Switching out wiki links

course_publishing.Rmd

@@ -25,7 +25,7 @@ _Computing for Cancer Informatics:_
 
 # Publishing with Bookdown
 
-To publish your content using Bookdown, you can utilize Github Pages by following the repository setup instructions provided [here](https://github.com/ottrproject/OTTR_Template/wiki/Starting-a-new-course-with-this-template#set-up-github-pages). It's important to note that Bookdown serves as a fundamental component for utilizing other publishing platforms such as Coursera or Leanpub. Therefore, if you intend to use Coursera or Leanpub, you will need to publish your content using Bookdown.
+To publish your content using Bookdown, you can utilize Github Pages by following the repository setup instructions provided [here](https://www.ottrproject.org/getting_started.html#7_Set_up_GitHub_Pages). It's important to note that Bookdown serves as a fundamental component for utilizing other publishing platforms such as Coursera or Leanpub. Therefore, if you intend to use Coursera or Leanpub, you will need to publish your content using Bookdown.
 
 As you modify the names of the chapters of your course and add more chapters (using the `.Rmd` files), you need to update the `_bookdown.yml` file accordingly.
 
@@ -65,20 +65,20 @@ The [`ottrpal` package](https://github.com/ottrproject/ottrpal) takes care of ha
 
 These converted files are stored in the `manuscript` folder. As a general rule, don't edit files in the `manuscript` folder. This folder should be auto generated by the `ottrpal` package and should not be edited.
 
-Note that if you wish to keep your quizzes and their answers hidden, there is some additional setup involved with this process and you will need to create a separate private OTTR_Quizzes repository to store these quizzes. Start with [these instructions](https://github.com/ottrproject/OTTR_Template/wiki/Making-quizzes-private) first if you want your quizzes and answers to be hidden.
+Note that if you wish to keep your quizzes and their answers hidden, there is some additional setup involved with this process and you will need to create a separate private OTTR_Quizzes repository to store these quizzes. Start with [these instructions](https://www.ottrproject.org/course_publishing.html#Setting_up_the__Quizzes_repository_checklist:) first if you want your quizzes and answers to be hidden.
 
 
 ## Leanpub Rendering
 
-The `ottrpal` package can handle most of the formatting tasks for links and other elements for you, as long as you have followed the formatting instructions provided in the `Setting up images` section of [this Wiki](https://github.com/ottrproject/OTTR_Template/wiki/Setting-up-images-and-graphics).
+The `ottrpal` package can handle most of the formatting tasks for links and other elements for you, as long as you have followed the [formatting instructions provided in the `Set up images` section](https://www.ottrproject.org/writing_content_courses.html#set-up-images).
 
 Github Actions in this repository will attempt to convert Bookdown to Leanpub for you by running `ottrpal::bookdown_to_leanpub()` function at the top of the repository.
 
 ### Setting up Leanpub-related GitHub Actions
 
 When you are ready to begin publishing to Leanpub, you will want to turn on a few Github Actions that are included in the template but by default, turned off.
 
-In your [config_automation.yml file](https://github.com/ottrproject/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots), you will need to turn on two Actions in particular:
+In your [config_automation.yml file](https://www.ottrproject.org/customize-robots.html), you will need to turn on two Actions in particular:
 
 - `render-leanpub: yes`
 - `check-quizzes:yes`
@@ -95,7 +95,7 @@ If you encounter issues with the `ottrpal` package, please file an issue in its
 
 ## Hosting your course on Leanpub
 
-_Finalizing your course on Leanpub can be tricky_. We have created a course, [Using Leanpub](https://ottrproject.org/Using_Leanpub/index.html), to help guide you.
+_Finalizing your course on Leanpub can be tricky_. We have created a course, [Using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html), to help guide you.
 
 To host your course on Leanpub, follow these steps:  
 
@@ -194,7 +194,7 @@ Upon merging to the `main` branch, a GitHub Action will automatically run `check
 
 ## Converting Quizzes from Leanpub to Coursera format
 
-[See more instructions on how to port a course made from these templates to Coursera](https://github.com/ottrproject/OTTR_Template/wiki/Publishing-on-Courseraa).
+[See more instructions on how to port a course made from these templates to Coursera](https://www.ottrproject.org/course_publishing.html#publishing-with-coursera).
 
 You can convert your quizzes to a nicely upload-able yaml file in this repository by running this command in the docker image
 
@@ -212,7 +212,7 @@ Additionally, the [`ottrpal`](https://github.com/ottrproject/ottrpal) package ha
 
 ## Setting up the _Quizzes repository checklist:
 
-- [ ] A [`GH_PAT` has been set in the main Template and the `_Quizzes` repository if you are using a separate `_Quizzes` repository](https://github.com/ottrproject/OTTR_Template/wiki/Setting-up-GitHub-secrets).
+- [ ] A [`GH_PAT` has been set in the main Template and the `_Quizzes` repository if you are using a separate `_Quizzes` repository](https://www.ottrproject.org/getting_started.html#6_Set_up_your_GitHub_personal_access_token).
 
