marp slides and material for git talk
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In order to participate, your environment should have:

  1. git is installed on your computer
  2. A text editor (such as atom) installed on your computer
  3. A github account setup
  4. You must know your password for github and your email

Give your Github username to the TAs! Once you've been invited, we can get started.

If you didn't bring a computer, or are unfamiliar with terminal commands, make a friend

BioData Club

Thanks to OHSU for hosting

Thanks to Philip, Ted, Lisa, Robin

Intro to Git

This talk will not cover, or expect, specific programming languages This talk will:

  1. Introduce a collaborative demo using git and Github
  2. Introduce vocabulary for using git and Github
  3. Understand a simple git workflow
  4. Talk about access control and Github


If you successfully finish workshop, you will

  • be able to collaborate on simple projects using git and Github
  • understand basic vocabulary for git
  • know what to study next and where to find resources

Why should you Care?

  • No more emailing document revisions
  • Simpler local directory/file structures
  • Remote storage
  • Stable workflow
  • Easily add new collaborators to project
  • The world's most boring time machine

Your Project!

After I assign you an issue of content,

  • add text contents of issue to the file
  • belonging to an existing repository
  • in alphabetical order.
  • Finally, use git to share your changes

A is for Amy who fell down the stairs
B is for Basil assaulted by bears
C is for Clara who wasted away
Z is for Zillah who drank to much gin

What is Git?

  • Source and version control
  • Ledger of work
  • Collaboration tool
  • Workflow management software

competes with : hg, svn, cvs

What is Github?

  • Git service provider
  • Account management and access control
  • Hosting platform
  • Ticket tracker / project management tool

competes with : GitLab, bitbucket,

What to store in Github?

  • source code (any language)
  • markdown / Jupyter / pdf
  • small public (images & data-sets)

What NOT to store?

  • PASSWORDS, access tokens, or private keys
  • PHI, large images, large data-sets
  • compiled binaries
  • Non-pars-able documents (Word, Photoshop, ...)

Vocabulary (I)

  • Working Copy - version of files I can currently edit
  • diff, status, log - What state am I in?
  • checkout - swaps current working copy to specific commit

Vocabulary (II)

  • remote labels that alias another location (host)

Vocabulary (III)

  • init / clone - Starts a Project

  • add/commit add to ledger history - Tracks Changes

  • fetch/merge Join multiple ledgers and handle merge conflicts

  • push - Share Changes

Merge Conflicts

$ git status
# On branch branch-b
# both modified:
$ cat
If you have questions, please
email a contributor.
$ cat
If you have a question, please open an issue on
github. If you have a solution, please submit
a pull request.

Workflow Map

simplest git workflow

Message Flag and Editor

If you don't use the -m message flag, you will likely be subject to vim. vim can be a very frustrating file editor, if you don't bother to learn it.

Look into how to change your default EDITOR for your operating system.


To exit vim, Hit the Esc key to enter "Command mode". Then you can type : to enter "Command-line mode". A colon (:) will appear at the bottom of the screen and you can type in one of the following commands. To execute a command, press the Enter key.

  • :q to quit (short for :quit)
  • :q! to quit without saving (short for :quit!)
  • :wq to write and quit

Defaults and config

$ git config --global "John Doe"
$ git config --global

The Fatal Lozenge

Rules of the Game (15 min)

  • 10 people per repository team {red, blue, black}
  • Each panel represents one entry from poem
  • Split panel text lines with <= 80 characters
  • Panels ordered alphabetically (by second word)
  • Your team is done when all panels added
  • Do a diff against origin/master before a merge
  • Review the log at least once (q to quit)
team == red

Git Commands

  • status, diff, log
  • clone, init
  • fetch, merge, commit, push, fetch
$ git clone
Cloning into 'ABC'...
remote: Counting objects: 500, done.
remote: Compressing objects: 100% (36/36), done.
remote: Total 500 (delta 27), reused 33 (delta 12), pack-reused 451
Receiving objects: 100% (500/500), 6.72 MiB | 1.71 MiB/s, done.
Resolving deltas: 100% (286/286), done.
Checking connectivity... done.


  • Complete the Game
  • Signal TAs for help if you get stuck!


$ cat secrets.json # this file should not be committed
import json

# this file should be committed

with open('secrets.json') as fd:
    pwd = json.load(fd)['password']



Can specify file types or specific files to not commit

Each line is a file type or filename

  • can use wildcard patterns: .csv
  • don't save my secrets.json

Github activities

  • Code reviews
  • Create / destroy user and organization accounts
  • Access control
  • Create / destroy repository
  • Issue creation / assignment / management
  • Gists

Collaborating without Permission

Collaboration within a team is different than from outside, as a consequence of access control.

  • fork - Copies repository
  • pull request - Shares changes back to source


  1. fork repository on Github
  2. clone forked repository to local directory
  3. add upstream directed toward original repository
  4. Edit files, save, commit, then push changes in forked repository
  5. pull request against original repository


Branching allows

  • encapsulation of features
  • simple diffs between features
  • easier pull requests

Collaboration Etiquette

  • Look for a file
  • Look for style guides
  • Read documentation before collaborating
  • Take code review feedback seriously and not personally
  • Identify an appropriate issue for your skill level
  • rebase -i to encapsulate solution to single issue

To Learn Next

  • checkout - use another version as working copy
  • branch - encapsulate work
  • rebase/rebase -i - edit branch history
  • Learn about branching models
  • Learn about version numbers

Additional Resources