3ca7ac07d1
- 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
89 lines
2.8 KiB
RPMSpec
89 lines
2.8 KiB
RPMSpec
#
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# spec file for package python-biopython
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#
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# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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# Tests require a network connection
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%bcond_with test
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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Name: python-biopython
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Version: 1.74
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Release: 0
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Summary: Python Tools for Computational Molecular Biology
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License: MIT AND BSD-3-Clause
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Group: Development/Libraries/Python
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Url: http://www.biopython.org
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Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
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Source100: python-biopython-rpmlintrc
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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module numpy-devel}
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BuildRequires: %{python_module setuptools}
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BuildRequires: %{python_module xml}
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BuildRequires: fdupes
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BuildRequires: flex
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BuildRequires: python-rpm-macros
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BuildRequires: python3-2to3
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Requires: python-numpy
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Requires: python-xml
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Recommends: python-matplotlib
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Recommends: python-mysql
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Recommends: python-networkx
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Recommends: python-psycopg2
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Recommends: python-pydot
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Recommends: python-pygraphviz
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Recommends: python-rdflib
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Recommends: python-reportlab
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%python_subpackages
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%description
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The Biopython Project is an international association of developers of freely
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available Python tools for computational molecular biology.
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%prep
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%setup -n biopython-%{version}
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# remove all execute bits from documentation and fix line endings
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find -type f -exec chmod -x {} 2>/dev/null ';'
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find -type f -exec sed -i 's/\r//' {} 2>/dev/null ';'
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# remove she-bang lines in .py files to keep rpmlint happy
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find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
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sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' Scripts/Structure/hsexpo
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%build
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export LANG=en_US.UTF-8
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%python_build
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%install
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export LANG=en_US.UTF-8
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%python_install
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%python_expand %fdupes %{buildroot}%{$python_sitearch}
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%if %{with test}
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%check
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export LANG=en_US.UTF-8
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%python_exec setup.py test
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%endif
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%files %{python_files}
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%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
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%doc Doc/
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%license LICENSE.rst
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%{python_sitearch}/Bio/
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%{python_sitearch}/BioSQL/
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%{python_sitearch}/biopython-%{version}-py*.egg-info
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%changelog
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