From ce0be688d936d2dc63e3820bca52eb728511cfc5 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 16 Dec 2021 20:21:16 -0500 Subject: [PATCH 1/2] Search and replace all with OTTR --- .github/PULL_REQUEST_TEMPLATE.md | 14 +++++++------- .github/automatic-issues/add-feedback-method.md | 2 +- .github/automatic-issues/add-to-library.md | 2 +- .github/automatic-issues/git-secrets.md | 4 ++-- .github/automatic-issues/images-checklist.md | 10 +++++----- .github/automatic-issues/set-repo-settings.md | 2 +- .github/automatic-issues/templates-to-edit.md | 14 +++++++------- .github/automatic-issues/update-enrollment.md | 4 ++-- .github/workflows/docker-build-test.yml | 4 ++-- .github/workflows/release-notes.yml | 12 ++++++------ .github/workflows/render-bookdown.yml | 1 + .github/workflows/render-preview.yml | 4 +++- .github/workflows/starting-course.yml | 2 +- 02-chapter_of_course.Rmd | 4 ++-- About.Rmd | 4 ++-- README.md | 12 ++++++------ _bookdown.yml | 2 +- _output.yml | 2 +- assets/big-image.html | 5 +++-- docs/02-chapter_of_course.md | 4 ++-- docs/404.html | 2 +- docs/About.md | 4 ++-- docs/about-the-authors.html | 6 +++--- docs/coursera/02-chapter_of_course.md | 4 ++-- docs/coursera/404.html | 2 +- docs/coursera/About.md | 4 ++-- docs/coursera/_output_coursera.yml | 2 +- docs/coursera/about-the-authors.html | 6 +++--- docs/coursera/assets/big-image.html | 2 +- docs/coursera/index.html | 2 +- docs/coursera/introduction.html | 6 +++--- docs/coursera/references.html | 2 +- docs/coursera/resources/image_to_slide_key.tsv | 4 ++-- docs/coursera/topic-of-section.html | 2 +- docs/index.html | 2 +- docs/introduction.html | 6 +++--- docs/references.html | 2 +- docs/topic-of-section.html | 2 +- output-proj.yml | 4 ++-- resources/image_to_slide_key.tsv | 4 ++-- scripts/git_repo_check.R | 4 ++-- style-sets/AnVIL/_output.yml | 2 +- style-sets/GDSCN/_output.yml | 2 +- style-sets/data-trail/_output.yml | 2 +- style-sets/itcr/_output.yml | 2 +- 45 files changed, 96 insertions(+), 92 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index fd3511c9..35d4d79c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -20,19 +20,19 @@ ### New Content Checklist -- [ ] New content/chapter is in an Rmd file with [this kind of format and headers](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/blob/main/02-chapter_of_course.Rmd). +- [ ] New content/chapter is in an Rmd file with [this kind of format and headers](https://github.com/jhudsl/OTTR_Template/blob/main/02-chapter_of_course.Rmd). -- [ ] New content/chapter contains [Learning Objectives and are in the correct format](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics#learning-objectives-formatting). +- [ ] New content/chapter contains [Learning Objectives and are in the correct format](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#learning-objectives-formatting). -- [ ] [Bookdown successfully re-renders and any new content files have been added to the _bookdown.yml](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Publishing-with-Bookdown). +- [ ] [Bookdown successfully re-renders and any new content files have been added to the _bookdown.yml](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-with-Bookdown). -- [ ] Spell check runs successfully in [Github actions style-n-check](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-set-up-and-customize-GitHub-actions-robots#spell-check)). +- [ ] Spell check runs successfully in [Github actions style-n-check](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#spell-check)). -- [ ] Any newly necessary packages that are needed have been added to the [Dockerfile and image](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Using-Docker#adding-packages-to-the-dockerfile). +- [ ] Any newly necessary packages that are needed have been added to the [Dockerfile and image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#adding-packages-to-the-dockerfile). -- [ ] Images are in the [correct format for rendering](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text). +- [ ] Images are in the [correct format for rendering](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text). -- [ ] Every new image has [alt text and is in a Google Slide](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics#accessibility). +- [ ] Every new image has [alt text and is in a Google Slide](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#accessibility). - [ ] Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this. diff --git a/.github/automatic-issues/add-feedback-method.md b/.github/automatic-issues/add-feedback-method.md index 7b7a7f69..b9330836 100644 --- a/.github/automatic-issues/add-feedback-method.md +++ b/.github/automatic-issues/add-feedback-method.md @@ -1,4 +1,4 @@ To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through. -[See these instructions](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Set-up-feedback-method) for suggestions on how to add a feedback method for this course. +[See these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Set-up-feedback-method) for suggestions on how to add a feedback method for this course. diff --git a/.github/automatic-issues/add-to-library.md