[Biopython-announce] Biopython 1.75 has been released

[Peter Cock]

Dear Biopythoneers,

Biopython 1.75 has been released as is available from our
website and on PyPI (e.g. pip install --upgrade biopython):

https://biopython.org/wiki/Download
https://pypi.python.org/pypi/biopython/1.75

Blog post:

https://www.open-bio.org/2019/11/07/biopython-1-75-released/

This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is
expected to work on the soon to be released Python 3.8. It has also
been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.

Note we intend to drop Python 2.7 support in early 2020.

The restriction enzyme list in Bio.Restriction has been updated to the
August 2019 release of REBASE.

Bio.SeqIO now supports reading and writing files in the native format
of Christian Marck's DNA Strider program ("xdna" format, also used by
Serial Cloner), as well as reading files in the native formats of GSL
Biotech's SnapGene ("snapgene") and Textco Biosoftware's Gene
Construction Kit ("gck").

Bio.AlignIO now supports GCG MSF mutliple sequence alignments as the
"msf" format (work funded by the National Marrow Donor Program).

The main Seq object now has string-like .index() and .rindex()
methods, matching the existing .find() and .rfind() implementations.
The MutableSeq object retains its more list-like .index() behaviour.

The MMTFIO class is added that allows writing of MMTF file format
files from a Biopython structure object. MMTFIO has a similar
interface to PDBIO and MMCIFIO, including the use of a Select class to
write out a specified selection. This final addition to read/write
support for PDB/mmCIF/MMTF in Biopython allows conversion between all
three file formats.

Values from mmCIF files are now read in as a list even when they
consist of a single value. This change improves consistency and
reduces the likelihood of making an error, but will require user code
to be updated accordingly.

Bio.PDB has been updated to support parsing REMARK 99 header entries
from PDB-style Astral files.

A new keyword parameter full_sequences was added to Bio.pairwise2's
pretty print method format_alignment to restore the output of local
alignments to the 'old' format (showing the whole sequences including
the un-aligned parts instead of only showing the aligned parts).

A new function charge_at_pH(pH) has been added to ProtParam and
IsoelectricPoint in Bio.SeqUtils.

The PairwiseAligner in Bio.Align was extended to allow generalized
pairwise alignments, i.e. alignments of any Python object, for example
three-letter amino acid sequences, three-nucleotide codons, and arrays
of integers.

A new module substitution_matrices was added to Bio.Align, which
includes an Array class that can be used as a substitution matrix. As
the Array class is a subclass of a numpy array, mathematical
operations can be applied to it directly, and C code that makes use of
substitution matrices can directly access the numerical values stored
in the substitution matrices. This module is intended as a replacement
of Bio.SubsMat, which is currently unmaintained.

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, and there has been further work
to follow the Python PEP8, PEP257 and best practice standard coding
style. We have also started to use the black Python code formatting
tool.

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

Chris MacRaild
Chris Rands
Damien Goutte-Gattat (first contribution)
Devang Thakkar
Harry Jubb
Joe Greener
Kiran Mukhyala (first contribution)
Konstantin Vdovkin
Mark Amery
Markus Piotrowski
Mike Moritz (first contribution)
Mustafa Anil Tuncel
Nick Negretti
Peter Cock
Peter Kerpedjiev
Sergio Valqui
Spencer Bliven

Thank you all,

Peter