Initial commit

.github/ISSUE_TEMPLATE/course-content-add.md

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+---
+name: New content idea
+about: Suggest an idea for the course
+title: ''
+labels: ''
+assignees:
+
+---
+
+## Describe the your scope of your content idea
+<!-- What will this cover and how does it relate to the current course material? -->
+
+## Describe the learning objectives for your content idea
+<!-- What will users learn from this new content? -->
+
+## Additional context or resources
+<!-- Add any other context or related resources we should know about? -->

.github/ISSUE_TEMPLATE/course-problem-report.md

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+---
+name: Course Problem Report
+about: Create a report to help improve the course
+title: [Problem]
+labels: bug
+assignees:
+
+---
+
+## Describe what is not working with the course
+<!-- A clear and concise description of what the bug is. -->
+
+## Steps to Reproduce
+<!-- Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+-->
+
+## Expected behavior
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Screenshots
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## Additional context
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/course-template-feature-request.md

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+---
+name: Course Template Feature Request
+about: Suggest an idea for the course templates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+## Is your feature request related to a problem? Please describe.
+<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
+
+## Describe the solution you'd like
+<!-- A clear and concise description of what you want to happen. -->
+
+## Describe alternatives you've considered
+<!--  A clear and concise description of any alternative solutions or features you've considered. -->
+
+## Additional context
+<!-- Add any other context or screenshots about the feature request here.  -->

.github/ISSUE_TEMPLATE/course-template-problem-report.md

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+---
+name: Course Template Problem Report
+about: Create a report to help improve the template and its documentation
+title: Problem
+labels: bug
+assignees: cansavvy
+
+---
+
+## Describe what is not working with the template or is unclear in the documentation
+<!-- A clear and concise description of what the bug is. -->
+
+## Please link to the specific course repository you are working on
+
+## To Reproduce
+<!-- Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error -->
+
+## Expected behavior
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Github actions links
+<!-- If applicable please link to the Github actions that has failed. -->
+
+## Screenshots
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## Additional context
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/new-course-add-to-sync.md

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+---
+name: Add your new course to syncs/OTTR updates
+about: Provide information about your new course (which uses the OTTR template) so that we can enroll it in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+## What is the name of your new repository?
+<!-- The name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## What username or organization is your new repository associated with?
+<!-- The name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->

.github/ISSUE_TEMPLATE/update-course-info-for-sync.md

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+---
+name: Update your course's info for syncs/OTTR updates
+about: Provide information about your moved/renamed course (which uses the OTTR template) so that it can continue to be enrolled in OTTR updates
+title: ''
+labels: ''
+assignees: cansavvy
+
+---
+
+<!-- Remove headings if they are not applicable to the changes/updates you made for your repo-->
+
+## If the name of your repository was changed ...
+
+### What was the old name?
+<!-- The old/original name of the repo. Ex the name of this repo is OTTR_Template -->
+
+### What is the new name?
+<!-- The new/modified name of the repo. Ex the name of this repo is OTTR_Template -->
+
+## If the repository was moved ...
+
+### What was the original username or organization your repository was associated with?
+<!-- The old/original name of the username or organization where the new repository was located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->
+
+### What is the new username or organization your repository was associated with?
+<!-- The new/modified name of the username or organization where the new repository is located . Ex this repository is part of the jhudsl organization. A personal repository would be associated with a username instead of the organization. -->

.github/ISSUE_TEMPLATE/url-error.md

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+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})

.github/PULL_REQUEST_TEMPLATE/add_to_sync_template.md

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+---
+name: Add new repository to sync
+about: Enroll your repository for OTTR updates
+title: OTTR Updates Enrollment
+labels: ''
+assignees: cansavvy
+---
+
+Added __ repository to sync.yml in order to enroll in OTTR updates.

.github/PULL_REQUEST_TEMPLATE/pull_request_template_general.md

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+---
+name: New Content or Feature
+about: New Content or Feature Update
+title: General Update
+labels: ''
+assignees:
+---
+
+
+<!--This PR Template was modified from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/.github/PULL_REQUEST_TEMPLATE.md-->
+
+### Purpose/implementation Section
+
+#### What changes are being implemented in this Pull Request?
+
+
+
+#### What was your approach?
+
+
+
+#### What GitHub issue does your pull request address?
+
+
+
+### Tell potential reviewers what kind of feedback you are soliciting.
+
+
+
+### New Content Checklist
+
+- [ ] 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.
+
+- [ ] [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](https://www.ottrproject.org/customize-robots.html#Spell_checking)).
+
+- [ ] Any newly necessary packages that are needed have been added to the [Dockerfile and image](https://www.ottrproject.org/customize-docker.html).
+
+- [ ] Images are in the [correct format for rendering](https://www.ottrproject.org/writing_content_courses.html#set-up-images).
+
+- [ ] Every new image has [alt text and is in a Google Slide](https://www.ottrproject.org/writing_content_courses.html#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.
+
+- [ ] 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/).

.github/automatic-issues/add-feedback-method.md

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+
+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.
+
+- [ ] [Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html).
+
+It's also a good idea to collect passive feedback via Google Analytics.
+
+- [ ] [Read our guide to Google Analytics here](https://www.ottrproject.org/more_features.html#google-analytics).