b/.github/automatic-issues/add-to-library.md index 9242eab3..312309ca 100644 --- a/.github/automatic-issues/add-to-library.md +++ b/.github/automatic-issues/add-to-library.md @@ -3,4 +3,4 @@ To help learners find your course, and for it to be tracked in the future, you m You should not worry about adding the course before it is ready to be made public but this issue is to remind you to do so. -[Follow these instructions](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Add-course-to-jhudsl-course-library) to add this new course to the jhudsl library. +[Follow these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Add-course-to-jhudsl-course-library) to add this new course to the jhudsl library. diff --git a/.github/automatic-issues/git-secrets.md b/.github/automatic-issues/git-secrets.md index 2b72fdb8..abd7c68c 100644 --- a/.github/automatic-issues/git-secrets.md +++ b/.github/automatic-issues/git-secrets.md @@ -1,7 +1,7 @@ **Note these steps are only pertinent if you are setting up this course outside of the jhudsl organization** -For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-GitHub-secrets). +For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-GitHub-secrets). It's important that these are set up and named exactly what they are below in order for Github actions to work correctly. @@ -23,4 +23,4 @@ For each new secret, click the `New repository secret` button and set each as fo Underneath `Select scopes`, check both `repo` and `workflow`. Then copy the PAT and save as the value. -- [ ] (Optionally) Set up your [`Leanpub` repository link to it](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Publishing-on-Leanpub) +- [ ] (Optionally) Set up your [`Leanpub` repository link to it](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-on-Leanpub) diff --git a/.github/automatic-issues/images-checklist.md b/.github/automatic-issues/images-checklist.md index 5653fd7d..6e576474 100644 --- a/.github/automatic-issues/images-checklist.md +++ b/.github/automatic-issues/images-checklist.md @@ -1,20 +1,20 @@ Use this checklist to make sure your slides and images are set up correctly! -See [Setting Up Images and Graphics](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics) for more info! +See [Setting Up Images and Graphics](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics) for more info! -- [ ] Create your [course's main Google Slides](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics) +- [ ] Create your [course's main Google Slides](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics) -- [ ] The slides use the [appropriate template](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics). +- [ ] The slides use the [appropriate template](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics). - [ ] Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this. - [ ] The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies. You can check this using [Color Oracle](https://colororacle.org/). -- [ ] Every image is [inserted into the text](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text) using one of these options: `leanbuild::include_slide()`, `knitr::include_image()`, or this format: `SOMETHING`. +- [ ] Every image is [inserted into the text](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text) using one of these options: `leanbuild::include_slide()`, `knitr::include_image()`, or this format: `SOMETHING`. -- [ ] Every image has [alternative text added to it](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text). +- [ ] Every image has [alternative text added to it](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text). - [ ] The beginning of each Rmd contains this chunk so the images are saved in the correct spot: diff --git a/.github/automatic-issues/set-repo-settings.md b/.github/automatic-issues/set-repo-settings.md index b21be2a9..a34faf72 100644 --- a/.github/automatic-issues/set-repo-settings.md +++ b/.github/automatic-issues/set-repo-settings.md @@ -1,5 +1,5 @@ -For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-your-repository-settings). +For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings). ### Needed settings: diff --git a/.github/automatic-issues/templates-to-edit.md b/.github/automatic-issues/templates-to-edit.md index 556a1dec..4124fd7c 100644 --- a/.github/automatic-issues/templates-to-edit.md +++ b/.github/automatic-issues/templates-to-edit.md @@ -1,20 +1,20 @@ -[Follow the Wiki instructions here](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Setting-up-your-repository-files#setting-up-the-repository) for details on how to complete the items in this issue. +[Follow the Wiki instructions here](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-files#setting-up-the-repository) for details on how to complete the items in this issue. The following files need to be edited to get this new course started! ### Picking a style -See more [about customizing style on this page in the guide](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Change-Title-&-Customize-style). +See more [about customizing style on this page in the guide](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style). By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set. #### Using