Initial commit

Author: KatherineCox

.github/AnVIL_Feedback_Script.sh

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+#!/bin/bash
+
+# Extract the title from the YAML front matter of index.Rmd
+title=$(awk '/^title:/{gsub(/^title: /,""); print}' "index.Rmd" | grep -v '^$')
+
+# Remove the outside quotation marks
+title=$(sed -e 's/^"//' -e 's/"$//' <<< "$title")
+
+# Replace spaces with '+'
+title=${title// /+}
+
+# Base url for the AnVIL Google Form
+url_base="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805="
+
+# Replace the url inside _output.yml
+perl -i -pe 's|https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform\?usp=pp_url&entry\.1565230805=.*"> Click|'${url_base}${title}'"> Click|g' _output.yml
+
+# Print for Github actions 
+echo "The feedback link is: ${url_base}${title}"

.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/PULL_REQUEST_TEMPLATE.md

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+<!--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 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/OTTR_Template/wiki/Publishing-with-Bookdown).
+
+- [ ] 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/OTTR_Template/wiki/Using-Docker#adding-packages-to-the-dockerfile).
+
+- [ ] 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/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.
+
+- [ ] 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-authors.md

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+- [ ] Fill in the `About.Rmd` page to give credit to authors and contributors.
+
+For more information about the `About.Rmd` page, see [the ottr instructions](https://www.ottrproject.org/more_features.html#Giving_credits_to_contributors).

.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.
+
+A feedback method (Google Form) has already been provided for AnVIL and GDSCN courses. Github actions automatically populates the Google Form with the `title` field from [`index.Rmd`](https://github.com/jhudsl/AnVIL_Template/blob/main/index.Rmd) using the [AnVIL Feedback Script](https://github.com/jhudsl/AnVIL_Template/blob/main/scripts/AnVIL_Feedback_Script.sh).
+
+- [ ] The `title` field has been filled out in the header yaml of `index.Rmd`.
+
+*No further action is needed on your part*. However, if you would like to change the feedback method, you can do so by editing [this line of code](https://github.com/jhudsl/AnVIL_Template/blob/7c501e9804cf88a151832bb0a9bbc1eae9d23fdf/_output.yml#L19) in `_output.yml`.
+
+[See these instructions](https://docs.google.com/document/d/1uhGafEkbtJL3ar3TVHqRFypwTbXjudHa7h2mXu53CkA/edit?usp=sharing) for how to manually create a feedback link for AnVIL / GDSCN content or events.

.github/automatic-issues/add-repo-to-anvil-collection.md

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+
+If you want this repository to be added to the AnVIL Collection, make sure you do the following:
+
+- Click the gear icon on the top right of the "Code" page next to "About"
+- [ ] Create a repository description
+- [ ] Add the homepage where your course will be rendered
+- [ ] Add a description of your course/content
+- [ ] Add the topic tag `anvil` or `gdscn`. You should also supply any other relevant tags.
+
+Following these steps will also automatically add this repository to the [AnVIL Collection](https://hutchdatascience.org/AnVIL_Collection/) if this repository is owned by one of the DaSL organizations.
+
+For more information on these settings see instructions in the [wiki pages](https://github.com/jhudsl/AnVIL_Template/wiki/The-AnVIL-Collection#adding-your-course-to-the-anvil-collection).
+
+For more information about adding repositories to the DaSL Collection, see the [AnVIL Collection README](https://github.com/fhdsl/AnVIL_Collection#readme).

.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 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.
+
+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://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-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://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/OTTR_Template/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/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-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](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:
+
+`````
+```{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 the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course).
+
+- [ ] This course repository is set to `public`.
+- [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings#add-jhudsl-robot-as-a-collaborator).
+- [ ] [GH_PAT has been set up as a GitHub secret](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token)
+
+- [ ] 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`.
+
+- [ ] [Github secret `GH_PAT` has been set](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#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.
+
+- [ ] [Set branch protections settings](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#9-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://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots) for what you will need in this course.