[Biopython] Biopython 1.78 released

[Peter Cock]

Blog post and twitter:

https://www.open-bio.org/2020/09/04/biopython-1-78-released/
https://twitter.com/Biopython/status/1301855658443255808

Biopython 1.78 has been released and is available from our website and PyPI.

https://biopython.org/wiki/Download
https://pypi.org/project/biopython/1.78/

The main change is that Bio.Alphabet is no longer used. In some cases
you will now have to specify expected letters, molecule type (DNA,
RNA, protein), or gap character explicitly. Please consult the updated
Tutorial and API documentation for guidance. This simplification has
sped up many Seq object methods. See
https://biopython.org/wiki/Alphabet for more information.

Bio.SeqIO.parse() is faster with “fastq” format due to small
improvements in the Bio.SeqIO.QualityIO module.

The SeqFeature object’s .extract() method can now be used for
trans-spliced locations via an optional dictionary of references.

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
additions to the test suite. There has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style, and all
of the tests have been reformatted with the black tool to match the
main code base.

Many thanks to the Biopython developers and community for making this
release possible, especially the following contributors:

Adam Sjøgren (first contribution)
Carlos Pena
Chris Daley
Chris Rands
Christian Brueffer
Damien Goutte-Gattat
João Rodrigues
João Vitor F Cavalcante (first contribution)
Marie Crane
Michiel de Hoon
Peter Cock
Sergio Valqui
Yogesh Kulkarni (first contribution)
Zheng Ruan