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BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

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Tuesday, July 21 • 02:20 - 02:25
Biopython Project Update 2020 🍐

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β†’ AbstractSlidesVideo

The presenter(s) will be available for live Q&A in this session (BCC West).

Peter Cock1 and the Biopython Contributors 2

1 Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, UK
2 See contributor listing on GitHub.

Website: http://biopython.org
Repository: https://github.com/biopython/biopython
License: Biopython License Agreement (BSD like, see http://www.biopython.org/DIST/LICENSE)

The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioin-
formatics Foundation, which develops a freely available Python library for biological computation [1]. This
talk will look ahead to the year to come, and give a summary of the project news since the 1.74 release in
July 2019, and the talk at BOSC 2019.
There have been three releases: Biopython 1.75 (November 2019), Biopython 1.76 (December 2019), and
Biopython 1.77 (expected May/June 2020). This year saw the adoption of the black Python coding style,
our final release to support Python 2, and substantial code cleanup to focus on Python 3 only.
In 2017 we started a re-licensing plan, to transition away from our liberal but unique Biopython License
Agreement to the similar but very widely used 3-Clause BSD License. We are reviewing the code base
authorship file-by-file, to gradually dual license the entire project. All new contributions are dual licensed,
and currently over 75% of the Python and C files in the main library have been dual licensed.
Another important effort had been improving the unit test coverage, which can be viewed at CodeCov.io.
Sadly, this has stalled at about 85% (excluding online tests) for some time.
We are using GitHub-integrated continuous integration testing on Linux (using TravisCI) and Windows
(using AppVeyor), including enforcing the Python PEP8, PEP257 and black coding style guidelines. We
recommend a simple git pre-commit hook using flake8 for our contributors, which aims to reduce the
human time costs in writing compliant code.
Finally, since our last update talk in July 2019, Biopython has had 37 named contributors including
15 newcomers. This reflects our policy of trying to encourage even small contributions. Our total named
contributor count is now at 275 since the project began, over twenty year ago.

References
[1] Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T.,
Kauff, F., Wilczynski, B., de Hoon, M.J. (2009) Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. doi:10.1093/bioinformatics/btp163


Speakers
avatar for Peter Cock

Peter Cock

The James Hutton Institute
Bioinformatician at the James Hutton Institute, a member of the BOSC organizing committee, treasurer of the Open Bioinformatics Foundation, and a core developer on the Biopython project.


Tuesday July 21, 2020 02:20 - 02:25 EDT
BOSC