|
|
a273212 |
%global pname MDAnalysis
|
|
|
a273212 |
%bcond_without check
|
|
|
a273212 |
|
|
|
a273212 |
Name: python-%{pname}
|
|
|
6f231a2 |
Version: 0.20.1
|
|
|
ecc4945 |
Release: 7%{?dist}
|
|
|
a273212 |
Summary: Analyze and manipulate molecular dynamics trajectories
|
|
|
a273212 |
License: GPLv2+ and BSD and MIT and CC-BY-ND
|
|
|
a273212 |
# BSD:
|
|
|
a273212 |
# MDAnalysis/lib/formats/*/xdrfile*
|
|
|
a273212 |
# MDAnalysis/lib/qcprot.pyx
|
|
|
a273212 |
# MDAnalysis/lib/src/transformations/transformations.c
|
|
|
a273212 |
# MDAnalysis/lib/transformations.py
|
|
|
a273212 |
# MIT:
|
|
|
a273212 |
# MDAnalysisTests-0.16.0/MDAnalysisTests/tempdir.py
|
|
|
a273212 |
# CC-BY-ND:
|
|
|
a273212 |
# doc/sphinx/source/_static/logos
|
|
|
a273212 |
# GPLv2+:
|
|
|
a273212 |
# everything else
|
|
|
a273212 |
URL: http://www.mdanalysis.org
|
|
|
a273212 |
Source0: https://files.pythonhosted.org/packages/source/M/%{pname}/%{pname}-%{version}.tar.gz
|
|
|
a273212 |
Source1: https://files.pythonhosted.org/packages/source/M/%{pname}Tests/%{pname}Tests-%{version}.tar.gz
|
|
|
a273212 |
Source2: https://github.com/%{pname}/mdanalysis/files/1935925/pypidoc.zip
|
|
|
a273212 |
# force rebuild of cythonized intermediate sources
|
|
|
a273212 |
Patch1: %{name}-cython.patch
|
|
|
6f231a2 |
Patch2: %{name}-flags.patch
|
|
|
a7844a6 |
# https://bugzilla.redhat.com/show_bug.cgi?id=1853117
|
|
|
a7844a6 |
Patch3: 2763.patch
|
|
|
6f231a2 |
# 32-bit archs: https://github.com/MDAnalysis/mdanalysis/issues/2342
|
|
|
6f231a2 |
# ppc64le, aarch64: https://github.com/MDAnalysis/mdanalysis/issues/2343
|
|
|
6f231a2 |
ExcludeArch: i686 armv7hl s390x ppc64le aarch64
|
|
|
a273212 |
# we don't want to provide private python extension libs in python3 dirs
|
|
|
a273212 |
# there are actually called lib...so, so this is needed
|
|
|
a273212 |
%global __provides_exclude_from ^%{python3_sitearch}/.*\\.so$
|
|
|
a273212 |
|
|
|
a273212 |
%global desc \
|
|
|
a273212 |
MDAnalysis is a python framework to analyze molecular dynamics trajectories\
|
|
|
a273212 |
generated by CHARMM, NAMD, LAMMPS, or Gromacs. It is mainly useful for geometric\
|
|
|
a273212 |
analyses, as there is no implemented potential model. \
|
|
|
a273212 |
\
|
|
|
a273212 |
It is inspired by the Schulten Group's MDtools for python, and the source for\
|
|
|
a273212 |
the DCD reading code is derived from VMD. MDAnalysis isGPL licensed, except for\
|
|
|
a273212 |
the dcd reading code (UIUC Open Source Licence) which comes from VMD (and is\
|
|
|
a273212 |
GPL-compatible). Gromacs trajectories are utilizing the Gromacs libxdrfile\
|
|
|
a273212 |
library (GPL). MDAnalysis exposes trajectory data transparently as NumPy arrays\
|
|
|
a273212 |
and as such it is easily extensible.