.github/automatic-issues/git-secrets.md

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+
+**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 on ottrproject.org](https://www.ottrproject.org/getting_started.html#6_Set_up_your_GitHub_personal_access_token).
+
+It's important that these are set up and named exactly what they are below in order for Github actions to work correctly.
+
+To set up these repository secrets, on your repository's main Github page, go to `Settings` and scroll down to see `Secrets` on the left side menu bar.
+
+- [ ] Set `GH_PAT`
+`Name`:  `GH_PAT`
+`value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+Underneath `Select scopes`, check both `repo` and `workflow`.
+Then copy the PAT and save as the value.

.github/automatic-issues/images-checklist.md

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+
+Use this checklist to make sure your slides and images are set up correctly!
+
+See [Setting Up Images and Graphics](https://www.ottrproject.org/writing_content_courses.html#Set_up_images) for more info!
+
+- [ ] Create your course's main Google Slides.
+
+- [ ] The slides use the appropriate template.
+
+- [ ] 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 using one of these options: `ottrpal::include_slide()`, `knitr::include_image()`, or this format: `<img src="blah.png" alt="SOMETHING">`.
+
+- [ ] Every image has alternative text added to it.
+
+- [ ] The beginning of each Rmd contains this chunk so the images are saved in the correct spot:
+
+`````
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+`````

.github/automatic-issues/set-repo-settings.md

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+
+For more information on these settings see instructions in [Starting a new OTTR course](https://www.ottrproject.org/getting_started.html#starting-a-new-ottr-course).
+
+- [ ] This course repository is set to `public`.
+- [ ] [Github secret `GH_PAT` has been set](https://www.ottrproject.org/getting_started.html#6_Set_up_your_GitHub_personal_access_token)
+  `Name`:  `GH_PAT`
+  `value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+  Underneath `Select scopes`, check both `repo` and `workflow`.
+  Then copy the PAT and save as the value.
+
+- [ ] GitHub pages is turned on
+  - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`.  
+  - [ ] Check `Enforce HTTPS`.
+
+- [ ] [Set branch protections settings](https://www.ottrproject.org/getting_started.html#8_Set_up_branch_rules)
+  - [ ] `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.
+  - [ ] Click `Save` at the bottom of the page!
+
+- [ ] [Customize GitHub actions](https://www.ottrproject.org/customize-robots.html) for what you will need in this course.

.github/automatic-issues/templates-to-edit.md

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+
+[Follow the instructions here in ottrproject.org](https://www.ottrproject.org/writing_content_courses.html) for details on how to start editing your OTTR course
+
+The following files need to be edited to get this new course started!
+
+### Files that need edited upon creating a new course.
+
+- [ ] `README.md` - Fill in all the `{ }`.
+- [ ] `index.Rmd` - `title:` should be updated.
+- [ ] `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.
+
+### 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://www.ottrproject.org/course_publishing.html#publishing-with-bookdown).
+- [ ] `book.bib` - any citations need to be added. See [instructions](https://www.ottrproject.org/more_features.html#citing-sources).
+
+### Picking a style
+
+See more [about customizing style on this page in the guide](https://www.ottrproject.org/customize-style.html).
+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://www.ottrproject.org/customize-style.html#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://www.ottrproject.org/writing_content_courses.html#Open_a_pull_request) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
+
+### 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://www.ottrproject.org/customize-docker.html).
+- The code chunk in `index.Rmd` should be edited to add the new package.

.github/automatic-issues/update-enrollment.md

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+
+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://www.ottrproject.org/getting_started.html#9_Enroll_your_repository_for_OTTR_updates) to enroll your course repository to receive these updates.
+  - [ ] Alternatively, [open an issue in the OTTR_Template repo](https://github.com/jhudsl/OTTR_Template/issues/new?assignees=cansavvy&labels=&projects=&template=new-course-add-to-sync.md&title=), providing us with the necessary information to add the course for you.
+
+In order for these syncs to happen we need credentials to do so. Our `jhudsl-robot` is what you need to give access to. 
+- [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://www.ottrproject.org/getting_started.html#5_Add_jhudsl-robot_as_a_collaborator).

.github/course_README_template.md

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+# {Course Name}
+
+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.}
+
+If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/).
+
+## About this course
+
+This course introduces {info on what this course introduces}
+
+## Learning Objectives
+
+This course will teach learners to:  
+
+- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here}
+- {More learning objectives}
+
+## Encountering problems?
+
+If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.
+
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />All materials in this course are licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> unless noted otherwise.

.github/switch_sync_repo.R

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+#!/usr/bin/env Rscript
+
+# This script switches the repo entry for the yaml file to whatever is specified
+# Written by Candace Savonen Jan 2022
+
+if (!("optparse" %in% installed.packages())){
+  install.packages("optparse")
+}
+
+library(optparse)
+
+option_list <- list(
+  optparse::make_option(
+    c("--repo"),
+    type = "character",
+    default = "jhudsl/OTTR_Template_Test",
+    help = "GitHub repository name, e.g. jhudsl/OTTR_Template_Test",
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Get test sync yaml path
+sync_file_path <- file.path(root_dir, ".github", "test-sync.yml")
+
+yaml_contents <- yaml::yaml.load_file(sync_file_path)
+
+# Only keep first grouping
+yaml_contents$group <- yaml_contents$group[[1]]
+
+# Switch out repo
+yaml_contents$group$repos <- opt$repo
+
+yaml::write_yaml(yaml_contents, sync_file_path)