2018-05-29 14:47:30 +00:00
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#
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# spec file for package python-biopython
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#
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- update to 1.80:
* This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It
has also been tested on PyPy3.7 v7.3.5.
* Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align``
to read and write ``Alignment`` objects.
* Because dict retains the item order by default since Python3.6, all
instances of ``collections.OrderedDict`` have been replaced by either standard
``dict`` or where appropriate by ``collections.defaultsdict``.
* The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class``
as a string array since the JASPAR 2018 release.
* The Local Composition Complexity functions from ``Bio.SeqUtils`` now
uses base 4 log instead of 2 as stated in the original reference Konopka
(2005), * Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260
* Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked
GZIP files with an internal empty block fixed).
* The experimental warning was dropped from ``Bio.phenotype`` (which was
new in Biopython 1.67).
* Sequences now have a ``defined`` attribute that returns a boolean
indicating if the underlying data is defined or not.
* The ``Bio.PDB`` module now includes a structural alignment module, using
the combinatorial extension algorithm of Shindyalov and Bourne, commonly
known as CEAlign. The module allows for two structures to be aligned based solely
on their 3D conformation, ie. in a sequence-independent manner. The method
is particularly powerful when the structures shared a very low degree of
sequence similarity. The new module is available in ``Bio.PDB.CEAligner`` with an
interface similar to other 3D superimposition modules.
* A new module ``Bio.PDB.qcprot`` implements the QCP superposition
algorithm in pure Python, deprecating the existing C implementation. This leads to a
slight performance improvement and to much better maintainability. The
refactored ``qcprot.QCPSuperimposer`` class has small changes to its API, to better
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=17
2023-01-04 14:21:39 +00:00
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# Copyright (c) 2023 SUSE LLC
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2018-05-29 14:47:30 +00:00
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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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2019-01-21 09:46:29 +00:00
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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2018-05-29 14:47:30 +00:00
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#
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2019-11-20 20:18:30 +00:00
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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2018-05-29 14:47:30 +00:00
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# Tests require a network connection
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%bcond_with test
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Accepting request 819377 from home:mcalabkova:branches:devel:languages:python:numeric
- Update to version 1.77
* **We have dropped support for Python 2 now.**
* ``pairwise2`` now allows the input of parameters with keywords and returns the
alignments as a list of ``namedtuples``.
* The codon tables have been updated to NCBI genetic code table version 4.5,
which adds Cephalodiscidae mitochondrial as table 33.
* Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
* A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
handle protein structure transformations using dihedral angles (internal
coordinates). The new framework supports lossless interconversion between
internal and cartesian coordinates, which, among other uses, simplifies the
analysis and manipulation of coordinates of proteins structures.
* ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
output.
* In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
CPUs under Linux thanks to Travis CI. Further post-release testing done by
Debian and other packagers and distributors of Biopython also covers these
CPUs.
* ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
re-written: it now applies ``.calculate()`` to chunks of the sequence
to maintain a low memory footprint for long sequences.
* Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and more of the code
style has been reformatted with the ``black`` tool.
OBS-URL: https://build.opensuse.org/request/show/819377
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=9
2020-07-08 10:10:38 +00:00
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%define skip_python2 1
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2021-02-21 06:56:38 +00:00
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%define skip_python36 1
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2018-05-29 14:47:30 +00:00
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Name: python-biopython
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2023-12-27 09:27:26 +00:00
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Version: 1.82
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2018-05-29 14:47:30 +00:00
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Release: 0
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Summary: Python Tools for Computational Molecular Biology
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2022-03-27 14:09:13 +00:00
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License: BSD-3-Clause AND MIT
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URL: https://biopython.org/
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2019-01-21 09:46:29 +00:00
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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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2018-05-29 14:47:30 +00:00
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BuildRequires: %{python_module devel}
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BuildRequires: %{python_module numpy-devel}
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2019-01-21 09:46:29 +00:00
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BuildRequires: %{python_module setuptools}
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2018-05-29 14:47:30 +00:00
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BuildRequires: %{python_module xml}
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2019-01-21 09:46:29 +00:00
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BuildRequires: fdupes
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BuildRequires: flex
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BuildRequires: python-rpm-macros
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2018-05-29 14:47:30 +00:00
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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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2019-11-20 20:18:30 +00:00
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%setup -q -n biopython-%{version}
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2018-05-29 14:47:30 +00:00
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find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
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2020-11-03 15:59:55 +00:00
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# Example scripts cannot be in a subdirectory
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2022-03-27 14:09:13 +00:00
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mv -v Doc/examples examples
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2018-05-29 14:47:30 +00:00
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%build
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export LANG=en_US.UTF-8
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%python_build
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%install
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export LANG=en_US.UTF-8
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%python_install
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2019-01-21 09:46:29 +00:00
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%python_expand %fdupes %{buildroot}%{$python_sitearch}
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2018-05-29 14:47:30 +00:00
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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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2019-11-20 20:18:30 +00:00
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%pytest
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2018-05-29 14:47:30 +00:00
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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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2020-11-03 15:59:55 +00:00
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%doc Doc/ examples/
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2018-05-29 14:47:30 +00:00
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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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