|
|
|
a273212 |
|
|
|
a273212 |
%description
|
|
|
a273212 |
%{desc}
|
|
|
a273212 |
|
|
|
a273212 |
%package -n python3-%{pname}
|
|
|
a273212 |
Summary: %{summary}
|
|
|
a273212 |
Requires: python3-biopython
|
|
|
a273212 |
Requires: python3-GridDataFormats >= 0.4.0
|
|
|
a273212 |
Requires: python3-gsd
|
|
|
a273212 |
Requires: python3-joblib
|
|
|
a273212 |
Requires: python3-matplotlib
|
|
|
a273212 |
Requires: python3-mmtf
|
|
|
a273212 |
Requires: python3-networkx
|
|
|
a273212 |
Requires: python3-numpy
|
|
|
a273212 |
Requires: python3-scipy
|
|
|
a273212 |
# optional deps
|
|
|
a273212 |
# this should also include matplotlib and scipy,
|
|
|
a273212 |
# but their lack is not handled gracefully
|
|
|
a273212 |
# https://github.com/MDAnalysis/mdanalysis/issues/1361
|
|
|
a273212 |
Recommends: python3-netcdf4
|
|
|
a273212 |
Recommends: python3-scikit-learn
|
|
|
a273212 |
Recommends: python3-seaborn
|
|
|
a273212 |
BuildRequires: python3-Cython
|
|
|
a273212 |
BuildRequires: python3-devel
|
|
|
a273212 |
BuildRequires: python3-gsd
|
|
|
a273212 |
BuildRequires: python3-numpy
|
|
|
a273212 |
BuildRequires: python3-setuptools
|
|
|
a273212 |
%if %{with check}
|
|
|
a273212 |
BuildRequires: python3-biopython
|
|
|
a273212 |
BuildRequires: python3-GridDataFormats >= 0.4.0
|
|
|
a273212 |
BuildRequires: python3-hypothesis
|
|
|
a273212 |
BuildRequires: python3-joblib
|
|
|
a273212 |
BuildRequires: python3-matplotlib
|
|
|
a273212 |
BuildRequires: python3-mmtf
|
|
|
a273212 |
BuildRequires: python3-mock
|
|
|
a273212 |
BuildRequires: python3-netcdf4
|
|
|
a273212 |
BuildRequires: python3-networkx
|
|
|
a273212 |
BuildRequires: python3-psutil
|
|
|
a273212 |
BuildRequires: python3-pytest-xdist
|
|
|
a273212 |
BuildRequires: python3-scikit-learn
|
|
|
a273212 |
BuildRequires: python3-tempdir
|
|
|
a273212 |
%endif
|
|
|
6f231a2 |
BuildRequires: gcc-c++
|
|
|
a273212 |
# MDAnalysis/coordinates/xdrfile/src
|
|
|
a273212 |
Provides: bundled(xdrfile) = 0.7.7
|
|
|
a273212 |
%{?python_provide:%python_provide python3-%{pname}}
|
|
|
a273212 |
|
|
|
a273212 |
%description -n python3-%{pname}
|
|
|
a273212 |
%{desc}
|
|
|
a273212 |
|
|
|
a273212 |
%package doc
|
|
|
a273212 |
Summary: Documentation for MDAnalysis
|
|
|
a273212 |
BuildArch: noarch
|
|
|
a273212 |
License: CC-BY-ND and GPLv2+
|
|
|
a273212 |
|
|
|
a273212 |
%description doc
|
|
|
a273212 |
MDAnalysis is a python framework to analyze molecular dynamics trajectories
|
|
|
a273212 |
generated by CHARMM, NAMD, LAMMPS, or Gromacs. It is mainly useful for geometric
|
|
|
a273212 |
analyses, as there is no implemented potential model.
|
|
|
a273212 |
|
|
|
a273212 |
This package contains the documentation
|
|
|
a273212 |
|
|
|
a273212 |
%prep
|
|
|
a273212 |
%setup -q -n %{pname}-%{version} -a 1
|
|
|
a273212 |
%patch1 -p1 -b .cython
|
|
|
6f231a2 |
%patch2 -p1 -b .flags
|
|
|
a7844a6 |
%patch3 -p1
|
|
|
a273212 |
# force rebuild of Egg Metadata
|
|
|
a273212 |
rm -r %{pname}.egg-info
|
|
|
a273212 |
rm -r %{pname}Tests-%{version}/%{pname}Tests.egg-info
|
|
|
a273212 |
chmod -x %{pname}Tests-%{version}/%{pname}Tests/data/dlpoly/CONFIG*
|
|
|
a273212 |
|
|
|
a273212 |
%build
|
|
|
a273212 |
%{py3_build}
|
|
|
a273212 |
|
|
|
a273212 |
pushd %{pname}Tests-%{version}
|
|
|
a273212 |
%{py3_build}
|
|
|
a273212 |
popd
|
|
|
a273212 |
|
|
|
a273212 |
mkdir -p doc/html
|
|
|
a273212 |
unzip -qq -o %{SOURCE2} -d doc/html
|
|
|
a273212 |
find doc/html -type d |xargs chmod 755
