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Git overview

Essentially, all version control does is store snapshots of your work in time, and keeps track of the parent-child relationships.

From [Pro Git]( Pro Git

You can think of your current set of working files as simply the child of the last node in this chain (that is, your files are the children of the most recent set of files known to the version control system).

git provides a large number of tools for manipulating this history. We’ll only touch on a few, but the number that you need to know for day-to-day use is actually quite small.

First, we’re going to need some terminology:

  • Repository: “Repo” for short; this is a copy of the history of your project. It is stored in a hidden directory within your project. People will talk about “cloning a repo” or “adding things to a repo”; these all manipulate the history in some way.
  • Working directory: This is your copy of a project. It’s just a directory with files and other directories in it. The repository is contained within a .git directory at the root directory of your project.

One of the distinguishing and great features about git is that the repo contains the entire history of the project, i.e. if your project moves, the history travels with it. So if you clone your work to a new computer, or a collaborator gets involved (more on how to do that later), they have the full project history available. This is called distributed version control.

What goes in my repository?

You should establish a new repo for each project you are working on. As we discussed previously) the project folder should contain everything related to a particular project, including inputs (data, images, notes), analysis scripts and outputs (figures, tables.) The content of your project will evolve over time and this will be tracked within the git repo.

But not all of your project folder contents will be stored within the git system. As a general guide, we suggest you make a folder called outputs. This is where you should save figures and other outputs from your analysis scripts. These outputs do not need to be tracked, as they can be reproduced at any time by rerunning the script. Later we’ll show you how to ignore certain files in git.

The commit cycle

Your project develops as you do work. During this process you make a series of small changes such as

  • writing some code
  • importing/entering new data
  • reorganising your files
  • making a figure
  • writing bits of reports or papers.

The idea with git is that you break up your project activity into a series of small tasks, each corresponding to a ‘commit’. So the cycle goes

Checkout project –> do work –> review changes –> commit

Anecdotal evidence suggests experienced programmers break up their project into lots of small pieces, and have lots of commits in their work cycle, while novices tend to have fewer, larger commits. some of the advantages of small commits are

  • helps you to focus on one small piece of a much larger puzzle
  • it’s easier to recover if something goes wrong
  • you have a greater sense of achievement.

In the software carpentry module we attended, Greg Wilson suggested we aim for work cycle of about 1 hr.

You should aim to only commit once a piece of code works, so that you leave your code in working order. Thus

Commits serve as checkpoints where individual files or an entire project can be safely reverted to when necessary.