Accepting request 750002 from home:TheBlackCat:branches:devel:languages:python:numeric
Update to version 1.75 OBS-URL: https://build.opensuse.org/request/show/750002 OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=7
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Todd R
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biopython-1.75.tar.gz
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biopython-1.75.tar.gz
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-------------------------------------------------------------------
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Wed Nov 20 20:17:31 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Update to version 1.75
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* The restriction enzyme list in Bio.Restriction has been updated to the August
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2019 release of REBASE.
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* ``Bio.SeqIO`` now supports reading and writing files in the native format of
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Christian Marck's DNA Strider program ("xdna" format, also used by Serial
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Cloner), as well as reading files in the native formats of GSL Biotech's
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SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").
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* ``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
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format (work funded by the National Marrow Donor Program).
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* The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
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methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
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The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.
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* The ``MMTFIO`` class has been added that allows writing of MMTF file format
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files from a Biopython structure object. ``MMTFIO`` has a similar interface to
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``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
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out a specified selection. This final addition to read/write support for
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PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
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* Values from mmCIF files are now read in as a list even when they consist of a
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single value. This change improves consistency and reduces the likelihood of
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making an error, but will require user code to be updated accordingly.
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* ``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
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PDB-style Astral files.
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* A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
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pretty print method ``format_alignment`` to restore the output of local
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alignments to the 'old' format (showing the whole sequences including the
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un-aligned parts instead of only showing the aligned parts).
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* A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
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``IsoelectricPoint`` in ``Bio.SeqUtils``.
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* The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
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pairwise alignments, i.e. alignments of any Python object, for example
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three-letter amino acid sequences, three-nucleotide codons, and arrays of
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integers.
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* A new module ``substitution_matrices`` was added to ``Bio.Align``, which
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includes an ``Array`` class that can be used as a substitution matrix. As
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the ``Array`` class is a subclass of a numpy array, mathematical operations
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can be applied to it directly, and C code that makes use of substitution
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matrices can directly access the numerical values stored in the substitution
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matrices. This module is intended as a replacement of ``Bio.SubsMat``,
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which is currently unmaintained.
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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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* 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. We have also
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started to use the ``black`` Python code formatting tool.
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-------------------------------------------------------------------
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Tue Jul 23 01:23:01 UTC 2019 - Todd R <toddrme2178@gmail.com>
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@ -16,17 +16,15 @@
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#
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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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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Version: 1.75
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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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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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@ -54,7 +52,7 @@ 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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%setup -q -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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@ -74,7 +72,7 @@ export LANG=en_US.UTF-8
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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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%pytest
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%endif
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%files %{python_files}
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