diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index d4d2515a..5aaad6e5 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' || 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](${{ steps.build-components.outputs.student_guide }}) \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea. diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index 8bb8ecb3..059e210e 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -30,7 +30,8 @@ jobs: toggle_bookdown: "${{ 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' || 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 index 431f7495..4a402262 100644 --- 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 index b5ced82d..d8a1a788 100644 --- 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]