cancer-imaging-informatics's Introduction

DaSL Course Templates

The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms less painful.

This template and guide helps you:

Edit and write a course in RMarkdown files and have it published to multiple different platforms:
Have Github action robots do your repetitive tasks like spell check and re-rendering.
Use automagic conversion to ease the lift of prepping the material for different platforms' formats.
Use our Docker image for consistency across authors as well as to help you avoid dependency hell.

Courses that have been made using this template:

To Get Started

Go to the Wiki page
Please take a look at the code of conduct.
If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please file an issue here! Your feedback is very much appreciated.

{Course Name}

This course was created from this GitHub 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.

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}.

All materials in this course are licensed CC-BY and can be repurposed freely with attribution.

cancer-imaging-informatics's People

Contributors

Watchers

cancer-imaging-informatics's Issues

New Course - Templates to Edit

Follow the Wiki instructions here for details on how to complete the items in this issue.

The following files need to be edited to get this new course started!

If you are creating an ITCR course:

Delete _output.yml and index.Rmd files
Keep the _output-itcr.yml and index-itcr.Rmd files but delete the -itcr parts of those file names.

If you are creating any other courses:

Delete the _output-itcr.yml and index-itcr.Rmd files.

Files that need edited upon creating a new course.

README.md - Fill in all the { }.
index.Rmd - the author:, title:, and description: should be updated.
About.Rmd - Replace information with your own author information and change the course title in the yaml header!
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.
code_output can be deleted if you don't plan to use code.

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.
book.bib - any citations need to be added. See instructions.

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.
The code chunk in index.Rmd should be edited to add the new package.

New Course - Set Github Secrets

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.

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.

For each new secret, click the New repository secret button and set each as follows, clicking Add secret as you fill each in appropriately:

Set DOCKERHUB_USERNAME
Name: DOCKERHUB_USERNAME
value: put your login username for https://hub.docker.com/
Set DOCKERHUB_TOKEN
Name:DOCKERHUB_TOKEN
value: put a access token for Dockerhub which you can create this by following these instructions.
Set GIT_TOKEN
Name: GIT_TOKEN
value: A personal access token following these instructions.
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

New Course - Template Update Enrollment

The original template: https://github.com/jhudsl/DaSL_Course_Template_Bookdown 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 to enroll your course repository to receive these updates.

New Course - Set Repository Settings