a style set -[Read more about the style sets here](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Change-Title-&-Customize-style#using-a-style-set). +[Read more about the style sets here](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style#using-a-style-set). - [ ] On a new branch, copy the `style-sets//index.Rmd` and `style-sets//_output.yml` to the top of the repository to overwrite the default `index.Rmd` and `_output.yml`. - [ ] Copy over all the files in the `style-sets//copy-to-assets` to the `assets` folder in the top of the repository. -- [ ] [Create a pull request](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/About-pull-request-review) with these changes, and double check the rendered preview to make sure that the style is what you are looking for. +- [ ] [Create a pull request](https://github.com/jhudsl/OTTR_Template/wiki/About-pull-request-review) with these changes, and double check the rendered preview to make sure that the style is what you are looking for. ### Files that need edited upon creating a new course. @@ -27,9 +27,9 @@ By default this course template will use the jhudsl data science lab style. Howe ### Files that need to be edited upon adding each new chapter (including upon creating a new course): -- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Publishing-with-Bookdown). -- [ ] `book.bib` - any citations need to be added. See [instructions](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Citations). +- [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-with-Bookdown). +- [ ] `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/DaSL_Course_Template_Bookdown/wiki/Using-Docker#starting-a-new-docker-image). +- `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. diff --git a/.github/automatic-issues/update-enrollment.md b/.github/automatic-issues/update-enrollment.md index df2344cc..76a1eb5e 100644 --- a/.github/automatic-issues/update-enrollment.md +++ b/.github/automatic-issues/update-enrollment.md @@ -1,7 +1,7 @@ -The original template: https://github.com/jhudsl/DaSL_Course_Template_Bookdown is always a work in progress. +The original template: https://github.com/jhudsl/OTTR_Template is always a work in progress. We are working on adding more features and smoothing out bugs as we go. If you want to receive updates from the original template to your course template, you will need to enroll this repository to the template updates by adding it to the `sync.yml` file. -[Follow these instructions](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Receiving-template-updates#how-to-enroll-a-repository-to-receive-template-updates) to enroll your course repository to receive these updates. +[Follow these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Receiving-template-updates#how-to-enroll-a-repository-to-receive-template-updates) to enroll your course repository to receive these updates. diff --git a/.github/workflows/docker-build-test.yml b/.github/workflows/docker-build-test.yml index 84fc0a1f..93107c11 100644 --- a/.github/workflows/docker-build-test.yml +++ b/.github/workflows/docker-build-test.yml @@ -36,9 +36,9 @@ jobs: - uses: actions/checkout@v2 - name: Don't re-test if this is a sync branch - if: ${{ github.head_ref == 'repo-sync/DaSL_Course_Template_Bookdown/default' }} + if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }} run: | - echo This was tested on DaSL_Course_Template_Bookdown no need to re-run + echo This was tested on OTTR_Template no need to re-run exit 1 # Set up Docker build diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml index dff1dda2..f962271c 100644 --- a/.github/workflows/release-notes.yml +++ b/.github/workflows/release-notes.yml @@ -12,23 +12,23 @@ jobs: runs-on: ubuntu-latest steps: - uses: mshick/add-pr-comment@v1 - if: ${{ github.head_ref == 'repo-sync/DaSL_Course_Template_Bookdown/default' }} + if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }} with: message: | **Please carefully review these changes and decide which are useful for your course.** - See the release notes: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/releases + See the release notes: https://github.com/jhudsl/OTTR_Template/releases - If you don't want the changes from a particular file, you can always [revert that particular commit](https://git-scm.com/docs/git-revert) before merging the sync PR. - If you will not want any updates on this file in the future, you may want to remove a file from being synced in your repo [by reconfiguring the sync file](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/blob/main/.github/sync.yml). + If you will not want any updates on this file in the future, you may want to remove a file from being synced in your repo [by reconfiguring the sync file](https://github.com/jhudsl/OTTR_Template/blob/main/.github/sync.yml). - If you want only some changes, but they are not on a whole file basis, you could check out the branch and make manual edits. To checkout the branch, navigate to your own repository you should be able to run: ``` - git checkout repo-sync/DaSL_Course_Template_Bookdown/default + git checkout