topics.md

Introduction to GitHub

1. Creating an account
   • It can be helpful to use a recognizable username.
   • May want to separate your personal account from your work account.
   • Associate your work email with account to get a free micro plan:
     • Improving GitHub for science
     • Request a discount
2. Docs
   • help.github.com
   • guides.github.com
   • TGI Code Review
3. Profile
   • Repositories, Followers, Starred, Following
4. Settings
   • Profile
     • It can be helpful to set your avatar. I recommend a portrait.
   • Emails
     • Associate your work email for free micro plan.
   • Security
     • Password security and two-factor authentication.
   • Notification center
     • Email vs. web vs. RSS
     • watching, automatically watching repos you have push access to
     • per-organization email routing
5. News Feed
   • Watching repos and followed users
6. Issues
   • Labels, Milestones
7. Pull Requests
   • Various links, dest repo, source repo, pull request.
   • Status (icon and link)
8. Creating a repo
9. Forking
10. Search
11. Keyboard Shortcuts
12. Setting up SSH key(s)
    • "Password-less" Git access
    • GitHub Help: Generating SSH Keys
    • ssh-add -K or Setup Keychain to Manage SSH Keys
13. Writing on GitHub
    • GitHub Help: Markdown Basics
    • GitHub Help: GitHub Flavored Markdown
    • GitHub Help: Writing on GitHub
      • References and Mentions

The Genome Organization

1. Personal Repos vs. Organization Repos
   • Create GitHub Organizational Repo
2. Organization RSS Feed
3. Where should we fork this repository?

Introduction to APIPE Code Review

1. How do I install 'hub'?
   • create, fork, pull-request
2. How do I fork a repository?
3. How do I make a pull request?
4. How do I review a pull request?
5. How do I know my pull request will be (or has been) reviewed?
6. How do I git checkout a pull request?
7. Merge Pull Request
8. Introduction to CI
   1. Travis CI
      • Travis CI Documentation
      • Examples: Perl, C++, Ruby, Python
   2. apipe-ci
      • Use Travis CI unless you need access to internal resources (not ideal).
      • Get APIPE to set it up.
      • Examples
      • genome/genome secret phrases:
        • Can one of the admins verify this patch?
        • CI, add author to whitelist. (.*CI\W+add\W+author\W+to\W+whitelist.*)
        • CI, test this. (.*CI\W+test\W+this.*)
        • CI, test this once. (.*CI\W+test\W+this\W+once.*)
        • CI, skip this. (.*CI\W+skip\W+this.*)
      • Details link.
   3. Lots of other services. Use what you want. Be aware of trade-offs.
      • drone.io
      • coveralls.io
9. Questions/Policies
   • To +1/+2 or not.
   • To require/encourage multiple +1/+2 or not.
   • How long to wait before merge.
   • How aggressive to be with closing pull requests.
   • Should you wait for new +1/+2 if you push new commits?
10. Comments
    • Make sure you leave a comment on the pull request if you push new commits. Otherwise no notification is sent.
    • Comment threading.
    • Mark moved Ptero repos from his username to genome and it transferred issues and pull requests successfully.

Looks good! A couple of small suggestions:

As part of creating an account, I would strongly advise (require?) that they set up 2 factor authentication of some sort.

As part of notifications, I might talk about the notification center vs. email and how to pick which notifications go where.

Thanks. I'll mention 2 factor and password security. "Email vs. web" is "notification center vs. email".

Looks good ! One thing I'd be interested in learning about and I'm not sure if it already falls in one of the above categories is the dev-cycle. Lets say if I'm working on two different sub projects on the same repo do I make a branch for each of them and work on them separately. When I commit these back do I merge them both locally and submit one pull request or do I submit separate pull requests for the branches, do I delete the branches after that, basically just a brief and basic overview of the git workflow. Obviously this could be a session in itself but I think it might be helpful when we talk about how pull requests usually deal with one specific issue in a repo.