sciware

Sciware

Intro to GitHub

https://sciware.flatironinstitute.org/21_IntroGithub

https://github.com/flatironinstitute/learn-sciware-dev/tree/master/21_IntroGithub

Rules of Engagement

Goal:

Activities where participants all actively work to foster an environment which encourages participation across experience levels, coding language fluency, technology choices*, and scientific disciplines.

*though sometimes we try to expand your options

Rules of Engagement

• Avoid discussions between a few people on a narrow topic
• Provide time for people who haven’t spoken to speak/ask questions
• Provide time for experts to share wisdom and discuss
• Work together to make discussions accessible to novices

(These will always be a work in progress and will be updated, clarified, or expanded as needed.)

Zoom Specific

• Dedicated Zoom moderator to field questions.
• Please stay muted if not speaking. (Host may mute you.)
• We are recording. Link will be posted to https://sciware.flatironinstitute.org/.

Future Sessions

• Tomorrow: GitHub Part 2: collaboration
• June 29: Showcase of code editors, development environments (show & tell)
• July 21 (preliminary): Shells, environments, command-lines

Today’s Agenda

• What is Git and GitHub?
• Setting up git and GitHub on your computer
• Getting code off of GitHub
• Putting code onto GitHub

Intro to Git and GitHub

Version control

• keeps track of the edit history to one or more files
• serves as a backup
• makes it easier to collaborate and combine multiple changes to the same file

an open-source, distributed, command-line, version-control tool

• released in 2005 by Linus Torvalds for Linux kernel (alternative to CVS, svn, ...)
• dominant tool for academic and industry software development
• distributed: no central server, every repo is fully functional, independent, and can "sync" with any other

GitHub

• A central website for storing and sharing git repositories
• Started in 2008 as a freemium service, now owned by Microsoft
• Provides repository management, permissions, collaboration tools, CI, etc.
• Alternatives: gitlab, bitbucket, …

Setting up GitHub on your Computer

Make sure git is installed

 > git version
git version 2.30.1

If this returns an error, please raise your hand or put a yellow sticky on your laptop.

Setting your name in Git

See what name is currently set

 > git config --global user.name

Set your full name

 > git config --global user.name "Mona Lisa"

Setting your email address

See what email address is currently set

 > git config --global user.email

Set an email address

 > git config --global user.email "youremail@flatironinstitute.org"

(Ideally set to the same email address you used for GitHub account)

Generate an SSH key

 > ssh-keygen -t ed25519

• We’re going to generate a new key (one you hopefully don’t have already)
• It is easiest to leave the passphrase blank

 > cat ~/.ssh/id_ed25519.pub
ssh-ed25519 AAA..... user@host

Copy this whole line to the clipboard

Add the SSH key to GitHub

• On GitHub:
  • Profile Photo > Settings > SSH and GPG keys > New SSH Key

Add the SSH key to GitHub

• Title should refer to the computer on which the key was generated.

• Paste key into text box.

Setup Git’s default text editor

So that you don’t get stuck in vi:

 > git config --global core.editor "nano -w"

How to set up your favorite editor with Git:

https://git-scm.com/book/en/v2/Appendix-C%3A-Git-Commands-Setup-and-Config#ch_core_editor

Questions?

Getting code from GitHub onto your computer

GitHub Jargon

• Directory containing the code
  • repository or repo, for short
• "Download the code"
  • clone the repo
• Your computer drive
  • local

Download the code to your computer in GitHub-ese is Clone the Repo to your local

Clone the repo

• Go to the repo on the GitHub website
  • https://github.com/ flatironinstitute/sciware21-git-intro
• Click Green Code button
• Choose SSH tab
• Click the clipboard icon to copy the repo path

Clone the repo (continued…)

• In a Terminal window, clone the repo:

 > git clone git@github.com:flatironinstitute/sciware21-git-intro
> cd sciware21-git-intro

• A directory will be created containing all of the files in the repo.
• The directory name will be the repo name.

What does git clone do?

• Using the git clone command connects the directory to the repo on GitHub in case you ever wanted to interact with it later.
• It generates hidden directory .git

 > ls -a

• It also saves the URL to the repo and names it origin

 > git remote -v
origin  git@github.com:flatironinstitute/sciware21-git-intro (fetch)
origin  git@github.com:flatironinstitute/sciware21-git-intro (push)

Questions?

Activity

Find a repo and clone it to your computer

https://github.com/explore

Survey

http://bit.ly/sciware-github1-2022

Putting code on GitHub

Make a project directory (folder)

 
> cd #out of sciware21-git-intro
> mkdir silly_repo
> cd silly_repo
> touch silly_code.py
> touch silly_file.txt

Create a repo on GitHub

• Go to your homepage on GitHub
• Click the Repositories tab
• Click the green New button
• Name the repository silly_repo

Initialize the directory to use with GitHub

> git init
> git status

Name the primary branch main

• It’s possible to have multiple branches of the code where different things are being worked on.
• The primary branch is usually called main.

> git branch -M main
> git status

Notice:

• branch name
• silly_file.txt is in red and is untracked

Specify which files that you want to transfer

Use the git add command to specify exactly which files you want to transfer to GitHub.

> git status
> git add silly_file.txt
> git status

Notice:

• silly_file.txt is now green
• silly_file.txt needs to be committed

Save the changes

• Use the git commit to save the local changes.
• Add a commit message to document the changes.
• Launch a text editor where you can type the commit message:

 > git commit

Alternatively, you can commit directly from the command line:

 > git commit -m "add silly file"
> git status

What’s in a commit message?

• Like a comment in your code
• Says what you changed and why

Connect the repo to GitHub

• Use git remote add to provide the URL to the GitHub repo.
• The repo that is in your personal profile is usually called origin

> git remote -v
> git remote add origin git@github.com:kelle/silly_repo.git
> git remote -v

Upload the repo contents to GitHub

• Use the git push command to upload the committed changes to the GitHub repo.

 
> git push origin main

Check GitHub

silly_file.txt should now be in the repo on the GitHub website.

Questions?

Activity

• Push silly_code.py to the repo
• Put one of your projects into a new GitHub repo

Troubleshooting

• Find GitHub buddies
• The best way to figure things out is by asking folks for help

Troubleshooting

• Avoid problems by keeping track of the state of your local.
• Inspect git status before and after every command until you gain confidence

https://medium.com/@kenwarner/command-line-ux-matters-too-improve-your-git-status-colors-170de858953d

Troubleshooting

• There are many resources for common git and GitHub problems on the internet.
• Consider discussing with a buddy before copy/pasting.

Tomorrow

Using GitHub to collaborate

Survey

http://bit.ly/sciware-github1-2022