repo-sync/OTTR_Template/default ``` - If you don't want any of the changes you can close the PR entirely. - You may want to unenroll your repository from the sync GitHub actions by [filing a PR](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) on `DaSL_Course_Template_Bookdown` - to delete [your repo name from this file](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/blob/main/.github/sync.yml) if this will continue to be the case. + You may want to unenroll your repository from the sync GitHub actions by [filing a PR](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) on `OTTR_Template` + to delete [your repo name from this file](https://github.com/jhudsl/OTTR_Template/blob/main/.github/sync.yml) if this will continue to be the case. repo-token: ${{ secrets.GH_PAT }} repo-token-user-login: 'github-actions[bot]' # The user.login for temporary GitHub tokens diff --git a/.github/workflows/render-bookdown.yml b/.github/workflows/render-bookdown.yml index 0db1b8c2..6c590e5e 100644 --- a/.github/workflows/render-bookdown.yml +++ b/.github/workflows/render-bookdown.yml @@ -79,6 +79,7 @@ jobs: --mount type=bind,target=/home/rstudio,source=$PWD \ jhudsl/course_template \ Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')" + cp -R assets/* docs/assets/ ##### If you do not wish to host your course on Coursera, you can delete this section ##### # Run Coursera version diff --git a/.github/workflows/render-preview.yml b/.github/workflows/render-preview.yml index 5aa3c181..2caacf0e 100644 --- a/.github/workflows/render-preview.yml +++ b/.github/workflows/render-preview.yml @@ -25,7 +25,8 @@ jobs: # We want a fresh run of the renders each time - name: Delete old docs/* - run: rm -r docs/* + run: | + rm -r docs/* # Run bookdown rendering - name: Run bookdown render @@ -35,6 +36,7 @@ jobs: --mount type=bind,target=/home/rstudio,source=$PWD \ jhudsl/course_template \ Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')" + cp -R assets/* docs/assets/ ##### If you do not wish to host your course on Coursera, you can delete this section ##### # Run Coursera version diff --git a/.github/workflows/starting-course.yml b/.github/workflows/starting-course.yml index 0de1580d..7926e23d 100644 --- a/.github/workflows/starting-course.yml +++ b/.github/workflows/starting-course.yml @@ -13,7 +13,7 @@ jobs: template-cleanup: name: Template Cleanup runs-on: ubuntu-latest - if: github.event.repository.name != 'DaSL_Course_Template_Bookdown' + if: github.event.repository.name != 'OTTR_Template' steps: # Check out current repository diff --git a/02-chapter_of_course.Rmd b/02-chapter_of_course.Rmd index 5fb11b27..1532c453 100644 --- a/02-chapter_of_course.Rmd +++ b/02-chapter_of_course.Rmd @@ -1,5 +1,5 @@ -*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Getting-started) +*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/OTTR_Template/wiki/Getting-started) Every chapter needs to start out with this chunk of code: @@ -20,7 +20,7 @@ This chapter will cover: For this chapter, we'll need the following packages attached: -*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Using-Docker#starting-a-new-docker-image). +*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). ```{r} library(magrittr) diff --git a/About.Rmd b/About.Rmd index d5d952a7..3bd9fc25 100644 --- a/About.Rmd +++ b/About.Rmd @@ -1,7 +1,7 @@ # About the Authors {-} -These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-give-credits). +These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits).     @@ -54,7 +54,7 @@ devtools::session_info() [Leanbuild]: https://github.com/jhudsl/leanbuild - # {Course Name} -[![Render Bookdown and Coursera](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/actions/workflows/render-bookdown.yml/badge.svg)](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/actions/workflows/render-bookdown.yml) +[![Render Bookdown and Coursera](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-bookdown.yml/badge.svg)](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-bookdown.yml) -This course was created from [this GitHub template](https://github.com/jhudsl/DaSL_Course_Template_Bookdown). +This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template). You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub. Will look something like: https://jhudatascience.org/{Course_Name}} -If you would like to contribute to this course material, take a look at the [getting started GitHub wiki pages](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki). +If you would like to contribute to this course material, take a look at the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki). ## About this course diff --git a/_bookdown.yml b/_bookdown.yml index 8dd4fc88..6558fad5 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,6 +1,6 @@ book_filename: "Course_Name" chapter_name: "Chapter " -repo: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/ +repo: https://github.com/jhudsl/OTTR_Template/ rmd_files: ["index.Rmd", "01-intro.Rmd", "02-chapter_of_course.Rmd", diff --git a/_output.yml b/_output.yml index 98500bfe..37d3f52a 100644 --- a/_output.yml +++ b/_output.yml @@ -10,6 +10,6 @@ bookdown::gitbook: before: | after: | -

