forked from pool/python-biopython
Accepting request 662924 from devel:languages:python:numeric
OBS-URL: https://build.opensuse.org/request/show/662924 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=2
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version https://git-lfs.github.com/spec/v1
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oid sha256:4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033
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size 16031832
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3
biopython-1.73.tar.gz
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biopython-1.73.tar.gz
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version https://git-lfs.github.com/spec/v1
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oid sha256:70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0
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size 15715102
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python-biopython-rpmlintrc
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python-biopython-rpmlintrc
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addFilter("devel-file-in-non-devel-package .*\.c")
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addFilter("devel-file-in-non-devel-package .*\.h")
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-------------------------------------------------------------------
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Fri Jan 4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Update to version 1.73
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* As in recent releases, more of our code is now explicitly available under
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either our original "Biopython License Agreement", or the very similar but
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more commonly used "3-Clause BSD License". See the ``LICENSE.rst`` file for
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more details.
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* The dictionary-like indexing in SeqIO and SearchIO will now explicitly preserve
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record order to match a behaviour change in the Python standard dict object.
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This means looping over the index will load the records in the on-disk order,
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which will be much faster (previously it would be effectively at random, based
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on the key hash sorting).
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* The "grant" matrix in Bio.SubsMat.MatrixInfo has been replaced as our original
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values taken from Gerhard Vogt's old webpages at EMBL Heidelberg were
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discovered to be in error. The new values have been transformed following
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Vogt's approach, taking the global maximum 215 minus the similarity scores
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from the original paper Grantham (1974), to give a distance measure.
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* Additionally, a number of small bugs and typos have been fixed with further
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additions to the test suite, and there has been further work to follow the
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Python PEP8, PEP257 and best practice standard coding style.
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* Double-quote characters in GenBank feature qualifier values in ``Bio.SeqIO``
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are now escaped as per the NCBI standard. Improperly escaped values trigger a
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warning on parsing.
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* There is a new command line wrapper for the BWA-MEM sequence mapper.
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* The string-based FASTA parsers in ``Bio.SeqIO.FastaIO`` have been optimised,
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which also speeds up parsing FASTA files using ``Bio.SeqIO.parse()``.
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- Update to version 1.72
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* Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
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SeqIO.write (especially when used in a for loop).
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* The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
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inclusive end co-ordinates to better handle searches at end points. This
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will require you to rebuild any existing MAF index files.
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* In this release more of our code is now explicitly available under either our
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original "Biopython License Agreement", or the very similar but more commonly
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used "3-Clause BSD License". See the ``LICENSE.rst`` file for more details.
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* The Entrez module now supports the NCBI API key. Also you can now set a custom
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directory for DTD and XSD files. This allows Entrez to be used in environments
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like AWS Lambda, which restricts write access to specific directories.
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Improved support for parsing NCBI Entrez XML files that use XSD schemas.
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* Internal changes to our C code mean that NumPy is no longer required at
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compile time - only at run time (and only for those modules which use NumPy).
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* Seq, UnknownSeq, MutableSeq and derived classes now support integer
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multiplication methods, matching native Python string methods.
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* A translate method has been added to Bio.SeqFeature that will extract a
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feature and translate it using the codon_start and transl_table qualifiers
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of the feature if they are present.
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* Bio.SearchIO is no longer considered experimental, and so it does not raise
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warnings anymore when imported.
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* A new pairwise sequence aligner is available in Bio.Align, as an alternative
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to the existing pairwise sequence aligner in Bio.pairwise2.
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-------------------------------------------------------------------
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Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com
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@@ -1,7 +1,7 @@
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#
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# spec file for package python-biopython
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#
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# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
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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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# 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 http://bugs.opensuse.org/
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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@@ -21,21 +21,22 @@
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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Name: python-biopython
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Version: 1.71
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Version: 1.73
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Release: 0
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Summary: Python Tools for Computational Molecular Biology
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License: MIT
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Group: Development/Libraries/Python
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Url: http://www.biopython.org
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Source: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
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BuildRequires: flex
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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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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module setuptools}
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BuildRequires: %{python_module numpy-devel}
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BuildRequires: %{python_module xml}
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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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@@ -69,7 +70,7 @@ export LANG=en_US.UTF-8
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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}%{$python_sitelib}
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%python_expand %fdupes %{buildroot}%{$python_sitearch}
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%if %{with test}
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%check
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@@ -78,7 +79,6 @@ export LANG=en_US.UTF-8
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%endif
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%files %{python_files}
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%defattr(-,root,root)
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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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