Contributing to OHSU BioData Club


Running a lesson

Making the lesson

The Mozilla Science Study Group handbook here and here has several very good points about making a lesson. This section summarizes bits of the handbook, but also adds pieces that are missing from it. Check out the lesson bank too.

From the handbook:

Expanding on this are other things to keep in mind.

Data: External data should not be used unless it is absolutely necessary. Instead, rely on built-in or sample datasets provided by the respective programming language or package.

Code: This is the main thing that should be emphasized. How the code is used, its specific applications, and its meaning should be the entire focus of the lesson. Here are some tips:

Lessons should be submitted as a Pull Request (PR) at least one full day before the session. Submitting the lessons as a Pull Request is also a great way to find out whether your lesson matches what is advertised in the Events repo. New lessons should be created from a copy of the lessons/template/lesson.md file. Follow the details and requests in the template lesson file and write up your lesson!

Submitting a PR can be done by (brief step-by-step):

  1. Forking the studyGroup repo
  2. (Optional) git clone your forked version onto your computer
  3. Use the lesson template and make your lesson
  4. Follow the file/folder naming rules (see below)
  5. git add and git commit that lesson
  6. git push your lesson to your forked studyGroup repo
  7. Submit a PR using Github’s Pull Request button on your forked version

In a more detailed step-by-step:

  1. Fork the studyGroup into your GitHub account. See this GitHub help for info on forking.
  2. After it is forked, git clone from your terminal or Git Bash of your new forked version of studyGroup onto your computer from your account. If you want it on your Desktop do:
      cd Desktop
      git clone https://github.com/YOUR-USERNAME/studyGroup.git 
    

…replacing YOUR-USERNAME with your own user name on GitHub (eg: mine would look like git clone https://github.com/lwjohnst86/studyGroup.git).

  1. Type ls to confirm that the studyGroup folder was created. Then cd studyGroup and git status or git log to confirm that you are now in the new repo.
  2. Add the original Study Group repo using this command:
      git remote add upstream https://github.com/UofTCoders/studyGroup.git
      git fetch upstream
    
  3. Create a new folder in the lessons folder of studyGroup on your computer, naming it appropriately (without spaces) to the lesson you are planning on teaching. Files and folders should be named as such:
    • Create the lesson template under whichever programming language you are teaching (e.g. under lesson/r or lesson/python.). Use the misc/ folder if you aren’t sure.
    • Name the new lesson folder, all small caps, so that it simply explains what the topic is (e.g. python/intro/, r/loops/).
    • If you need more than one word, keep all small caps and use a dash (-) for a space (e.g. misc/bash-intro/, misc/jekyll-ghpages/).
  4. Copy the lessons/template/lesson.md into the new folder and write up your lesson in there, filling out requested information. This is a Markdown file (.md). The reason it should be Markdown or plain text is because GitHub renders the Markdown file into HTML so it’s nicer to read on the site and for others.

  5. Save the new file in the git history:
      git add ./lessons/yourlesson/lesson.md
      git commit -m "Added file on lesson"
    
  6. Push up to your GitHub repo:
      git push origin gh-pages
    
  7. Submit a Pull Request from your GitHub account into the UofTCoders. Make sure the base fork is set to UofTCoders/studyGroup (and not mozillascience/studyGroup). Check the GitHub help on Pull Requests.

Note: For those wanting to contribute regularly or who edit their repositories often, it’s best to create a new branch for each PR you make. For example, if you want to clean up some bits of the repo, you can follow a workflow such as this:

## Good to name the branch to reflect what you are doing.
git checkout -b cleaningUp 
## Make edits/changes/cleaning up
git add files-changed
git commit
git push origin cleaningUp

You can now make a pull request of the cleaningUp branch. Once the pull request has been completed, you can delete the now old branch via:

git checkout gh-pages ## Move back to main branch
git branch --delete cleaningUp
## If you want to delete the remote branch too do:
git push origin --delete cleaningUp
## Update your main branch from the new upstream branch
git pull upstream gh-pages

Giving the lesson

Come 10 min early, to make sure everything is set up.

Before you begin:

A few tips:


Fixing and updating the website

There are two ways of fixing or adding to the website, either by:

If you want to view the website before submitting a Pull Request to make sure your changes are as you expect, you’ll need to: