[Biopython] Biopython 1.73 released

[Peter Cock]

Dear Biopythoneers,

Biopython 1.73 has been released and is available from our website and PyPI.

https://biopython.org/wiki/Download
https://pypi.org/project/biopython/1.73/

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It
has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

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.

The dictionary-like indexing in Bio.SeqIO and Bio.SearchIO will now
explicitly preserve record order to match a behaviour change in the
Python standard dict object. This means looping over the index will
load the records in the on-disk order, which will be much faster
(previously it would be effectively at random, based on the key hash
sorting).

The “grant” matrix in Bio.SubsMat.MatrixInfo has been replaced as our
original values taken from Gerhard Vogt’s old webpages at EMBL
Heidelberg were discovered to be in error. The new values have been
transformed following Vogt’s approach, taking the global maximum 215
minus the similarity scores from the original paper Grantham (1974),
to give a distance measure.

Double-quote characters in GenBank feature qualifier values in
Bio.SeqIO are now escaped as per the NCBI standard. Improperly escaped
values trigger a warning on parsing.

There is a new command line wrapper for the BWA-MEM sequence mapper.

The string-based FASTA parsers in Bio.SeqIO.FastaIO have been
optimised, which also speeds up parsing FASTA files using
Bio.SeqIO.parse().

Additionally, a number of small bugs and typos have been fixed with
further additions to the test suite, and there has been further work
to follow the Python PEP8, PEP257 and best practice standard coding
style.

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

- Alona Levy-Jurgenson (first contribution)
- Ariel Aptekmann
- Brandon Invergo
- Catherine Lesuisse
- Chris Rands
- Darcy Mason (first contribution)
- Devang Thakkar (first contribution)
- Ivan Antonov (first contribution)
- Jeremy LaBarage (first contribution)
- Juraj Szász (first contribution)
- Kai Blin
- Konstantin Vdovkin (first contribution)
- Manuel Nuno Melo (first contribution)
- Maximilian Greil
- Nick Negretti (first contribution)
- Peter Cock
- Rona Costello (first contribution)
- Spencer Bliven
- Wibowo 'Bow' Arindrarto
- Yi Hsiao (first contribution)

Thank you all,

Peter


For reference, checksums:

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biopython-1.73-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
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biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl
d3cab98752b83cef121b7a1e8b81853c  biopython-1.73-cp27-cp27m-win32.whl
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biopython-1.73-cp34-cp34m-manylinux1_x86_64.whl
1b0d7ba1b4c097b318213431d9b6b99e  biopython-1.73-cp34-cp34m-win32.whl
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biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl
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biopython-1.73-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
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biopython-1.73-cp37-cp37m-manylinux1_x86_64.whl
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d1d2e6154c2c89d6bb0e77f4a3578686  biopython-1.73.tar.gz
478d71daf63e9b57775fbd5aaa8f48f1  biopython-1.73.zip

$ sha256sum biopython-1.73*
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biopython-1.73-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
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biopython-1.73-cp27-cp27m-manylinux1_i686.whl
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biopython-1.73-cp27-cp27m-manylinux1_x86_64.whl
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biopython-1.73-cp27-cp27m-win_amd64.whl
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biopython-1.73-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
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biopython-1.73-cp34-cp34m-manylinux1_i686.whl
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biopython-1.73-cp34-cp34m-win_amd64.whl
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biopython-1.73-cp35-cp35m-win_amd64.whl
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biopython-1.73-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
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biopython-1.73-cp36-cp36m-manylinux1_i686.whl
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biopython-1.73-cp37-cp37m-manylinux1_i686.whl
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biopython-1.73-cp37-cp37m-win_amd64.whl
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biopython-1.73.tar.gz
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biopython-1.73.zip