From 061a2d5331d330161fd82ff8d6d63eff5d0bf3262140f3d44b70eaab1119358b Mon Sep 17 00:00:00 2001 From: Dominique Leuenberger Date: Tue, 29 May 2018 14:47:30 +0000 Subject: [PATCH] Accepting request 605802 from devel:languages:python computational molecular biology for python OBS-URL: https://build.opensuse.org/request/show/605802 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=1 --- .gitattributes | 23 +++++ .gitignore | 1 + biopython-1.71.tar.gz | 3 + python-biopython.changes | 176 +++++++++++++++++++++++++++++++++++++++ python-biopython.spec | 89 ++++++++++++++++++++ 5 files changed, 292 insertions(+) create mode 100644 .gitattributes create mode 100644 .gitignore create mode 100644 biopython-1.71.tar.gz create mode 100644 python-biopython.changes create mode 100644 python-biopython.spec diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +## Default LFS +*.7z filter=lfs diff=lfs merge=lfs -text +*.bsp filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.gem filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.jar filter=lfs diff=lfs merge=lfs -text +*.lz filter=lfs diff=lfs merge=lfs -text +*.lzma filter=lfs diff=lfs merge=lfs -text +*.obscpio filter=lfs diff=lfs merge=lfs -text +*.oxt filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.rpm filter=lfs diff=lfs merge=lfs -text +*.tbz filter=lfs diff=lfs merge=lfs -text +*.tbz2 filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.ttf filter=lfs diff=lfs merge=lfs -text +*.txz filter=lfs diff=lfs merge=lfs -text +*.whl filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..57affb6 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.osc diff --git a/biopython-1.71.tar.gz b/biopython-1.71.tar.gz new file mode 100644 index 0000000..aa5fa08 --- /dev/null +++ b/biopython-1.71.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4f1770a29a5b18fcaca759bbc888083cdde2b301f073439ff640570d4a93e033 +size 16031832 diff --git a/python-biopython.changes b/python-biopython.changes new file mode 100644 index 0000000..1faf983 --- /dev/null +++ b/python-biopython.changes @@ -0,0 +1,176 @@ +------------------------------------------------------------------- +Wed May 9 03:23:14 UTC 2018 - toddrme2178@gmail.com + +- Update to version 1.71 + * Encoding issues have been fixed in several parsers when reading data files + with non-ASCII characters, like accented letters in people's names. This would + raise ``UnicodeDecodeError: 'ascii' codec can't decode byte ...`` under some + system locale settings. + * Bio.KEGG can now parse Gene files. + * The multiple-sequence-alignment object used by Bio.AlignIO etc now supports + a per-column annotation dictionary, useful for richly annotated alignments + in the Stockholm/PFAM format. + * The SeqRecord object now has a translate method, following the approach used + for its existing reverse_complement method etc. + * The output of function ``format_alignment`` in ``Bio.pairwise2`` for displaying + a pairwise sequence alignment as text now indicates gaps and mis-matches. + * Bio.SeqIO now supports reading and writing two-line-per-record FASTA files + under the format name "fasta-2line", useful if you wish to work without + line-wrapped sequences. + * Bio.PDB now contains a writer for the mmCIF file format, which has been the + standard PDB archive format since 2014. This allows structural objects to be + written out and facilitates conversion between the PDB and mmCIF file formats. + * Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc + wrapper and include a new wrapper for fuzzpro. + * The restriction enzyme list in Bio.Restriction has been updated to the + November 2017 release of REBASE. + * New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) + were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain + no dedicated stop codons; the stop codons in these codes have a context + dependent encoding as either STOP or as amino acid. + * In this release more of our code is now explicitly available under either our + original "Biopython License Agreement", or the very similar but more commonly + used "3-Clause BSD License". See the ``LICENSE.rst`` file for more details. + * IO functions such as ``SeqIO.parse`` now accept any objects which can be passed + to the builtin ``open`` function. Specifically, this allows using + ``pathlib.Path`` objects under Python 3.6 and newer, as per `PEP 519 + `_. + * Bio.SearchIO can now parse InterProScan XML files. + * For Python 3 compatibility, comparision operators for the entities within a + Bio.PDB Structure object were implemented. These allow the comparison of + models, chains, residues, and atoms with the common operators (==, !