Bump biopython from 1.76 to 1.77

[dependabot-preview[bot]]

Bumps biopython from 1.76 to 1.77.

Changelog

Sourced from biopython's changelog.

25 May 2020: Biopython 1.77

This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been tested on PyPy3.6.1 v7.1.1-beta0.

We have dropped support for Python 2 now.

pairwise2 now allows the input of parameters with keywords and returns the alignments as a list of namedtuples.

The codon tables have been updated to NCBI genetic code table version 4.5, which adds Cephalodiscidae mitochondrial as table 33.

Updated Bio.Restriction to the January 2020 release of REBASE.

A major contribution by Rob Miller to Bio.PDB provides new methods to handle protein structure transformations using dihedral angles (internal coordinates). The new framework supports lossless interconversion between internal and cartesian coordinates, which, among other uses, simplifies the analysis and manipulation of coordinates of proteins structures.

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:

• Alexander Decurnou (first contribution)
• Andrei Istrate (first contribution)
• Andrey Raspopov
• Austin Varela (first contribution)
• Chris Daley
• Chris Rands
• Deepak Khatri
• Hielke Walinga (first contribution)
• Kai Blin
• Karthikeyan Singaravelan (first contribution)
• Markus Piotrowski
• Michiel de Hoon
• Peter Cock
• Rob Miller
• Sergio Valqui
• Steve Bond
• Sujan Dulal (first contribution)
• Tianyi Shi (first contribution)

Commits

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[codecov[bot]]

Codecov Report

Merging #171 into dev will decrease coverage by 0.72%. The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev     #171      +/-   ##
==========================================
- Coverage   89.15%   88.43%   -0.73%     
==========================================
  Files          10       10              
  Lines         830      830              
==========================================
- Hits          740      734       -6     
- Misses         90       96       +6     

Impacted Files	Coverage Δ
iss/download.py	85.93% <0.00%> (-9.38%)	:arrow_down:

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[HadrienG]

@dependabot rebase