[Biopython-announce] Biopython 1.79 released!

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Thu Jun 3 19:02:33 EDT 2021

Dear Biopythoneers,

Biopython 1.79 has been released and is available from our website
<https://biopython.org/wiki/Download> and PyPI

This is the final release supporting Python version 3.6. It also supports
Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1.

The major changes in this version are listed below:

- The Seq and MutableSeq classes in Bio.Seq now inherit from the same base
class, ensuring their mutual consistency. In addition, both classes now
store sequence data as bytes and bytearray objects, respectively.

- Empty or unknown sequences can now be created directly by passing None to
the Seq class, instead of using UnknownSeq. This latter class is now
deprecated and will be removed in a future version of Biopython.

- A new module Bio.PDB.SASA implements the Shrake-Rupley algorithm to
calculate solvent accessible areas natively, without requiring third-party
tools such as DSSP or NACCESS.

- Other minor improvements to the Bio.PDB module include a new
center_of_mass() method to calculate the center of mass or center of
gravity of any Entity subclass (e.g. Structure, Chain, or Residue).

- Changes in the KEGG KGML_Pathway module now produce output files
compliant with KGML v0.7.2. In addition, Bio.UniProt.GOA now parses GPI
files version 1.2.

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.

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:

- Damien Goutte-Gattat
- Gert Hulselmans
- João Rodrigues
- Markus Piotrowski
- Sergio Valqui
- Suyash Gupta
- Vini Salazar (first contribution)
- Leighton Pritchard
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