Source Control

Intro to Git

Git is a version control tool. It is used to keep track of how text gradually changes in code. Here are the commands to get started:

$ git clone https://github.com/[OWNER]/[REPO].git # Download a repo from Github
$ git status # View changed files
$ git diff [FILE] # View what the changes are in the repo, differences in just a set of files in the repo
$ git add NEW_FILE # Tell git that you want it to start track changes in this file from now on
$ git stage TRACKED_FILE # Specify what files you want to save
$ git commit –m “DESCRIBE WHAT YOU CHANGED” # Locally save changes in staged files and start tracking changes in newly added files
$ git push # Sync github server’s version of the repo's files with local repo. Allows everyone to see your changes.

Github Usage

Make a github.com account and give the username to Jeff (jeffrey.maurer@pennmedicine.upenn.edu). We can add you as a contributor if you are here long-term in the dry lab. We prefer that as few hands touch the main branches as possible.

In .gitignore, add “*_small*” and “*_toy*” for projects where new ground will be broken, requiring small test data.

Intro to Virtual Environments

The lab’s hippa directory has a software directory that has a virtual environment subdirectory. Read the README.md file for usage. We intend for all analyses to be done in a virtual environment in the future to ensure our work is fully and easily reproducible.