[Biopython-announce] Biopython 1.74 has been released

[Peter Cock]

Dear Biopythoneers,

Biopython 1.74 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/1.74

Blog post:

https://www.open-bio.org/2019/07/16/biopython-1-74-released/

This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7.
However, it will be the last release to support Python 3.4 which is
now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and
PyPy3.5 v6.0.0.

(Please note we will be dropping support for Python 2.7 in early 2020.)

Over half 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.

Our core sequence objects (Seq, UnknownSeq, and MutableSeq) now have a
string-like .join() method.

The NCBI now allows longer accessions in the GenBank file LOCUS line,
meaning the fields may not always follow the historical column based
positions. We no longer give a warning when parsing these. We now
allow writing such files (although with a warning as support for
reading them is not yet widespread).

Support for the mysqlclient package, a fork of MySQLdb, has been added.

We now capture the IDcode field from PDB Header records.

Bio.pairwise2‘s pretty-print output from format_alignment has been
optimized for local alignments: If they do not consist of the whole
sequences, only the aligned section of the sequences are shown,
together with the start positions of the sequences (in 1-based
notation). Alignments of lists will now also be prettily printed.

Bio.SearchIO now supports parsing the text output of the HHsuite
protein sequence search tool. The format name is hhsuite2-text and
hhsuite3-text, for versions 2 and 3 of HHsuite, respectively.

Bio.SearchIO HSP objects has a new attribute called output_index. This
attribute is meant for capturing the order by which the HSP were
output in the parsed file and is set with a default value of -1 for
all HSP objects. It is also used for sorting the output of
QueryResult.hsps.

Bio.SeqIO.AbiIO has been updated to preserve bytes value when parsing.
The goal of this change is make the parser more robust by being able
to extract string-values that are not utf-8-encoded. This affects all
tag values, except for ID and description values, where they need to
be extracted as strings to conform to the SeqRecord interface. In this
case, the parser will attempt to decode using utf-8 and fall back to
the system encoding if that fails. This change affects Python 3 only.

Bio.motifs.mast has been updated to parse XML output files from MAST
over the plain-text output file. The goal of this change is to parse a
more structured data source with minimal loss of functionality upon
future MAST releases. Class structure remains the same plus an
additional attribute Record.strand_handling required for diagram
parsing.

Bio.Entrez now automatically retries HTTP requests on failure. The
maximum number of tries and the sleep between them can be configured
by changing Bio.Entrez.max_tries and Bio.Entrez.sleep_between_tries.
(The defaults are 3 tries and 15 seconds, respectively.)

All tests using the older print-and-compare approach have been
replaced by unit tests following Python’s standard testing framework.

On the documentation side, all the public modules, classes, methods
and functions now have docstrings (built in help strings). In addition
to displaying the Biopython API documentation via epydoc, we now also
have the Biopython API documentation via Sphinx (which we hope to make
the default in future). Furthermore, the PDF version of the Biopython
Tutorial and Cookbook now uses syntax coloring for code snippets.

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:

- Andrey Raspopov (first contribution)
- Antony Lee
- Benjamin Rowell (first contribution)
- Bernhard Thiel
- Brandon Invergo
- Catherine Lesuisse
- Chris Rands
- Deepak Khatri (first contribution)
- Gert Hulselmans
- Jared Andrews
- Jens Thomas (first contribution)
- Konstantin Vdovkin
- Lenna Peterson
- Mark Amery
- Markus Piotrowski
- Micky Yun Chan (first contribution)
- Nick Negretti
- Peter Cock
- Peter Kerpedjiev
- Ralf Stephan
- Rob Miller
- Sergio Valqui
- Victor Lin
- Wibowo 'Bow' Arindrarto
- Zheng Ruan

Thank you all,

Peter

--

P.S.

For reference, checksums:

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