Changelog for python-biopython-1.73-2.2.x86_64.rpm :
Fri Jan 4 13:00:00 2019 Todd R
- Update to version 1.73

* 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 SeqIO and 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.

* 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.

* 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()``.
- Update to version 1.72

* Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
SeqIO.write (especially when used in a for loop).

* The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
inclusive end co-ordinates to better handle searches at end points. This
will require you to rebuild any existing MAF index files.

* In this release 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 Entrez module now supports the NCBI API key. Also you can now set a custom
directory for DTD and XSD files. This allows Entrez to be used in environments
like AWS Lambda, which restricts write access to specific directories.
Improved support for parsing NCBI Entrez XML files that use XSD schemas.

* Internal changes to our C code mean that NumPy is no longer required at
compile time - only at run time (and only for those modules which use NumPy).

* Seq, UnknownSeq, MutableSeq and derived classes now support integer
multiplication methods, matching native Python string methods.

* A translate method has been added to Bio.SeqFeature that will extract a
feature and translate it using the codon_start and transl_table qualifiers
of the feature if they are present.

* Bio.SearchIO is no longer considered experimental, and so it does not raise
warnings anymore when imported.

* A new pairwise sequence aligner is available in Bio.Align, as an alternative
to the existing pairwise sequence aligner in Bio.pairwise2.

Wed May 9 14:00:00 2018 toddrme2178AATTgmail.com
- Update to version 1.71

* 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.

* In this release 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.

* 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, comparision 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 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.
- Update to version 1.70

* Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our
original logo and the current Python logo, this shows a yellow and blue snake
forming a double helix.

* For installation Biopython now assumes ``setuptools`` is present, and takes
advantage of this to declare we require NumPy at install time (except under
Jython). This should help ensure ``pip install biopython`` works smoothly.

* Bio.AlignIO now supports Mauve\'s eXtended Multi-FastA (XMFA) file format
under the format name \"mauve\" (contributed by Eric Rasche).

* Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return
text-mode handles for use under Python 3.

* Two new arguments for reading and writing blast-xml files have been added
to the Bio.SearchIO functions (read/parse and write, respectively). They
are \'use_raw_hit_ids\' and \'use_raw_query_ids\'. Check out the relevant
SearchIO.BlastIO documentation for a complete description of what these
arguments do.

* Bio.motifs was updated to support changes in MEME v4.11.4 output.

* The Bio.Seq sequence objects now have a ``.count_overlap()`` method to
supplement the Python string like non-overlap based ``.count()`` method.

* The Bio.SeqFeature location objects can now be compared for equality.

* Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw
instead, or another library or program if more advanced plotting functionality
is needed.

* In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
_DistanceMatrix) has a new method \'format_phylip\' to write Phylip-compatible
distance matrix files (contributed by Jordan Willis).

* 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.
- Use license tag

Wed May 24 14:00:00 2017 toddrme2178AATTgmail.com
- Implement single-spec version
- Fix source URL.
- updated to version 1.69

* We now expect and take advantage of NumPy under PyPy, and compile most of the
Biopython C code modules as well.

* Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the
format name \"maf\", using new module Bio.AlignIO.MafIO which also offers
indexed access to these potentially large files using SQLite3 (contributed by
Andrew Sczesnak, with additional refinements from Adam Novak).

* Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The
underlying format (ABIF) remains the same as AB1 files and so the string
\'abif\' is the expected format argument in the main SeqIO functions. AbiIO
determines whether the file is AB1 or FSA based on the presence of specific
tags.

* The Uniprot parser is now able to parse \"submittedName\" elements in XML files.

* The NEXUS parser handling of internal node comments has been improved, which
should help if working with tools like the BEAST TreeAnnotator. Slashes are
now also allowed in identifiers.

* New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue,
and cell line ontology (contributed by Steve Marshall).

* For consistency the Bio.Seq module now offers a complement function (already
available as a method on the Seq and MutableSeq objects).

* The SeqFeature object\'s qualifiers is now an explicitly ordered dictionary
(note that as of Python 3.6 the Python dict is ordered by default anyway).
This helps reproduce GenBank/EMBL files on input/output.

* The Bio.SeqIO UniProt-XML parser was updated to cope with features with
unknown locations which can be found in mass spec data.

* The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type
from the LOCUS/ID line explicitly in the record.annotations dictionary.
The Bio.SeqIO EMBL parser was updated to cope with more variants seen in
patent data files, and the related IMGT parser was updated to cope with
IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed.
The GenBank output now uses colon space to match current NCBI DBLINK lines.

* The Bio.Affy package supports Affymetrix version 4 of the CEL file format,
in addition to version 3.

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

* Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default),
PDBML/XML and mmtf format protein structures. This is inline with the RCSB
recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython
already has support for parsing mmCif files.

* 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.

Thu Nov 17 13:00:00 2016 alinm.elenaAATTgmail.com
- updated to version 1.68

Mon Dec 9 13:00:00 2013 toddrme2178AATTgmail.com
- Update to version 1.63

* 2to3 no longer needed for python 3
- Added additional dependencies

Thu Sep 19 14:00:00 2013 highwaystar.ruAATTgmail.com
- upgrade to version 1.62

* The translation functions will give a warning on any partial codons

* Phylo module now supports the file formats NeXML and CDAO

* New module Bio.UniProt adds parsers for the GAF, GPA and GPI
formats from UniProt-GOA.

* The BioSQL module is now supported in Jython.

* Feature labels on circular GenomeDiagram figures now support
the label_position argument (start, middle or end)

* The code for parsing 3D structures in mmCIF files was updated
to use the Python standard library\'s shlex module instead of C code
using flex.

* The Bio.Sequencing.Applications module now includes a BWA
command line wrapper.

* Bio.motifs supports JASPAR format files with multiple
position-frequence matrices.

Wed Feb 1 13:00:00 2012 saschpeAATTsuse.de
- Ran spec-cleaner
- Set license to MIT (looks like it)

Wed Jan 11 13:00:00 2012 toddrme2178AATTgmail.com
- Cleaned up spec file

Thu Sep 8 14:00:00 2011 alinm.elenaAATTgmail.com
- Initial commit