This content was published with bookdown by:

+

This content was published with bookdown by:

The Johns Hopkins Data Science Lab

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

diff --git a/assets/big-image.html b/assets/big-image.html index c1af1d99..f12179e7 100644 --- a/assets/big-image.html +++ b/assets/big-image.html @@ -7,6 +7,7 @@ -
- + +
+
\ No newline at end of file diff --git a/docs/02-chapter_of_course.md b/docs/02-chapter_of_course.md index a78a644f..50d70e06 100644 --- a/docs/02-chapter_of_course.md +++ b/docs/02-chapter_of_course.md @@ -1,5 +1,5 @@ -*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Getting-started) +*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/OTTR_Template/wiki/Getting-started) Every chapter needs to start out with this chunk of code: @@ -18,7 +18,7 @@ This chapter will cover: For this chapter, we'll need the following packages attached: -*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/Using-Docker#starting-a-new-docker-image). +*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). ```r diff --git a/docs/404.html b/docs/404.html index eaa068a2..e697ed92 100644 --- a/docs/404.html +++ b/docs/404.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/About.md b/docs/About.md index 7f32a12c..b8538881 100644 --- a/docs/About.md +++ b/docs/About.md @@ -1,7 +1,7 @@ # About the Authors {-} -These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-give-credits). +These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits).     @@ -109,7 +109,7 @@ These credits are based on our [course contributors table guidelines](https://gi [Leanbuild]: https://github.com/jhudsl/leanbuild - - - +
    \ No newline at end of file diff --git a/docs/coursera/index.html b/docs/coursera/index.html index fdb625d1..516223be 100644 --- a/docs/coursera/index.html +++ b/docs/coursera/index.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/coursera/introduction.html b/docs/coursera/introduction.html index 3bbc05fb..355a084c 100644 --- a/docs/coursera/introduction.html +++ b/docs/coursera/introduction.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    @@ -226,7 +226,7 @@

    1.2 Target Audience

    1.3 Curriculum

    The course covers…

    -

    *If you haven’t yet read the getting started Wiki pages; start there

    +

    *If you haven’t yet read the getting started Wiki pages; start there

    Every chapter needs to start out with this chunk of code:

    @@ -241,7 +241,7 @@

    1.4 Learning Objectives

    1.5 Libraries

    For this chapter, we’ll need the following packages attached:

    -

    *Remember to add any additional packages you need to your course’s own docker image.

