Biopython 1.76 released
Biopython 1.76 has been released and is available from our website and PyPI.
Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.
This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement“, or the very similar but more commonly used “3-Clause BSD License“. See the LICENSE.rst file for more details.
In addition to the mainstream x86_64 aka AMD64 CPU architecture, we now also test every contribution on the ARM64, ppc64le, and s390x CPUs under Linux thanks to Travis CI. Further post-release testing done by Debian and other packagers and distributors of Biopython also covers these CPUs.
The Bio.motifs.PositionSpecificScoringMatrix.search() method has been re-written: it now applies .calculate() to chunks of the sequence to maintain a low memory footprint for long sequences.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the black tool.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Chris Daley (first contribution)
- Chris Rands
- Christian Brueffer
- Ilya Flyamer (first contribution)
- Jakub Lipinski (first contribution)
- Michael R. Crusoe (first contribution)
- Michiel de Hoon
- Peter Cock
- Sergio Valqui