From c380a570fb3defef1a145ec086ec4b818c020b76 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 12:41:54 -0400 Subject: [PATCH 1/8] Make sure output.yml gets a commit --- .github/workflows/pull_request.yml | 8 +++++++- _output.yml | 2 +- config_automation.yml | 3 +++ 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index d4d2515a..577ace03 100644 --- 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' # Run bookdown rendering - name: Run bookdown render diff --git a/_output.yml b/_output.yml index 7d6b017c..7ff6ae59 100644 --- a/_output.yml +++ b/_output.yml @@ -18,4 +18,4 @@ bookdown::gitbook:

Style adapted from: rstudio4edu-book (CC-BY 2.0)

Click here to provide feedback

-# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows. \ No newline at end of file +# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows. You can deactivate this behavior in config_automation.yml. \ No newline at end of file diff --git a/config_automation.yml b/config_automation.yml index ccc06112..8e28f58d 100644 --- a/config_automation.yml +++ b/config_automation.yml @@ -22,6 +22,9 @@ render-coursera: yes ##### Rendering of student guide (if applicable) 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 rendering-docker-image: 'jhudsl/base_ottr:main' From bd1ea0c32779548c5066f1bfbfd5b1e7a13cd1ac Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:03:22 -0400 Subject: [PATCH 2/8] Fix name --- .github/workflows/pull_request.yml | 3 ++- student-guide/_bookdown.yml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 577ace03..952a1ff7 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -216,7 +216,8 @@ 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_docx_link=$(echo "https://github.com/$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" >> $GITHUB_OUTPUT diff --git a/student-guide/_bookdown.yml b/student-guide/_bookdown.yml index b5ced82d..5c247d77 100644 --- a/student-guide/_bookdown.yml +++ b/student-guide/_bookdown.yml @@ -1,4 +1,4 @@ -book_filename: "Course_Name" +book_filename: "Student_Guide" chapter_name: "Chapter " repo: https://github.com/jhudsl/AnVIL_Template/ rmd_files: ["index.Rmd", From b53f1fcceb061ef625f301e0617ddcb432142edd Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:05:40 -0400 Subject: [PATCH 3/8] Update render all to match --- .github/workflows/render-all.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index 8bb8ecb3..d6870ff6 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -30,7 +30,8 @@ jobs: toggle_bookdown: "${{ 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: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}} + run: | + bash scripts/AnVIL_Feedback_Script.sh + git add _output.yml + git commit -m 'Set up feedback link' # Run bookdown rendering - name: Run bookdown render From fc42f8cc95f721f5f42304813f21eafc487f1443 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:12:53 -0400 Subject: [PATCH 4/8] fix download object for docx --- .github/workflows/pull_request.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index 952a1ff7..b84bd309 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -216,12 +216,12 @@ jobs: course_name=$(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-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx") + student_guide=$(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 ${{steps.commit.outputs.changes}} @@ -236,7 +236,7 @@ jobs: Re-rendered previews from the latest commit: - :eyes: Quick [preview of course website here](${{ 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. From 26755058f4cea349a8a4c7244defbf13f38d668a Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:13:04 -0400 Subject: [PATCH 5/8] sync more files (for now) --- .github/sync.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/sync.yml b/.github/sync.yml index 053695ae..2dc9ab5e 100644 --- a/.github/sync.yml +++ b/.github/sync.yml @@ -39,6 +39,10 @@ group: dest: assets/style.css - source: assets/toc_close.css dest: assets/toc_close.css + - source: config_automation.yml + dest: config_automation.yml + - source: student-guide/_bookdown.yml + dest: student-guide/_bookdown.yml # Repositories to receive changes repos: | fhdsl/AnVIL_Book_Epigenetics_Intro From 7ddd146cf3214d0380c3e08548b81b539cf038e2 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:24:54 -0400 Subject: [PATCH 6/8] Need to commit student guide? --- .github/workflows/pull_request.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index b84bd309..8d3f3e54 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -169,6 +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' # Run TOC-less version # Rendered content for Leanpub and Coursera is very similar. From 054c8ed764fd10f7a91ac07e6166871a189b5548 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:41:19 -0400 Subject: [PATCH 7/8] Oops yaml obj was wrong --- .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 8d3f3e54..5e2ab3ef 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -159,7 +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 diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index d6870ff6..74cf10b1 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -79,7 +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 From 6985ece792201136d4307d22b55762aa09b10363 Mon Sep 17 00:00:00 2001 From: avahoffman Date: Fri, 9 Aug 2024 13:48:58 -0400 Subject: [PATCH 8/8] Forgot to commit on main --- .github/workflows/render-all.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index 74cf10b1..6bfc7aa3 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -89,6 +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' # 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