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

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

Obtaining the source code

If you don't want to make any changes, you can simply download a zipped up archive of the latest code from github. Very easy - and you don't even need to install git on your computer to do this.

If you want to make changes, then there are two ways of getting the code tree onto your machine. 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.

Forking without a github account

Getting a copy of the repository without github account is very simple:

 git clone git://github.com/biopython/biopython.git

This command creates a local copy of the Biopython source on your machine (your own personal branch of the code, with the full history to date). You can now make local changes and commit them to this local copy.

However, if you want other people to see your changes you need to take care of publishing your branch yourself. 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

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

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 git@github.com:<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, selecte 'edit' and then add them to the 'Repository Collaborators' section. You will need to know their username on GitHub.

Making changes

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, it can be deleted by selected 'edit' and then 'delete repository' from the bottom of the edit page.

Other information

There is a lot of different nice guides to using git on the web:

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