=, >, ...) + Comparisons are based on IDs and take the parents of the entity up to the + model level into account. For consistent behaviour of all entities the operators + for atoms were modified to also consider the parent IDs. NOTE: this represents a + change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic + the behaviour of previous versions, comparison will have to be done for Atom IDs + and alternative locations specifically. + * 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. +- Update to version 1.70 + * Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our + original logo and the current Python logo, this shows a yellow and blue snake + forming a double helix. + * For installation Biopython now assumes ``setuptools`` is present, and takes + advantage of this to declare we require NumPy at install time (except under + Jython). This should help ensure ``pip install biopython`` works smoothly. + * Bio.AlignIO now supports Mauve's eXtended Multi-FastA (XMFA) file format + under the format name "mauve" (contributed by Eric Rasche). + * Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return + text-mode handles for use under Python 3. + * Two new arguments for reading and writing blast-xml files have been added + to the Bio.SearchIO functions (read/parse and write, respectively). They + are 'use_raw_hit_ids' and 'use_raw_query_ids'. Check out the relevant + SearchIO.BlastIO documentation for a complete description of what these + arguments do. + * Bio.motifs was updated to support changes in MEME v4.11.4 output. + * The Bio.Seq sequence objects now have a ``.count_overlap()`` method to + supplement the Python string like non-overlap based ``.count()`` method. + * The Bio.SeqFeature location objects can now be compared for equality. + * Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw + instead, or another library or program if more advanced plotting functionality + is needed. + * In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously + _DistanceMatrix) has a new method 'format_phylip' to write Phylip-compatible + distance matrix files (contributed by Jordan Willis). + * Additionally, a number of small bugs 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. +- Use license tag + +------------------------------------------------------------------- +Wed May 24 14:28:23 UTC 2017 - toddrme2178@gmail.com + +- Implement single-spec version +- Fix source URL. +- updated to version 1.69 + * We now expect and take advantage of NumPy under PyPy, and compile most of the + Biopython C code modules as well. + * Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the + format name "maf", using new module Bio.AlignIO.MafIO which also offers + indexed access to these potentially large files using SQLite3 (contributed by + Andrew Sczesnak, with additional refinements from Adam Novak). + * Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The + underlying format (ABIF) remains the same as AB1 files and so the string + 'abif' is the expected format argument in the main SeqIO functions. AbiIO + determines whether the file is AB1 or FSA based on the presence of specific + tags. + * The Uniprot parser is now able to parse "submittedName" elements in XML files. + * The NEXUS parser handling of internal node comments has been improved, which + should help if working with tools like the BEAST TreeAnnotator. Slashes are + now also allowed in identifiers. + * New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue, + and cell line ontology (contributed by Steve Marshall). + * For consistency the Bio.Seq module now offers a complement function (already + available as a method on the Seq and MutableSeq objects). + * The SeqFeature object's qualifiers is now an explicitly ordered dictionary + (note that as of Python 3.6 the Python dict is ordered by default anyway). + This helps reproduce GenBank/EMBL files on input/output. + * The Bio.SeqIO UniProt-XML parser was updated to cope with features with + unknown locations which can be found in mass spec data. + * The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type + from the LOCUS/ID line explicitly in the record.annotations dictionary. + The Bio.SeqIO EMBL parser was updated to cope with more variants seen in + patent data files, and the related IMGT parser was updated to cope with + IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed. + The GenBank output now uses colon space to match current NCBI DBLINK lines. + * The Bio.Affy package supports Affymetrix version 4 of the CEL file format, + in addition to version 3. + * The restriction enzyme list in Bio.Restriction has been updated to the + February 2017 release of REBASE. + * Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default), + PDBML/XML and mmtf format protein structures. This is inline with the RCSB + recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython + already has support for parsing mmCif