We are currently testing the benefits of migration to Git distributed version control.
This is the official repository. Currently it is synchronized with the main CVS trunk every hour, so it should be up to date most of the time. All developers and potential contributors are encouraged to try out this repository. Instructions on developing Biopython with Git follow below.
You will need to install Git on your computer. Git (http://git-scm.com/) is available for all major operating systems. Please use the appropriate installation method as described below.
Git is now packaged in all major Linux distributions, you should find it in your package manager.
You can install Git from the git-core package. e.g.,
sudo apt-get install git-core
You'll probably also want to install the following packages: gitk git-gui git-doc
Mac OS X
Download the .dmg disk image from http://code.google.com/p/git-osx-installer/
msysGit is a port of Git that runs natively on Windows via the MinGW library. Because Git was not originally designed to run on Windows, and since this is a port, some bugs exist, though are rarely encountered in everyday use of Git. See their website for download and installation instructions. Additionally, you can watch Scott Chacon's screencast on installing msysGit on Windows, and see this GitHub guide.
Cygwin provides a Linux-like environment for Windows. It includes access to repositories of many software packages available commonly in Linux distributions, including Git. You can find the git package under the "devel" category.
Creating a GitHub account (Optional)
Once you have Git installed on your machine, you can obtain the code and start developing. Since the code is hosted at GitHub, however, you may wish to take advantage of the site's offered features by signing up for a GitHub account. While a GitHub account is completely optional and not required for obtaining the Biopython code or participating in development, a GitHub account will enable all other Biopython developers to track (and review) your changes to the code base, and will help you track other developers' contributions. This fosters a social, collaborative environment for the Biopython community.
If you don't already have a GitHub account, you can create one here (the free plan is absolutely enough). Once you have created your account, upload an SSH public key by clicking on 'Account' after logging in. For more information on generating and uploading an SSH public key, see this GitHub guide.
Obtaining the source code
If you want to make changes, then there are two ways of getting the source code tree onto your machine: by simply "cloning" the repository, or by "forking" the repositon GitHub. They're not that different, in fact both will result in a directory on your machine containing a full copy of the repository on your machine. However, if you have a GitHub account, you can make your repository a public branch of the project. If you do so, other people will be able to easily review your code, make their own branches from it or merge it back to the trunk.
In fact you can change this later, using the .git/config file, but to make it easier I'll describe the two possibilities separately.
Cloning the repository without a GitHub account
Getting a copy of the repository (called "cloning" in Git terminology) without GitHub account is very simple:
git clone git://github.com/biopython/biopython.git
This command creates a local copy of the entire Biopython repository on your machine (your own personal copy of the official repository with its complete history). You can now make local changes and commit them to this local copy.
If you want other people to see your changes, however, you need to take care of publishing your branch to a public server yourself. Alternatively, using GitHub takes care of this for you.
Forking Biopython using a GitHub account
If you are logged in to GitHub, you can go to the Biopython repository page
and click on a button named 'Fork'. This will create a fork (basically a copy) of the official Biopython repository, still on publically viewable on GitHub, but listed under your personal account.
Now, assuming that you have Git installed on your computer, execute the following commands locally on your machine:
git clone firstname.lastname@example.org:<your username>/biopython.git
Where <your username>, not surprisingly, stands for your GitHub username. You have just created a local copy of the biopython repository on your machine.
You may want to also link your branch with the official distribution:
git remote add official_dist git://github.com/biopython/biopython.git
You can find more info here: http://github.com/guides/keeping-a-git-fork-in-sync-with-the-forked-repo
To add additional contributors to your branch on GitHub, select 'edit' and then add them to the 'Repository Collaborators' section. You will need to know their username on GitHub.
Now you can make changes to your branch. Since your local branch is a full repository, you can commit your changes as often as you like. In fact, you should commit as often as possible, because smaller commits are much better to manage and document. Let us assume you've made changes to the file Bio/x.py. You need to add this file to your change-set:
git add Bio/x.py
and now you commit:
git commit -m "added feature Y in Bio.x"
Your commits in Git are local, i.e. they affect only your working branch on your computer, and not the whole Biopython tree or even your fork on GitHub. You don't need an internet connection to commit, so you can do it very often.
Once you think your changes are fine and should be reviewed by others, you can push your changes back to the GitHub server:
git push origin
If you think you changes are worth including in the main Biopython distribution, then file an (enhancement) bug on Bugzilla, and include a link to your updated branch (i.e. your branch on GitHub, or another public Git server). You could also attach a patch on Bugzilla. If the changes are accepted, one of the Biopython developers will have to check this code into our CVS repository, and within the hour this should update the main Biopython branch on GitHub.
On GitHub itself, you can inform keepers of the main branch of your changes by sending a 'pull request' from the main page of your branch. Once the file has been committed to the main branch, you may want to delete your now redundant bug fix branch on GitHub. Branches can be deleted by selecting 'edit' and then 'delete repository' from the bottom of the edit page.
This section describes the steps to evaluate and integrate changes for Biopython core developers, or anyone accepting changes on a branch. The following commands will show you a diff of modifications on another branch. First add a reference to the remote repository, and fetch the changes locally:
git remote add username/biopython-mods git://github.com/username/biopython-mods.git git fetch username/biopython-mods
To double check the branch is integrated:
git branch -r
Finally, get the diff of the modifications:
git diff origin/master username/biopython-mods/master
If you later want to remove the reference to the branch:
git branch -r -d username/biopython-mods/master
Alternatively, from within GitHub you can use the fork-queue to cherry pick commits from other people's forked branches. See this github blog post for details. While this defaults to applying the changes to your current branch, you would typically do this using a new integration branch, then fetch it to your local machine to test everything, before merging it to your main branch.
There is a lot of different nice guides to using Git on the web: