163,6 +169,8 @@ jobs:
           mv _bookdown.yml _output.yml student-guide
           mv tmp1/_bookdown.yml tmp1/_output.yml .
           rm -r tmp1
+          git add student-guide/*
+          git commit -m 'Create student guide' || echo "No changes to commit"
           
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
@@ -210,11 +218,12 @@ jobs:
           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/$course_name.docx")          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          student_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx")          
+          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
           echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
           echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
           echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
-          echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
+          echo "student_guide=$student_guide" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
@@ -229,7 +238,7 @@ jobs:
             Re-rendered previews from the latest commit:
             - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
             - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
-            - Download the [.docx file](${{ steps.build-components.outputs.docx_link }})
+            - Download the Student Guide [.docx file](${{ steps.build-components.outputs.student_guide }})
 
             \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
 

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
@@ -30,7 +30,8 @@ jobs:
       toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}"
       toggle_coursera: "${{ env.RENDER_COURSERA }}"
       toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
-      make_book_txt: "${{ env.MAKE_BOOK_TXT }}"
+      toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
+      toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
 
@@ -61,8 +62,11 @@ jobs:
 
       # Make sure the link for AnVIL feedback is prepopulated for the specific course
       - name: Set up feedback link
-        id: feedback
-        run: bash scripts/AnVIL_Feedback_Script.sh
+        if: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}}
+        run: |
+          bash scripts/AnVIL_Feedback_Script.sh
+          git add _output.yml
+          git commit -m 'Set up feedback link' || echo "No changes to commit"
 
       # Run bookdown rendering
       - name: Run bookdown render
@@ -75,7 +79,7 @@ jobs:
       # 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'}}
+        if: ${{needs.yaml-check.outputs.toggle_student_guide == 'yes'}}
         id: student_guide
         run: |
           mkdir tmp1
@@ -85,6 +89,8 @@ jobs:
           mv _bookdown.yml _output.yml student-guide
           mv tmp1/_bookdown.yml tmp1/_output.yml .
           rm -r tmp1
+          git add student-guide/*
+          git commit -m 'Create student guide' || echo "No changes to commit"
 
       # 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/config_automation.yml b/config_automation.yml
@@ -20,7 +20,10 @@ render-leanpub: no
 render-coursera: no
 
 ##### Rendering of student guide (if applicable)
-render-student-guide: no
+render-student-guide: yes
+
+##### Auto-generate a feedback link for the AnVIL Feedback Form: https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform
+feedback-link: yes
 
 # What docker image should be used for rendering?
 # The default is jhudsl/course_template:main

diff --git a/student-guide/_bookdown.yml b/student-guide/_bookdown.yml
@@ -1,8 +1,10 @@
-book_filename: "Course_Name"
+book_filename: "Student_Guide"
 chapter_name: "Chapter "
-repo: https://github.com/jhudsl/AnVIL_Template/
+repo: https://github.com/fhdsl/GDSCN_BioDIGS_Book/
 rmd_files: ["index.Rmd",
-            "09-student_guide.Rmd",
+            "08-student_anvil_guide.Rmd",
+            "08-student_using_galaxy.Rmd",
+            "08-student_using_rstudio.Rmd",
             "References.Rmd"]
 new_session: yes
 bibliography: [book.bib]