files. + * Additionally, a number of small bugs 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. + +------------------------------------------------------------------- +Thu Nov 17 10:10:59 UTC 2016 - alinm.elena@gmail.com + +- updated to version 1.68 + +------------------------------------------------------------------- +Mon Dec 9 16:00:01 UTC 2013 - toddrme2178@gmail.com + +- Update to version 1.63 + * 2to3 no longer needed for python 3 +- Added additional dependencies + +------------------------------------------------------------------- +Thu Sep 19 02:06:32 UTC 2013 - highwaystar.ru@gmail.com + +- upgrade to version 1.62 + * The translation functions will give a warning on any partial codons + * Phylo module now supports the file formats NeXML and CDAO + * New module Bio.UniProt adds parsers for the GAF, GPA and GPI +formats from UniProt-GOA. + * The BioSQL module is now supported in Jython. + * Feature labels on circular GenomeDiagram figures now support + the label_position argument (start, middle or end) + * The code for parsing 3D structures in mmCIF files was updated + to use the Python standard library's shlex module instead of C code + using flex. + * The Bio.Sequencing.Applications module now includes a BWA + command line wrapper. + * Bio.motifs supports JASPAR format files with multiple + position-frequence matrices. + +------------------------------------------------------------------- +Wed Feb 1 14:09:33 UTC 2012 - saschpe@suse.de + +- Ran spec-cleaner +- Set license to MIT (looks like it) + +------------------------------------------------------------------- +Wed Jan 11 14:56:08 UTC 2012 - toddrme2178@gmail.com + +- Cleaned up spec file + +------------------------------------------------------------------- +Thu Sep 8 19:36:32 UTC 2011 - alinm.elena@gmail.com + +- Initial commit + diff --git a/python-biopython.spec b/python-biopython.spec new file mode 100644 index 0000000..907df32 --- /dev/null +++ b/python-biopython.spec @@ -0,0 +1,89 @@ +# +# spec file for package python-biopython +# +# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# +# All modifications and additions to the file contributed by third parties +# remain the property of their copyright owners, unless otherwise agreed +# upon. The license for this file, and modifications and additions to the +# file, is the same license as for the pristine package itself (unless the +# license for the pristine package is not an Open Source License, in which +# case the license is the MIT License). An "Open Source License" is a +# license that conforms to the Open Source Definition (Version 1.9) +# published by the Open Source Initiative. + +# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# + + +# Tests require a network connection +%bcond_with test + +%{?!python_module:%define python_module() python-%{**} python3-%{**}} +Name: python-biopython +Version: 1.71 +Release: 0 +Summary: Python Tools for Computational Molecular Biology +License: MIT +Group: Development/Libraries/Python +Url: http://www.biopython.org +Source: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz +BuildRequires: flex +BuildRequires: fdupes +BuildRequires: python-rpm-macros +BuildRequires: python3-2to3 +BuildRequires: %{python_module devel} +BuildRequires: %{python_module setuptools} +BuildRequires: %{python_module numpy-devel} +BuildRequires: %{python_module xml} +Requires: python-numpy +Requires: python-xml +Recommends: python-matplotlib +Recommends: python-mysql +Recommends: python-networkx +Recommends: python-psycopg2 +Recommends: python-pydot +Recommends: python-pygraphviz +Recommends: python-rdflib +Recommends: python-reportlab +BuildRoot: %{_tmppath}/%{name}-%{version}-build +%python_subpackages + +%description +The Biopython Project is an international association of developers of freely +available Python tools for computational molecular biology. + +%prep +%setup -n biopython-%{version} +# remove all execute bits from documentation and fix line endings +find -type f -exec chmod -x {} 2>/dev/null ';' +find -type f -exec sed -i 's/\r//' {} 2>/dev/null ';' +# remove she-bang lines in .py files to keep rpmlint happy +find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';' +sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' Scripts/Structure/hsexpo + +%build +export LANG=en_US.UTF-8 +%python_build + +%install +export LANG=en_US.UTF-8 +%python_install +%python_expand %fdupes %{buildroot}%{$python_sitelib} + +%if %{with test} +%check +export LANG=en_US.UTF-8 +%python_exec setup.py test +%endif + +%files %{python_files} +%defattr(-,root,root) +%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst +%doc Doc/ +%license LICENSE.rst +%{python_sitearch}/Bio/ +%{python_sitearch}/BioSQL/ +%{python_sitearch}/biopython-%{version}-py*.egg-info + +%changelog