    +

    *Remember to add any additional packages you need to your course’s own docker image.

    library(magrittr)
    diff --git a/docs/coursera/references.html b/docs/coursera/references.html index 16109192..96bf6629 100644 --- a/docs/coursera/references.html +++ b/docs/coursera/references.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/coursera/resources/image_to_slide_key.tsv b/docs/coursera/resources/image_to_slide_key.tsv index 7f50a3ec..1cf33393 100644 --- a/docs/coursera/resources/image_to_slide_key.tsv +++ b/docs/coursera/resources/image_to_slide_key.tsv @@ -1,3 +1,3 @@ image_url page_id image_id -https://raw.githubusercontent.com/jhudsl/DaSL_Course_Template_Bookdown/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png SLIDES_API1620647862_0 SLIDES_API1831894727_0 -https://raw.githubusercontent.com/jhudsl/DaSL_Course_Template_Bookdown/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png SLIDES_API133532727_0 SLIDES_API739649856_0 +https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png SLIDES_API1620647862_0 SLIDES_API1831894727_0 +https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png SLIDES_API133532727_0 SLIDES_API739649856_0 diff --git a/docs/coursera/topic-of-section.html b/docs/coursera/topic-of-section.html index 896aefc8..99f7f899 100644 --- a/docs/coursera/topic-of-section.html +++ b/docs/coursera/topic-of-section.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/index.html b/docs/index.html index fdb625d1..516223be 100644 --- a/docs/index.html +++ b/docs/index.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/introduction.html b/docs/introduction.html index 3bbc05fb..355a084c 100644 --- a/docs/introduction.html +++ b/docs/introduction.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    @@ -226,7 +226,7 @@

    1.2 Target Audience

    1.3 Curriculum

    The course covers…

    -

    *If you haven’t yet read the getting started Wiki pages; start there

    +

    *If you haven’t yet read the getting started Wiki pages; start there

    Every chapter needs to start out with this chunk of code:

    @@ -241,7 +241,7 @@

    1.4 Learning Objectives

    1.5 Libraries

    For this chapter, we’ll need the following packages attached:

    -

    *Remember to add any additional packages you need to your course’s own docker image.

    +

    *Remember to add any additional packages you need to your course’s own docker image.

