Dirk Mueller
34b75af993
* The old parser stores information in a
Bio.Blast.NCBIXML.Blast object, with attribute names based on
plain-text Blast output. The new parser stores information in
a Bio.Blast.Record object. This class follows the DTD that
describes the XML in terms of attribute names and dictionary
key names, class structure, and object types. This makes it
easier to find the detailed description of each field in the
NCBI Blast documentation.
* The old parser stores alignment information directly as seen
in the BLAST XML output, i.e. as strings with dashes to
represent gaps. The new parser stores the alignment
information as a Bio.Align.Alignment object, which can then
be used to e.g. print the alignment in a different format.
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=25
85 lines
2.5 KiB
RPMSpec
85 lines
2.5 KiB
RPMSpec
#
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# spec file for package python-biopython
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#
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# Copyright (c) 2024 SUSE LLC
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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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%{?!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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%define skip_python2 1
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%define skip_python36 1
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Name: python-biopython
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Version: 1.84
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Release: 0
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Summary: Python Tools for Computational Molecular Biology
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License: BSD-3-Clause AND MIT
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URL: https://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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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 -q -n biopython-%{version}
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find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
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# Example scripts cannot be in a subdirectory
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mv -v Doc/examples examples
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%build
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export LANG=en_US.UTF-8
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%python_build
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%install
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export LANG=en_US.UTF-8
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%python_install
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%python_expand %fdupes %{buildroot}%{$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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%pytest
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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/ examples/
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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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