[Biopython-dev] biopython on github

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Mon Feb 23 13:31:00 UTC 2009

On Sun, Feb 15, 2009 at 4:29 PM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> Hi,
> I have uploaded a git-converted branch of biopython on github, in case
> you want to try it and see how it works.
> You can find it here:
> - http://github.com/biopython/biopython/

Hi people,
so, I am still testing biopython on git.

The function to convert a cvs repository to git works well: I have
just updated the branch on github to the latest cvs commit in
open-bio, and it has correctly imported all the new commits without
mixing them with the old ones.

Now, if you look at http://github.com/biopython/biopython/network ,
you can see the results from all these experiments: the black line
represent the code imported from cvs, and the other ones are
experiments (well, don't care about the red one).

For example, let's say you want to test the fix to the SwissProt
parser commented by Andrea.
You could create a new experimental branch, make it publicly
accessible, and put all the changes there: only when you will consider
it finish, you will merge it with the official one.
The advantage of doing this is that two people or more are able to
work on the same patch at the same time, and without having to touch
the official code.

> To work with it, the optimal protocol is:
> - create an account on github.com. Upload an ssh public key by
> clicking on 'account' after having logged in.
> It is not mandatory to use github, but it will help you understanding
> how git works, and it allows other people to follow your branches and
> your work.
> - 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 at 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
> p.s.: to convert to git from cvs I have followed the instructions here:
> - http://www.kernel.org/pub/software/scm/git/docs/v1.4.4.4/cvs-migration.html
> This seems to be a good tutorial on git, too:
> - http://www.kernel.org/pub/software/scm/git/docs/v1.4.4.4/tutorial.html
> --
> My blog on bioinformatics (now in English): http://bioinfoblog.it


My blog on bioinformatics (now in English): http://bioinfoblog.it

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