Prep for OTTR name switch over (#362)

* Search and replace all with OTTR

* Update all links

.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.
 

.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. 

.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.

.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)

.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: `<img src="blah.png" alt="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: `<img src="blah.png" alt="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:
 

.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:
 

.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/<set-name>/index.Rmd` and `style-sets/<set-name>/_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/<set-name>/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.

.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.

.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

.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

.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

.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

.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

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)

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
 
-<!-- Fill out this table using these instructions: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-give-credits
+<!-- Fill out this table using these instructions: https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits
 
 For JHU courses, You will need to add Ira as a credit: