# Where to go from here – contributing to Biopython

## 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 mailing list and issues or pull requests on GitHub.

Additionally, if you think you’ve found a new bug, you can submit it to our issue tracker at https://github.com/biopython/biopython/issues (this replaced the older Open Bioinformatics Foundation hosted RedMine tracker). This way, it won’t get buried in anyone’s Inbox and forgotten about.

## Mailing lists and helping newcomers

We encourage all our uses to sign up to the main Biopython mailing list. Once you’ve got the hang of an area of Biopython, we’d encourage you to help answer questions from beginners. After all, you were a beginner once.

## Contributing Documentation

We’re happy to take feedback or contributions - either via a bug-report or on the Mailing List. While reading this tutorial, perhaps you noticed some topics you were interested in which were missing, or not clearly explained. There is also Biopython’s built-in documentation (the docstrings, these are also online), where again, you may be able to help fill in any blanks.

## Contributing cookbook examples

As explained in Chapter Cookbook – Cool things to do with it, Biopython now has a wiki collection of user contributed “cookbook” examples, http://biopython.org/wiki/Category:Cookbook – maybe you can add to this?

## Maintaining a distribution for a platform

We currently provide source code archives (suitable for any OS, if you have the right build tools installed), and pre-compiled wheels via https://github.com/biopython/biopython-wheels to cover the major operating systems.

Most major Linux distributions have volunteers who take these source code releases, and compile them into packages for Linux users to easily install (taking care of dependencies etc). This is really great and we are of course very grateful. If you would like to contribute to this work, please find out more about how your Linux distribution handles this. There is a similar process for conda packages via https://github.com/conda-forge/biopython-feedstock thanks to the conda-forge team.

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

Windows

  – You must first make sure you have a C compiler on your Windows computer, and that you can compile and install things (this is the hard bit - see the Biopython installation instructions for info on how to do this).

RPMs

  – RPMs are pretty popular package systems on some Linux 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 the Biopython installation instructions 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.

Macintosh

  – Since Apple moved to Mac OS X, things have become much easier on the Mac. We generally treat it as just another Unix variant, and installing Biopython from source is just as easy as on Linux. The easiest way to get all the GCC compilers etc installed is to install Apple’s X-Code. We might be able to provide click and run installers for Mac OS X, but to date there hasn’t been any demand.

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, make a pull request on GitHub and write to our Biopython mailing list. You’ve done it. Thanks!

## Contributing Unit Tests

Even if you don’t have any new functionality to add to Biopython, but you want to write some code, please consider extending our unit test coverage. We’ve devoted all of Chapter The Biopython testing framework to this topic.

## 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 in the contributing documentation at http://biopython.org/wiki/Contributing. We also try to add code to the distribution along with tests (see Chapter The Biopython testing framework for more info on the regression testing framework) and documentation, so that everything can stay as workable and well documented as possible (including docstrings). 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!

Please note that to make a code contribution you must have the legal right to contribute it and license it under the Biopython license. If you wrote it all yourself, and it is not based on any other code, this shouldn’t be a problem. However, there are issues if you want to contribute a derivative work - for example something based on GPL or LPGL licensed code would not be compatible with our license. If you have any queries on this, please discuss the issue on the mailing list or GitHub.

Another point of concern for any additions to Biopython regards any build time or run time dependencies. Generally speaking, writing code to interact with a standalone tool (like BLAST, EMBOSS or ClustalW) doesn’t present a big problem. However, any dependency on another library - even a Python library (especially one needed in order to compile and install Biopython like NumPy) would need further discussion.

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/wiki/Scriptcentral) which has pointers to freely available code in Python for bioinformatics.

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!

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