[Biopython] Biopython 1.71 released

Wed Apr 4 15:39:22 UTC 2018

Dear Biopythoneers,

Source distributions of Biopython 1.71 are now available from the
downloads page on the official Biopython website, and the release is
also on the Python Package Index (PyPI)including pre-compiled Wheel
Packages for Linux, Mac OS X and Windows.

http://biopython.org/wiki/Download
https://pypi.python.org/pypi/biopython/1.71

This annoucment is also online here:

https://news.open-bio.org/2018/04/04/biopython-1-71-released/

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we
have now dropped support for Python 3.3). It has also been tested on
PyPy2.7 v5.10.0 and PyPy3.5 v5.10.1.

Python 3 is the primary development platform for Biopython. We will
drop support for Python 2.7 no later than 2020, in line with the
end-of-life or sunset date for Python 2.7 itself.

Setup changes:

We now explicitly recommend installation using “pip install
biopython”, rather than the classic “python setup.py install”
approach. In a related change, we depend on the Python package
setuptools (rather than the older package distutils in the Python
standard library) and have made the dependency on NumPy explicit and
automatic.

License changes:

As of Biopython 1.69, we have started to dual-license Biopython under
both our original liberal “Biopython License Agreement”, and the very
similar but more commonly used “3-Clause BSD License”. A growing
number of the Python files are explicitly available under either
license, but most of the code remains under the “Biopython License
Agreement” only. See the LICENSE file for more details.

Code changes:

Encoding issues have been fixed in several parsers when reading data
files with non-ASCII characters, like accented letters in people’s
names. This would raise UnicodeDecodeError: 'ascii' codec can't decode
byte ... under some system locale settings.

Bio.KEGG can now parse Gene files.

The multiple-sequence-alignment object used by Bio.AlignIO etc now
supports a per-column annotation dictionary, useful for richly
annotated alignments in the Stockholm/PFAM format.

The SeqRecord object now has a translate method, following the
approach used for its existing reverse_complement method etc.

The output of function format_alignment in Bio.pairwise2 for
displaying a pairwise sequence alignment as text now indicates gaps
and mis-matches.

Bio.SeqIO now supports reading and writing two-line-per-record FASTA
files under the format name “fasta-2line”, useful if you wish to work
without line-wrapped sequences.

Bio.PDB now contains a writer for the mmCIF file format, which has
been the standard PDB archive format since 2014. This allows
structural objects to be written out and facilitates conversion
between the PDB and mmCIF file formats.

Bio.Emboss.Applications has been updated to fix a wrong parameter in
fuzznuc wrapper and include a new wrapper for fuzzpro.

The restriction enzyme list in Bio.Restriction has been updated to the
November 2017 release of REBASE.

New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2)
were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31
contain no dedicated stop codons; the stop codons in these codes have
a context dependent encoding as either STOP or as amino acid.

IO functions such as SeqIO.parse now accept any objects which can be
passed to the builtin open function. Specifically, this allows using
pathlib.Path objects under Python 3.6 and newer, as per PEP 519.

Bio.SearchIO can now parse InterProScan XML files.

For Python 3 compatibility, comparison operators for the entities
within a Bio.PDB Structure object were implemented. These allow the
comparison of models, chains, residues, and atoms with the common
operators (==, !=, >, …) Comparisons are based on IDs and take the
parents of the entity up to the model level into account. For
consistent behaviour of all entities the operators for atoms were
modified to also consider the parent IDs. NOTE: this represents a
change in behaviour in respect to v1.70 for Atom comparisons. In order
to mimic the behaviour of previous versions, comparison will have to
be done for Atom IDs and alternative locations specifically.

Additionally, a number of small bugs 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.

Acknowledgements:

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

- Adhemar Zerlotini
- Ariel Aptekmann
- Chris Rands
- Christian Brueffer
- Erik Cederstrand (first contribution)
- Fei Qi (first contribution)
- Francesco Gastaldello
- James Jeffryes (first contribution)
- Jerven Bolleman (first contribution)
- Joe Greener (first contribution)
- Joerg Schaarschmidt (first contribution)
- João Rodrigues
- Jeroen Van Goey
- Jun Aruga (first contribution)
- Kai Blin
- Kozo Nishida
- Lewis A. Marshall (first contribution)
- Markus Piotrowski
- Michiel de Hoon
- Nicolas Fontrodona (first contribution)
- Peter Cock
- Philip Bergstrom (first contribution)
- rht (first contribution)
- Saket Choudhary
- Shuichiro MAKIGAKI (first contribution)
- Shyam Saladi (first contribution)
- Siong Kong
- Spencer Bliven
- Stefans Mezulis
- Steve Bond
- Yasar L. Ahmed (first contribution)
- Zachary Sailer (first contribution)
- Zaid Ur-Rehman (first contribution)

Thank you all.

P.S. You can follow @Biopython on Twitter

Checksums:

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