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Accepting request 717710 from home:TheBlackCat:branches:devel:languages:python:numeric

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- Update to version 1.74
  * 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
    unittests 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). 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.

OBS-URL: https://build.opensuse.org/request/show/717710
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=5
This commit is contained in:
Todd R 2019-07-23 01:28:49 +00:00 committed by Git OBS Bridge
parent 562201f9d3
commit 3ca7ac07d1
4 changed files with 55 additions and 6 deletions
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biopython-1.73.tar.gz
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python-biopython.changes
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@ -1,3 +1,53 @@
-------------------------------------------------------------------
Tue Jul 23 01:23:01 UTC 2019 - Todd R <toddrme2178@gmail.com>
- Update to version 1.74
* 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
unittests 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). 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.
-------------------------------------------------------------------
Fri Jan 4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>

5
python-biopython.spec
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@ -21,10 +21,10 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-biopython
Version: 1.73
Version: 1.74
Release: 0
Summary: Python Tools for Computational Molecular Biology
License: MIT
License: MIT AND BSD-3-Clause
Group: Development/Libraries/Python
Url: http://www.biopython.org
Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
@ -47,7 +47,6 @@ Recommends: python-pydot
Recommends: python-pygraphviz
Recommends: python-rdflib
Recommends: python-reportlab
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%python_subpackages
%description