From ee4d158b8b0b7ee0845ec923288ad9634b626606 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 10:04:24 -0500 Subject: [PATCH 1/6] Add warning to not set branch settings right away --- .github/automatic-issues/set-repo-settings.md | 2 ++ .github/automatic-issues/templates-to-edit.md | 3 +-- output-proj.yml | 16 ---------------- 3 files changed, 3 insertions(+), 18 deletions(-) delete mode 100644 output-proj.yml diff --git a/.github/automatic-issues/set-repo-settings.md b/.github/automatic-issues/set-repo-settings.md index a34faf72..fab99096 100644 --- a/.github/automatic-issues/set-repo-settings.md +++ b/.github/automatic-issues/set-repo-settings.md @@ -6,6 +6,8 @@ For more information on these settings see instructions in the [getting started - [ ] Github pages is turned on. - [ ] `Enforce HTTPS`has been checked +\* Don't set these settings right away! Wait a few minutes after starting your repository. + - [ ] `main` branch has been set up: - [ ] `Require pull request reviews before merging` box is checked. - [ ] `Require status checks to pass before merging` box is checked. diff --git a/.github/automatic-issues/templates-to-edit.md b/.github/automatic-issues/templates-to-edit.md index 4124fd7c..86afbc86 100644 --- a/.github/automatic-issues/templates-to-edit.md +++ b/.github/automatic-issues/templates-to-edit.md @@ -19,11 +19,10 @@ By default this course template will use the jhudsl data science lab style. Howe ### Files that need edited upon creating a new course. - [ ] `README.md` - Fill in all the `{ }`. -- [ ] `index.Rmd` - the `author:`, `title:`, and `description:` should be updated. +- [ ] `index.Rmd` - `title:` should be updated. - [ ] `About.Rmd` - Replace information with your own author information and change the course title in the yaml header! - [ ] `01-intro.Rmd` - replace the information there with information pertinent to this new course. - [ ] `02-chapter_of_course.Rmd` - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted. -- [ ] `code_output` can be deleted if you don't plan to use code. ### Files that need to be edited upon adding each new chapter (including upon creating a new course): diff --git a/output-proj.yml b/output-proj.yml deleted file mode 100644 index 0b37a96c..00000000 --- a/output-proj.yml +++ /dev/null @@ -1,16 +0,0 @@ -bookdown::gitbook: - css: assets/style.css - includes: - before_body: assets/big-image.html - after_body: assets/footer.html - highlight: tango - config: - toc: - collapse: section - before: | - - after: | -

This content was published with bookdown by:

-

The Johns Hopkins Data Science Lab

- -

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

From 734c2bc5bd5ca38f07c763a4a9b8ea1428ad692f Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 10:07:46 -0500 Subject: [PATCH 2/6] Update issue --- .github/automatic-issues/templates-to-edit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/automatic-issues/templates-to-edit.md b/.github/automatic-issues/templates-to-edit.md index 86afbc86..271ca4a2 100644 --- a/.github/automatic-issues/templates-to-edit.md +++ b/.github/automatic-issues/templates-to-edit.md @@ -20,7 +20,6 @@ By default this course template will use the jhudsl data science lab style. Howe - [ ] `README.md` - Fill in all the `{ }`. - [ ] `index.Rmd` - `title:` should be updated. -- [ ] `About.Rmd` - Replace information with your own author information and change the course title in the yaml header! - [ ] `01-intro.Rmd` - replace the information there with information pertinent to this new course. - [ ] `02-chapter_of_course.Rmd` - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted. @@ -30,5 +29,6 @@ By default this course template will use the jhudsl data science lab style. Howe - [ ] `book.bib` - any citations need to be added. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Citations). ### Files that need to be edited upon adding new packages that the book's code uses: + - `docker/Dockerfile` needs to have the new package added so it will be installed. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). - The code chunk in `index.Rmd` should be edited to add the new package. From 2c70e55333771e59e21a6a8fe2b0c671184a2c08 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 10:10:26 -0500 Subject: [PATCH 3/6] Update transfer rendered name --- .github/workflows/transfer-rendered-files.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml index 57bc2e70..aebe8fd3 100644 --- a/.github/workflows/transfer-rendered-files.yml +++ b/.github/workflows/transfer-rendered-files.yml @@ -12,7 +12,7 @@ on: workflow_dispatch: # Only run after the render finishes running workflow_run: - workflows: [ "Build, Render, and Push" ] + workflows: [ "Bookdown to Leanpub repo copy over" ] branches: [ main ] types: - completed From fd88ae0afef585220ddc3e2dd8756ad47d0c7315 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 10:14:26 -0500 Subject: [PATCH 4/6] Add more info about github pages --- .github/automatic-issues/set-repo-settings.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/automatic-issues/set-repo-settings.md b/.github/automatic-issues/set-repo-settings.md index fab99096..cc183539 100644 --- a/.github/automatic-issues/set-repo-settings.md +++ b/.github/automatic-issues/set-repo-settings.md @@ -3,14 +3,15 @@ For more information on these settings see instructions in the [getting started ### Needed settings: -- [ ] Github pages is turned on. -- [ ] `Enforce HTTPS`has been checked +#### Turn on GitHub pages +- [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`. +- [ ] Check `Enforce HTTPS`. -\* Don't set these settings right away! Wait a few minutes after starting your repository. +#### Set protections for main branch +\* Don't set these settings right away! Wait a few minutes after starting your repository. - [ ] `main` branch has been set up: - [ ] `Require pull request reviews before merging` box is checked. - [ ] `Require status checks to pass before merging` box is checked. - [ ] Underneath that `Require branches to be up to date before merging` box is checked. - -- [ ] All these settings have been saved! +- [ ] Click `Save` at the bottom of the page! From 4801f28ea763f06d5a10809f88fd0095da6f914e Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 10:23:52 -0500 Subject: [PATCH 5/6] Add more formatting tips to 02- --- 02-chapter_of_course.Rmd | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/02-chapter_of_course.Rmd b/02-chapter_of_course.Rmd index 1532c453..becbc27e 100644 --- a/02-chapter_of_course.Rmd +++ b/02-chapter_of_course.Rmd @@ -128,8 +128,25 @@ but they need a ; separator [@rmarkdown2021; @Xie2018]. In text, we can put citations like this @rmarkdown2021. +### FYI boxes + +::: {.fyi} +Please click on the subsection headers in the left hand +navigation bar (e.g., 2.1, 4.3) a second time to expand the +table of contents and enable the `scroll_highlight` feature +([see more](introduction.html#scroll-highlight)). +::: + +### Dropdown summaries + +
You can hide additional information in a dropdown menu +Here's more words that are hidden +
+ ## Print out session info +You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html). + ```{r} sessionInfo() ``` From 126fe34f225d32d346b6299a76948d092eede7d5 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Mon, 20 Dec 2021 13:10:16 -0500 Subject: [PATCH 6/6] Fix github actions --- .github/workflows/transfer-rendered-files.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml index aebe8fd3..3bf592a0 100644 --- a/.github/workflows/transfer-rendered-files.yml +++ b/.github/workflows/transfer-rendered-files.yml @@ -12,7 +12,7 @@ on: workflow_dispatch: # Only run after the render finishes running workflow_run: - workflows: [ "Bookdown to Leanpub repo copy over" ] + workflows: [ "Render Bookdown and Coursera" ] branches: [ main ] types: - completed