 - [ ] [Your Leanpub course as been created on Leanpub](#hosting-your-course-on-leanpub)
   - [ ] Writing mode in this course is set to `GitHub` and your main OTTR_Template repository is linked.
@@ -223,7 +223,7 @@ Additionally, the [`ottrpal`](https://github.com/ottrproject/ottrpal) package ha
    - [ ] `Require status checks to pass before merging` box is checked.
      - [ ] Underneath that `Require branches to be up to date before merging` box is checked.
 
-- [ ] This repo has been enrolled in [automatic updates from the original template](https://github.com/ottrproject/OTTR_Template/wiki/Receiving-template-updates).
+- [ ] This repo has been enrolled in [automatic updates from the original template](https://www.ottrproject.org/getting_started.html#8_Enroll_your_repository_for_OTTR_updates_(Not_required_but_highly_encouraged)).
 
 - [ ] Your Book.txt file is up to date.
 
@@ -549,6 +549,3 @@ These resources are used throughout this Coursera course in the form of ungraded
 Note about links in the plug-ins: The plug-ins used throughout the course feature links to other resources. To follow these links, right-click on them and open in a new tab or window.
 Regardless of the format you choose for the instructional content, you must take and pass the quizzes here on Coursera if you want to earn a Coursera certificate.
 ```
-
-
-

customize-docker.Rmd

@@ -205,7 +205,7 @@ For your personalized docker image, you can store the Dockerfile anywhere. In or
 
 It may be easiest to store it in the OTTR-made repository you are working from.
 
-In whichever repository you choose to store your Dockerfile, its recommended you use a GitHub action to automatically test it when you make changes. You can use our Docker handling [GitHub action here as a starting point](https://github.com/ottrproject/ottr-docker/blob/main/.github/workflows/docker-test.yml).
+In whichever repository you choose to store your Dockerfile, its recommended you use a GitHub action to automatically test it when you make changes. You can use our Docker handling [GitHub action here as a starting point](https://github.com/ottrproject/ottr-docker/blob/main/.github/workflows/pull_request.yml).
 
 You will need to modify this GHA for your own purposes:
 

customize-robots.Rmd

@@ -52,7 +52,7 @@ Leanpub needs a particular format for it to upload correctly. This action will l
 
 ### Check for broken URLs
 
-In the `config_automation.yml` file there are two different URL checkers. 
+In the `config_automation.yml` file there are two different URL checkers.
 
 1) One that is run during pull requests. It is set by:
 ```
@@ -65,7 +65,7 @@ If it fails, you can click on the output comment on your pull request that says
 GitHub Actions runs a check on all the URLs upon creating a pull request to the `main` branch.
 If it fails, you can click on the output comment on your pull request that says "Download errors here". This will give you a print out of the broken URLs it found.
 
-2) The other URL check runs on a set interval to see if any URLs referenced are no longer valid. This one is set by: 
+2) The other URL check runs on a set interval to see if any URLs referenced are no longer valid. This one is set by:
 ```
 url-check-periodically: yes
 ```
@@ -120,7 +120,7 @@ In the config_automation.yml file it looks like:
 docker-test: no
 ```
 By default it is set to `no` which means it won't run automatically unless you change this to `yes`.
-This is only relevant if you have [your own Docker image you are managing for your course](https://github.com/ottrproject/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image). If changes are made to Docker-relevant files: `Dockerfile`, `install_github.R`, or `github_package_list.tsv`, this will test re-build the Docker image. If it is successfully built, then it makes sense to merge it to `main` but the Docker Image will not be pushed to `Dockerhub` automatically. [Follow these instructions to push your Docker image to Dockerhub](https://github.com/ottrproject/OTTR_Template/wiki/Using-Docker#pushing-the-docker-image).
+This is only relevant if you have [your own Docker image you are managing for your course](https://www.ottrproject.org/customize-docker.html). If changes are made to Docker-relevant files: `Dockerfile`, `install_github.R`, or `github_package_list.tsv`, this will test re-build the Docker image. If it is successfully built, then it makes sense to merge it to `main` but the Docker Image will not be pushed to `Dockerhub` automatically. [Follow these instructions to push your Docker image to Dockerhub](https://www.ottrproject.org/customize-docker.html#Testing_a_modified_Docker_image).
 
 <br>
 
@@ -134,9 +134,9 @@ render-bookdown: yes
 render-leanpub: yes
 render-coursera: yes
 ```
-For publishing to Leanpub, make sure that the render Leanpub option is set to yes: `render-leanpub: yes`.  See more details about publishing to Leanpub [here](https://github.com/ottrproject/OTTR_Template/wiki/Publishing-on-Leanpub).
+For publishing to Leanpub, make sure that the render Leanpub option is set to yes: `render-leanpub: yes`.  See more details about publishing to Leanpub [here](https://www.ottrproject.org/course_publishing.html#publishing-with-leanpub).
 
