Biopython 1.71 released

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.

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 PEP8PEP257 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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