    library(magrittr)
    diff --git a/docs/references.html b/docs/references.html index 16109192..96bf6629 100644 --- a/docs/references.html +++ b/docs/references.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/docs/topic-of-section.html b/docs/topic-of-section.html index 47567a2e..c121ca2d 100644 --- a/docs/topic-of-section.html +++ b/docs/topic-of-section.html @@ -181,7 +181,7 @@
  • About the Authors
  • References
  • -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/output-proj.yml b/output-proj.yml index bd63db5b..0b37a96c 100644 --- a/output-proj.yml +++ b/output-proj.yml @@ -8,9 +8,9 @@ bookdown::gitbook: toc: collapse: section before: | - + after: | -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/resources/image_to_slide_key.tsv b/resources/image_to_slide_key.tsv index 7f50a3ec..1cf33393 100644 --- a/resources/image_to_slide_key.tsv +++ b/resources/image_to_slide_key.tsv @@ -1,3 +1,3 @@ image_url page_id image_id -https://raw.githubusercontent.com/jhudsl/DaSL_Course_Template_Bookdown/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png SLIDES_API1620647862_0 SLIDES_API1831894727_0 -https://raw.githubusercontent.com/jhudsl/DaSL_Course_Template_Bookdown/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png SLIDES_API133532727_0 SLIDES_API739649856_0 +https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-2-1.png SLIDES_API1620647862_0 SLIDES_API1831894727_0 +https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/_bookdown_files/02-chapter_of_course_files/figure-html/unnamed-chunk-3-1.png SLIDES_API133532727_0 SLIDES_API739649856_0 diff --git a/scripts/git_repo_check.R b/scripts/git_repo_check.R index ed839677..e1d74124 100644 --- a/scripts/git_repo_check.R +++ b/scripts/git_repo_check.R @@ -13,7 +13,7 @@ option_list <- list( c("--repo"), type = "character", default = NULL, - help = "GitHub repository name, e.g. jhudsl/DaSL_Course_Template_Bookdown", + help = "GitHub repository name, e.g. jhudsl/OTTR_Template", ), optparse::make_option( c("--git_pat"), @@ -39,7 +39,7 @@ check_git_repo <- function(repo, git_pat = NULL, silent = TRUE, return_repo = FA # exists and return a TRUE/FALSE # Inputs: - # repo: the name of the repository, e.g. jhudsl/DaSL_Course_Template_Bookdown + # repo: the name of the repository, e.g. jhudsl/OTTR_Template # git_pat: A personal access token from GitHub. Only necessary if the repository being # checked is a private repository. # silent: TRUE/FALSE of whether the warning from the git ls-remote command diff --git a/style-sets/AnVIL/_output.yml b/style-sets/AnVIL/_output.yml index 7440ec76..247b59b3 100644 --- a/style-sets/AnVIL/_output.yml +++ b/style-sets/AnVIL/_output.yml @@ -10,7 +10,7 @@ bookdown::gitbook: before: | after: | -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/style-sets/GDSCN/_output.yml b/style-sets/GDSCN/_output.yml index 5a59f74d..b950a3b4 100644 --- a/style-sets/GDSCN/_output.yml +++ b/style-sets/GDSCN/_output.yml @@ -10,7 +10,7 @@ bookdown::gitbook: before: | after: | -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/style-sets/data-trail/_output.yml b/style-sets/data-trail/_output.yml index 4c7c20fc..bf0596bf 100644 --- a/style-sets/data-trail/_output.yml +++ b/style-sets/data-trail/_output.yml @@ -10,7 +10,7 @@ bookdown::gitbook: before: | after: | -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    diff --git a/style-sets/itcr/_output.yml b/style-sets/itcr/_output.yml index 4554097c..87b4a01d 100644 --- a/style-sets/itcr/_output.yml +++ b/style-sets/itcr/_output.yml @@ -10,7 +10,7 @@ bookdown::gitbook: before: | after: | -

    This content was published with bookdown by:

    +

    This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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

    From f7289995c99286d7691603f46d66c8709d317d63 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 17 Dec 2021 11:19:34 -0500 Subject: [PATCH 2/2] Update all links --- docs/404.html | 2 +- docs/about-the-authors.html | 2 +- docs/coursera/404.html | 2 +- docs/coursera/about-the-authors.html | 2 +- docs/coursera/assets/big-image.html | 2 +- docs/coursera/index.html | 2 +- docs/coursera/introduction.html | 2 +- docs/coursera/references.html | 2 +- docs/coursera/topic-of-section.html | 2 +- docs/index.html | 2 +- docs/introduction.html | 2 +- docs/references.html | 2 +- docs/topic-of-section.html | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/404.html b/docs/404.html index 43f6aab2..377a68f3 100644 --- a/docs/404.html +++ b/docs/404.html @@ -211,7 +211,7 @@

    - +

    Page not found

    diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html index 86a1d0b3..7722b554 100644 --- a/docs/about-the-authors.html +++ b/docs/about-the-authors.html @@ -211,7 +211,7 @@

    - +

    About the Authors

    diff --git a/docs/coursera/404.html b/docs/coursera/404.html index 43f6aab2..377a68f3 100644 --- a/docs/coursera/404.html +++ b/docs/coursera/404.html @@ -211,7 +211,7 @@

    - +

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    diff --git a/docs/coursera/about-the-authors.html b/docs/coursera/about-the-authors.html index 3ba7806c..5d9d76ae 100644 --- a/docs/coursera/about-the-authors.html +++ b/docs/coursera/about-the-authors.html @@ -211,7 +211,7 @@

    - +

    About the Authors

    diff --git a/docs/coursera/assets/big-image.html b/docs/coursera/assets/big-image.html index 0da49e04..7336841a 100644 --- a/docs/coursera/assets/big-image.html +++ b/docs/coursera/assets/big-image.html @@ -7,6 +7,6 @@
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