-For publishing to Coursera, make sure render Coursera option is set to yes: `render-coursera: yes`. See more details about publishing to Coursera [here](https://github.com/ottrproject/OTTR_Template/wiki/Publishing-on-Coursera).
+For publishing to Coursera, make sure render Coursera option is set to yes: `render-coursera: yes`. See more details about publishing to Coursera [here](https://www.ottrproject.org/course_publishing.html#publishing-with-coursera).
 
 <br>
 

customize-style.Rmd

@@ -30,9 +30,9 @@ For example, if you are creating an ITCR course, you will need the files in `sty
 
 1. 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`.
 1. Copy over all the files in the `style-sets/<set-name>/copy-to-assets` to the `assets` folder in the top of the repository.
-1. [Create a pull request](https://github.com/ottrproject/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.
+1. [Create a pull request](https://www.ottrproject.org/writing_content_courses.html#about-ottr-and-pull-requests) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
 
-[Read here](https://bookdown.org/yihui/bookdown/output-formats.html) for more about how to customize your `_output.yml` file -- which is ultimately a part of how bookdown works. 
+[Read here](https://bookdown.org/yihui/bookdown/output-formats.html) for more about how to customize your `_output.yml` file -- which is ultimately a part of how bookdown works.
 
 <br>
 

editing_website.Rmd

@@ -367,7 +367,7 @@ to your branch.
 You can adjust what checks are run by editing the
 `config_automation.yml` file. This is further discussed in this section
 about [the GitHub
-Actions](https://github.com/ottrproject/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots).
+Actions](https://www.ottrproject.org/customize-robots.html).
 
 If you need more information on failed GitHub actions you can scroll to
 the bottom of your pull request where the status of the checks are shown

faqs.Rmd

@@ -7,7 +7,7 @@ output:
 
 ## Search on OTTR docs
 
-Search on the OTTR docs for what you are looking for. Note that first few entries are sponsored, the actually helpful stuff will be below that. 
+Search on the OTTR docs for what you are looking for. Note that first few entries are sponsored, the actually helpful stuff will be below that.
 
 <script async src="https://cse.google.com/cse.js?cx=22c03a049bf7a472a">
 </script>
@@ -42,7 +42,7 @@ Execution halted
 ```
 _What does this mean?:_
 
-Your Google Slides presentation you have tried to retrieve a slide from with `ottrpal::include_slide()` is not public. Your Google Slide document must be set to `Anyone with a link`. See [this article for more details.](https://support.wix.com/en/article/setting-permissions-for-google-drive-files-and-folders#:~:text=Settings%20Permissions%20for%20a%20Google,edit%20and%20comment%20as%20well.) The renders will fail if this is not set! See the [setting up images and graphics section](https://github.com/ottrproject/OTTR_Template/wiki/Setting-up-images-and-graphics) for more details.
+Your Google Slides presentation you have tried to retrieve a slide from with `ottrpal::include_slide()` is not public. Your Google Slide document must be set to `Anyone with a link`. See [this article for more details.](https://support.wix.com/en/article/setting-permissions-for-google-drive-files-and-folders#:~:text=Settings%20Permissions%20for%20a%20Google,edit%20and%20comment%20as%20well.) The renders will fail if this is not set! See the [setting up images and graphics section](https://www.ottrproject.org/writing_content_courses.html#set-up-images) for more details.
 
 ***
 
@@ -118,7 +118,7 @@ bookdown::word_document2:
   toc: true
 ```
 
-Commit the changes to your `_output.yml` and see if the preview GitHub action runs appropriately. 
+Commit the changes to your `_output.yml` and see if the preview GitHub action runs appropriately.
 
 ### `Error in if (title == x2) return(head) : the condition has length > 1`: Run bookdown render error
 
@@ -158,6 +158,6 @@ Check that the config file is up-to-date. It should look like this: https://gith
 
 ## Contact Info
 
-If you have a question that's not addressed by this website or just wanna chat with us about something else, please email us at itcrtrainingnetwork@gmail.com OR you can [leave a GitHub issue here](https://github.com/ottrproject/OTTR_Template/issues/new). 
+If you have a question that's not addressed by this website or just wanna chat with us about something else, please email us at itcrtrainingnetwork@gmail.com OR you can [leave a GitHub issue here](https://github.com/ottrproject/OTTR_Template/issues/new) and assign or "at" a team member in the description/a comment (`@carriewright11`, `@kweav`, or `@avahoffman`).
 
 We greatly appreciate any feedback! We are always looking for ways to improve OTTR so more open source courses can be made!