02' Git Basics

Before we resume our Introduction to Python, we will start with a short introduction to version control systems and in particular Git.¹

A version control system (VCS) manages files and tracks changes to those files. It stores the complete history and allows you to recover files at any stage of the history (think "undo" to the beginning). Any serious software project uses version control but its uses go beyond software, e.g., documents and data can also be version controlled.

A set of changes is called a commit. It typically contains changes to multiple files. It also contains a timestamp, information about the user who made the changes, and a commit message that explains the changes. The history consists of all the commits. The VCS stores the history in a storage area called a repository.

Modern distributed VCS such as Git or mercurial make it easy for multiple developers to work on the same project. They have support for merging changes from different people into a single new file, and for resolving conflicts, i.e., the case when the same part of a file was changed (the changes "collided"). Online platforms such as GitHub or Bitbucket provide free repositories in the cloud (but you don't need these platforms to use a VCS!).

We will use Git. For the class you should get into the habit to version-control your work: in class notes, home works, and projects. You will later use GitHub to submit code that you develop as part of your assignments and projects.

1. Tutorial
2. Set up your own GitHub repositories
3. Class resources on GitHub
4. Additional resources

Tutorial

Let's use git to manage what we have done so far.

Configuring Git

The first time you use git you need to tell it who you are: this information will be the user information in the commit history. (Use your own name and email address!)

git config --global user.name "Darth Vader"
git config --global user.email "dvader@empire.gov"
git config --global color.ui "auto"

You also tell it how to color output and what editor to use to write commit messages ².

# choose your favorite editor
# Windows users: First try without executing this command.
#                If you have problems with 'git commit' later, ask!
git config --global core.editor "nano -w"

You can see a list of all your configuration settings with git config --list.

Git commands always follow the pattern git <verb> [options] [arguments ...]. In particular, --help is always an option. Also try git help and git help tutorial.

Creating a repository

You alread should have a PHY494 directory in your home directory with a layout like the following (where 01_shell might contain other folders and documents):

~/PHY494/
        01_shell/
        02_python/
		         gutentag.py

Make the PHY494 directory a repository with the git init command:

cd ~/PHY494
git init

That's it. Although, not much happened yet… except, check with

ls -la

A new hidden directory ~/PHY494/.git/ appeared. This is your actual repository where Git stores all its information. Do not change anything in this directory (unless you really know what you are doing) and do not delete the .git directory. If you delete it, your repository is irrevocably gone (and there is no undo for that!).

Now try the (possibly) most-used git command:

git status

Adding files

Prepare the files to be committed to the repository: git add adds files and directories to a "staging area":

git add .
git status

(Use git reset FILENAME to unstage any files that you might have added accidentally.)

The files are not committed yet. You can do more work, add more files…

Committing

git commit

• When your editor pops up, enter a commit message: Convention:
  • first line (<60 char): one line summary
  • second line: blank
  • third and following lines: more details The first line is mandatory (you cannot have a commit without a message), the rest is optional.
• After you wrote and saved the message (in nano, ^O; in vim, i to write, ESC :wq to save and exit) and exited (^X in nano), your changes will be committed to the repository.
• You can also supply the message as an argument: git commit -m "one line summary of changes".
• Check the status with git status…

For a new commit, add files and commit again.

History

Read the history with

git log

Removing and renaming files

Removing files and directories via git allows you to get them back later.

git rm FILENAME
git rm -r DIRECTORY

Renaming is the same as removing the old file and adding the new one but there is also a simple command

git mv OLD NEW

The git rm and git mv commands are similar to the git add command in that they stage these changes; you still have to commit them.

Working with remote repositories

Initialize a local repository from a remote source:

git clone URL

If you haven't done so earlier, clone the repository where code and data will be posted:

cd ~
git clone https://github.com/ASU-CompMethodsPhysics-PHY494/PHY494-resources-2016.git
cd PHY494-resources-2016

Note:

• The local name of your repository can be any name you like but it is customary (and less confusing) if you go with the default, which is the remote repository name without the ".git" suffix, i.e., PHY494-resources-2016 for us.

• For all other git commands you must be inside your local repository:

    cd ~/PHY494-resources-2016
  

Update your local repository with any "upstream" changes:

git pull

Update the remote repository with you local changes (commits):

git push

(For "pushing" to work, you must be allowed to write to the remote repository; this will not work for PHY494-resources-2016 but we will use it below for your own GitHub repositories).

Contributing to Open Source on GitHub

GitHub enables you to easily contribute to other projects. This includes

• filing bug reports or feature requests (raising issues); for instance, if you do not agree with some of the Star Wars data from the previous lessons, raise an issue in the issue tracker for the PHY494-auxilliary repository.
• proposing to add your own code and changes through pull requests (but this is too advanced for a our short introduction today — see the additional resources under More…).

Set up your own GitHub repositories

1. Go to https://github.com and create a new account. It is free.³ Remember your GitHub username and the password.
2. Create a new repository PHY494-class.
3. Note the repository URL https://github.com/USERNAME/PHY494-class.git

4. Add the remote repository to your repository (replace USERNAME with your GitHub username):

    git remote add origin https://github.com/USERNAME/PHY494-class.git
   

   We named the remote "origin", which is a common choice for the main repository. You can have many different remotes, just give them different names. You can list them with

    git remote -v
   

5. push your local history to the remote repository:

    git push --set-upstream origin master
   

   You need to enter your username and password ⁴.

   You only need the --set-upstream origin master (or -u origin master) for the first time (it tells git which "branches" to associate with each other in local and remote) ⁵. All further push operations will then simply be

    git push
   

   Look at the web interface at https://github.com/USERNAME/PHY494-class and see your changes appear.

For the rest of the semester, commit what you did during each class session to the repository.

Class resources on GitHub

Notebooks and files are being made available on GitHub in the repository ASU-CompMethodsPhysics-PHY494/PHY494-resources-2016. If you have not done so already:

cd ~
git clone https://github.com/ASU-CompMethodsPhysics-PHY494/PHY494-resources-2016.git

Update:

cd ~/PHY494-resources-2016
git pull

You should get a new file, 02_python/02-intro-python.ipynb. Copy it to your class directory:

cp ~/PHY494-resources-2016/02_python/02-intro-python.ipynb ~/PHY494/02_python/

and create a new commit with it:

cd ~/PHY494/02_python/
git add 02-intro-python.ipynb
git commit -m "Lesson 02 Intro to Python notebook"

Open the notebook (jupyter notebook) and then we will continue with 02 Introduction to Python.

At the end of today's class, commit your changes to the notebook and push to your github repository.

More…

• For a longer introductory tutorial see the Software Carpentry lesson on Version Control with Git.
• Interactive in-browser lesson Try Git, takes 15 minutes.
• Blischak JD, Davenport ER, Wilson G (2016). A Quick Introduction to Version Control with Git and GitHub. PLoS Comput Biol 12(1): e1004668. doi:10.1371/journal.pcbi.1004668
• For in-depth discussion read the Pro Git book by Scott Chacon and Ben Straub.

Footnotes