GitMigration

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Migration from CVS to Git

We are currently testing the benefits of migration to git distributed version control.

Currently we have a git repository hosted at github.com:

http://github.com/biopython/biopython/

This is the official branch, it's 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.

Below you can find rudimentary instructions on how to develop biopython with git.

Prerequisites

Installing git

First, you need to have git installed on your computer.

Git (http://git-scm.com/) is now available for all major operating systems, you can get it

  • Linux: Git is now packaged in all major linux distributions, you should find it in your package manager.
  • Mac OS X: http://code.google.com/p/git-osx-installer/
  • Windows: There are two options: [[MsysGit][1]] or running the compiled git under Cygwin. You can find more information in [[this github guide][2]]


Getting a github account (Optional)

Once you have git installed on your machine, you can get the code and start developing, However, since the code is hosted at github, you can use more features if you sign up for github account. This is completely optional but if you do sign up all other developers will be able to see (and review) the changes you have made.

If you dan't already have a github account:

  • create one here http://github.com/plans (the free plan is absolutely enough)
  • Upload an ssh public key by clicking on 'account' after having logged in

Getting the source

- go to the biopython repo:

http://github.com/biopython/biopython/tree/master

and you will see a button named 'Fork': click on it. It will create a fork of the official biopython repository your personal account. Here the word 'fork' is not used in the common way it is, but just to indicate that you are going to work on a modified version of the official code, and it's not even a git command.


- now, install git on your computer, and execute the following commands: $: git clone git@github.com:<your username>/biopython.git $: git remote add official_dist git://github.com/biopython/biopython.git

With the first command, you will download a copy of the repository on your local computer, which will be the one you will modify (technically, you are creating a new branch on your computer). With the second command, you are adding a reference to the official biopython repository, so in the future you will be able to easily import the official code and compare it with yours.

Here it is an explanation on these two commands: http://github.com/guides/keeping-a-git-fork-in-sync-with-the-forked-repo

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