Chapter 5 Where to go from here -- contributing to Biopython

5.1 Maintaining a distribution for a platform

We try to release Biopython to make it as easy to install as possible for users. Thus, we try to provide the Biopython libraries in as many install formats as we can. Doing this from release to release can be a lot of work for developers, and sometimes requires them to maintain packages they are not all that familiar with. This section is meant to provide tips to encourage other people besides developers to maintain platform builds.

In general, this is fairly easy -- all you would need to do is produce the system specific package whenever we make a release. You should then check the package (of course!) to make sure it installs everything properly. Then you just send it to one of the main developers, they stick the package on the web site and just like that, you've contributed to Biopython! Snazzy.

Below are some tips for certain platforms to maybe get people started with helping out:

RPMs

-- RPMs are pretty popular package systems on some platforms. There is lots of documentation on RPMs available at http://www.rpm.org to help you get started with them. To create an RPM for your platform is really easy. You just need to be able to build the package from source (having a C compiler that works is thus essential) -- see section 1.3.1 for more info on this.

To make the RPM, you just need to do:

python setup.py bdist_rpm

This will create an RPM for your specific platform and a source RPM in the directory dist. This RPM should be good and ready to go, so this is all you need to do! Nice and easy.

Windows

-- Windows products typically have a nice graphical installer that installs all of the essential components in the right place. We can use Disttutils to create a installer of this type fairly easily.

You must first make sure you have a C compiler on your Windows computer, and that you can compile and install things (see section 1.3.2 for info on how to do this.

Once you are setup with a C compiler, making the installer just requires doing:

python setup.py bdist_wininst

Now you've got a Windows installer. Congrats!

Macintosh

-- We would love to find someone who wants to maintain a Macintosh distribution, and make it available in a Macintosh friendly format like bin-hex. This would basically include finding a way to compile everything on the Mac, making sure all of the code written by us UNIX-based developers works well on the Mac, and providing any Mac-friendly hints for us.

Once you've got a package, please test it on your system to make sure it installs everything in a good way and seems to work properly. Once you feel good about it, send it off to one of the biopython developers (write to our main list serve at biopython@biopython.org if you're not sure who to send it to) and you've done it. Thanks!

5.2 Bug Reports + Feature Requests

Getting feedback on the Biopython modules is very important to us. Open-source projects like this benefit greatly from feedback, bug-reports (and patches!) from a wide variety of contributors.

The main forums for discussing feature requests and potential bugs are the biopython development lists:

biopython@biopython.org -- An unmoderated list for discussion of anything to do with biopython.
biopython-dev@biopython.org -- A more development oriented list that is mainly used by developers (but anyone is free to contribute!).

Additionally, if you think you've found a bug, you can submit it to our bug-tracking page at http://www.biopython.org/biopython-bugs/. This way, it won't get buried in anyone's Inbox and forgotten about.

5.3 Contributing Code

There are no barriers to joining biopython code development other than an interest in creating biology-related code in python. The best place to express an interest is on the biopython mailing lists -- just let us know you are interested in coding and what kind of stuff you want to work on. Normally, we try to have some discussion on modules before coding them, since that helps generate good ideas -- then just feel free to jump right in and start coding!

The main biopython release tries to be fairly uniform and interworkable, to make it easier for users. You can read about some of (fairly informal) coding style guidelines we try to use in biopython on the wiki site at http://biopython.org/wiki/html/BioPython/PythonStyle.html. We also try to add code to the distribution along with tests (see section 4.2 for more info on the regression testing framework) and documentation, so that everything can stay as workable and well documented as possible. This is, of course, the most ideal situation, under many situations you'll be able to find other people on the list who will be willing to help add documentation or more tests for your code once you make it available. So, to end this paragraph like the last, feel free to start working!

Additionally, if you have code that you don't think fits in the distribution, but that you want to make available, we maintain Script Central (http://biopython.org/ScriptCentral.shtml) which has pointers to freely available code in python for bioinformatics. Just let us know on the mailing list, and we'll be happy to add links to your code.

Hopefully this documentation has got you excited enough about biopython to try it out (and most importantly, contribute!). Thanks for reading all the way through!