diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index de76459..2ce0dec 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -249,9 +249,8 @@ jobs: - name: Build components of the comment id: build-components run: | - 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") - student_guide=$(echo "https://github.com/$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/docs/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" >> $GITHUB_OUTPUT diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml index 177b4a9..5f7c4dd 100644 --- a/.github/workflows/render-all.yml +++ b/.github/workflows/render-all.yml @@ -31,6 +31,7 @@ jobs: toggle_website: "${{ env.RENDER_WEBSITE }}" 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 }}" diff --git a/_output.yml b/_output.yml index 068b3a3..743fcf2 100644 --- a/_output.yml +++ b/_output.yml @@ -16,6 +16,6 @@ bookdown::gitbook:

The Johns Hopkins Data Science Lab

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

-

Click here to provide feedback

+

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. +# 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 diff --git a/config_automation.yml b/config_automation.yml index dd249e5..dcc9d6c 100644 --- a/config_automation.yml +++ b/config_automation.yml @@ -25,8 +25,12 @@ render-website: rmd render-leanpub: no render-coursera: no +## Automate the creation of Book.txt file? yes/no +## This is only relevant if render-leanpub is yes, otherwise it will be ignored +make-book-txt: yes + ##### 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 diff --git a/student-guide.Rmd b/student-guide.Rmd new file mode 100644 index 0000000..529480b --- /dev/null +++ b/student-guide.Rmd @@ -0,0 +1,20 @@ + +# Student Guide + +## Activity One + +Many of the AnVIL books that are designed for teaching a class or workshop contain information aimed at the instructor. + +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. + +By default, repositories based on `AnVIL_Template` create a docx file containing this chapter as an example. Once you have adjusted `student-guide/bookdown.yml` to include the chapters you want in your student guide, you can link to it by replacing `{repo-name}` in the following URL: + +`https://github.com/jhudsl/{repo-name}/raw/main/student-guide/docs/Student_Guide.docx` + +When someone clicks this link, they will download the docx file. For example, here is the link for the student guide from `AnVIL_Template`: + +https://github.com/jhudsl/AnVIL_Template/raw/main/student-guide/docs/Student_Guide.docx + +## Activity Two + +Steps of the guide could go here. \ No newline at end of file diff --git a/student-guide/09-student_guide.md b/student-guide/09-student_guide.md deleted file mode 100644 index 33df504..0000000 --- a/student-guide/09-student_guide.md +++ /dev/null @@ -1,10 +0,0 @@ - -# Student Guide - -## Activity One - -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 - -Steps of the guide could go here. diff --git a/student-guide/References.md b/student-guide/References.md deleted file mode 100644 index 98d65dc..0000000 --- a/student-guide/References.md +++ /dev/null @@ -1,2 +0,0 @@ - -# References diff --git a/student-guide/Student_Guide.docx b/student-guide/Student_Guide.docx deleted file mode 100644 index f8e07c2..0000000 Binary files a/student-guide/Student_Guide.docx and /dev/null differ diff --git a/student-guide/_bookdown.yml b/student-guide/_bookdown.yml index 5c247d7..4c4664c 100644 --- a/student-guide/_bookdown.yml +++ b/student-guide/_bookdown.yml @@ -1,8 +1,8 @@ -book_filename: "Student_Guide" chapter_name: "Chapter " -repo: https://github.com/jhudsl/AnVIL_Template/ +repo: https://github.com/jhudsl/AnVIL_Book_Champions/ rmd_files: ["index.Rmd", - "09-student_guide.Rmd", + "student-guide.Rmd", + "About.Rmd", "References.Rmd"] new_session: yes bibliography: [book.bib] @@ -10,4 +10,5 @@ delete_merged_file: true language: ui: chapter_name: "Chapter" -output_dir: "student-guide" +book_filename: "Student_Guide" # Do not change +output_dir: "student-guide/docs" # Do not change diff --git a/student-guide/index.md b/student-guide/index.md deleted file mode 100644 index 7f3abf5..0000000 --- a/student-guide/index.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: "AnVIL Book Name" -date: "August 27, 2024" -site: bookdown::bookdown_site -documentclass: book -bibliography: book.bib -biblio-style: apalike -link-citations: yes -description: Description about Course/Book. -favicon: assets/AnVIL_style/anvil_favicon.ico ---- - - -# About this Book {-} - -This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063). - -## Skills Level {-} - -::: {.notice} -_Genetics_ - - -_Programming skills_ - -::: - -## AnVIL Collection {-} - -Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ - -# Learning Objectives {-} - - - - - - - - diff --git a/student-guide/reference-keys.txt b/student-guide/reference-keys.txt deleted file mode 100644 index be361e9..0000000 --- a/student-guide/reference-keys.txt +++ /dev/null @@ -1,4 +0,0 @@ -student-guide -activity-one -activity-two -references diff --git a/style-sets/AnVIL_FH/_output.yml b/style-sets/AnVIL_FH/_output.yml index 7cba311..7d6b017 100644 --- a/style-sets/AnVIL_FH/_output.yml +++ b/style-sets/AnVIL_FH/_output.yml @@ -2,6 +2,7 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # css: [assets/style.css, assets/AnVIL_style/anvil.css] includes: + in_header: GA_Script.html before_body: assets/AnVIL_style/big-image_anvil.html after_body: assets/AnVIL_style/footer.html highlight: tango diff --git a/style-sets/AnVIL_JHU/_output.yml b/style-sets/AnVIL_JHU/_output.yml index a3a7145..743fcf2 100644 --- a/style-sets/AnVIL_JHU/_output.yml +++ b/style-sets/AnVIL_JHU/_output.yml @@ -2,6 +2,7 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # css: [assets/style.css, assets/AnVIL_style/anvil.css] includes: + in_header: GA_Script.html before_body: assets/AnVIL_style/big-image_anvil.html after_body: assets/AnVIL_style/footer.html highlight: tango diff --git a/style-sets/GDSCN/_output.yml b/style-sets/GDSCN/_output.yml index 4156fd7..df9a9f2 100644 --- a/style-sets/GDSCN/_output.yml +++ b/style-sets/GDSCN/_output.yml @@ -2,6 +2,7 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # css: [assets/style.css, assets/GDSCN_style/gdscn.css] includes: + in_header: GA_Script.html before_body: assets/GDSCN_style/big-image_gdscn.html after_body: assets/GDSCN_style/footer.html highlight: tango diff --git a/style-sets/GDSCN_JHU/_output.yml b/style-sets/GDSCN_JHU/_output.yml index 2bbb202..0651f27 100644 --- a/style-sets/GDSCN_JHU/_output.yml +++ b/style-sets/GDSCN_JHU/_output.yml @@ -2,6 +2,7 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # css: [assets/style.css, assets/GDSCN_style/gdscn.css] includes: + in_header: GA_Script.html before_body: assets/GDSCN_style/big-image_gdscn.html after_body: assets/GDSCN_style/footer.html highlight: tango diff --git a/style-sets/fhdasl/_output.yml b/style-sets/fhdasl/_output.yml index 0a86496..108c33e 100644 --- a/style-sets/fhdasl/_output.yml +++ b/style-sets/fhdasl/_output.yml @@ -1,6 +1,7 @@ bookdown::gitbook: css: assets/style.css includes: + in_header: GA_Script.html before_body: assets/big-image_fhdasl.html after_body: assets/footer.html split_bib: false