Chapter 4 - Distributed Version Control (Git/GitHub)#

Authors: Daniel J. B. Clarke

Maintainers: Daniel J. B. Clarke

Version: 0.1

License: CC-BY-NC-SA 4.0

Setup#

Download & Install Git#

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Download Git : https://git-scm.com/download

Git Documentation: https://git-scm.com/doc

Git Cheat Sheets: https://training.github.com/downloads/github-git-cheat-sheet/ https://ndpsoftware.com/git-cheatsheet.html

Fig. 6 https://git-scm.com#

Create an Account on GitHub#

GitHub is a complete developer platform to build, scale, and deliver software. It’s primary use is for software development and version control using git.

GitHub Sign Up: https://github.com/signup

GitHub Documentation: https://docs.github.com

Fig. 7 https://github.com#

Download & Install Visual Studio Code#

Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux.

Visual Studio Code Download: https://code.visualstudio.com/download

Visual Studio Code Documentation: https://code.visualstudio.com/docs

Fig. 8 https://code.visualstudio.com#

Install Git Lens Visual Studio Code Extension#

GitLens supercharges Git within VS Code – Visualize code authorship at a glance via Git blame annotations and CodeLens, seamlessly navigate and explore Git repositories.

Install in Visual Studio Code:

ext install eamodio.gitlens

Fig. 9 https://gitlens.amod.io/#

Configuring Git#

First Time Git Setup#

The first thing you should do when you install Git is to set your user name and email address. This is important because every Git commit uses this information, and it’s immutably baked into the commits you start creating (for more information, see git’s docs on the subject).

Run these commands in your terminal after git is installed, replacing the name and email address with your own:

git config --global user.name "John Doe"
git config --global user.email johndoe@example.com

Configuring GitHub#

Creating an RSA Key-Pair for Secure GitHub Access #

Generating a new SSH key #

Adding a new SSH key to GitHub #

Creating a GitHub Repository#

Fork the Demo Project on GitHub#

https://github.com/ maayanlab /github-project-demo

Using Git#

Clone your Fork#

The username will change from maayanlab to your github username for your fork.

You can use Visual Studio Code and/or the git command line to clone the repository from the url.

Open & Explore the Project’s History#

History can be accessed both using Git Lens or via command line with git log --all --graph

Each item is a change to the code, changes can also be performed concurrently in other “branches”.

Navigating Git#

Git Workflow at a Glance#

Staging a Commit#

After making changes to a file, we’re able to review the “diff” in visual studio code(git diff --cached). Once satisfied we can “stage” files with the “+” (or git add ) and commit them with a message (git commit).

Effects of a Commit#

Commit exists in our local repo, but not in the remote repo “origin” until we “sync” (git push)

origin/master is where github’s branch is

master is where our branch is

HEAD is where our workspace is

Browsing the Past#

Our workspace now has the state it did before we made the change

We can always get back to the state at any commit (git checkout).

Creating a New Branch#

A branch is useful to work from a previous state, they are inevitable when multiple people are working on the same project at the same time.

Cherry-Picking#

Cherry-pick applies the changes in a commit on top of the current branch

Merge#

A merge will converge two branches into one, applying changes from both on top of each other. Most of the time this works automatically, some time manual review is required to address parallel changes to the same thing.

Merge Conflict Resolution#

A conflict will occur if two people edit the same line. We must accept one or the other, or manually merge the divergent code, save and stage the updated file.

Merge Commit#

A commit message is automatically generated during a merge.

When done, our branch contains changes from master, the without-test branch, and our test.py capitalization changes.

Our previous local master branch is now redundant and no longer needed, let’s clean it up by moving it to be the same as new-branch.

Git Reset#

Pushing to GitHub#

Changes are then available on github through the UI and to other collaborators using git to update.

Getting New Repository Changes#

Visual Studio Code runs git fetch periodically automatically, but git fetch will obtain new changes made to the remote repository that aren’t yet incorporated into your local branch.