|
|
|
a273212 |
|
|
|
a273212 |
%install
|
|
|
a273212 |
%{py3_install}
|
|
|
a273212 |
find %{buildroot}%{python3_sitearch}/%{pname} -type f -name "*.so" | xargs chmod 755
|
|
|
a273212 |
|
|
|
a273212 |
pushd %{pname}Tests-%{version}
|
|
|
a273212 |
%{py3_install}
|
|
|
a273212 |
popd
|
|
|
a273212 |
|
|
|
a273212 |
%if %{with check}
|
|
|
a273212 |
%check
|
|
|
a273212 |
# https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests#recommended
|
|
|
a273212 |
# skip some tests for now
|
|
|
a273212 |
# https://github.com/MDAnalysis/mdanalysis/issues/1969
|
|
|
a273212 |
# https://github.com/MDAnalysis/mdanalysis/issues/1970
|
|
|
a273212 |
# GSD test needs a native-endian sample, so skip on big-endian for now
|
|
|
a273212 |
# https://github.com/MDAnalysis/mdanalysis/issues/1829
|
|
|
a273212 |
cd %{pname}Tests-%{version}/%{pname}Tests
|
|
|
a273212 |
PYTHONPATH=%{buildroot}%{python3_sitelib}:%{buildroot}%{python3_sitearch} \
|
|
|
a273212 |
pytest-%{python3_version} \
|
|
|
a273212 |
-v \
|
|
|
a273212 |
--disable-pytest-warnings \
|
|
|
a273212 |
--numprocesses=auto \
|
|
|
a273212 |
-k 'not test_hes \
|
|
|
a273212 |
and not test_clustering_KMeans_direct \
|
|
|
a273212 |
and not test_clustering_method_w_no_distance_matrix \
|
|
|
a273212 |
%ifarch s390x
|
|
|
a273212 |
and not test_clustering_three_ensembles_two_identical \
|
|
|
a273212 |
and not test_rmsd \
|
|
|
a273212 |
and not (test_rms and test_custom_weighted) \
|
|
|
a273212 |
and not (test_rms and test_mass_weighted) \
|
|
|
a273212 |
and not (test_chainreader and test_time) \
|
|
|
a273212 |
and not test_dcd \
|
|
|
a273212 |
and not (test_lammps and test_Timestep_time) \
|
|
|
a273212 |
and not (test_lammps and test_dt) \
|
|
|
a273212 |
and not test_rename_aux \
|
|
|
a273212 |
and not test_iter_as_aux_lowf \
|
|
|
a273212 |
and not test_iter_as_aux_highf \
|
|
|
a273212 |
%endif
|
|
|
a273212 |
%ifarch ppc64 s390x
|
|
|
a273212 |
and not test_gsd \
|
|
|
a273212 |
%endif
|
|
|
a273212 |
and not test_clustering_two_methods_one_w_no_distance_matrix' \
|
|
|
a273212 |
|
|
|
a273212 |
%endif
|
|
|
a273212 |
|
|
|
a273212 |
%files -n python3-%{pname}
|
|
|
a273212 |
%license LICENSE
|
|
|
a273212 |
%doc AUTHORS CHANGELOG README SUMMARY.txt
|
|
|
a273212 |
%{python3_sitearch}/%{pname}-%{version}-py%{python3_version}.egg-info
|
|
|
a273212 |
%{python3_sitearch}/%{pname}
|
|
|
a273212 |
%exclude %{python3_sitelib}/%{pname}Tests-%{version}-py%{python3_version}.egg-info
|
|
|
a273212 |
%exclude %{python3_sitelib}/%{pname}Tests
|
|
|
a273212 |
|
|
|
a273212 |
%files doc
|
|
|
a273212 |
%license LICENSE
|
|
|
a273212 |
%doc doc/html/*
|
|
|
a273212 |
|
|
|
a273212 |
%changelog
|
|
|
ecc4945 |
* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 0.20.1-7
|
|
|
ecc4945 |
- Rebuilt for Python 3.10
|
|
|
ecc4945 |
|
|
|
4429956 |
* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.20.1-6
|
|
|
4429956 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
|
|
|
4429956 |
|
|
|
d43d246 |
* Tue Jul 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.20.1-5
|
|
|
d43d246 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
|
|
d43d246 |
|
|
|
a7844a6 |
* Thu Jul 02 2020 Christoph Junghans <junghans@votca.org> - 0.20.1-4
|
|
|
a7844a6 |
- Fix build with matplotlib 3.3.0rc1 (bug #1853117)
|
|
|
a7844a6 |
|
|
|
c629d29 |
* Tue May 26 2020 Miro HronĨok <mhroncok@redhat.com> - 0.20.1-3
|
|
|
c629d29 |
- Rebuilt for Python 3.9
|
|
|
c629d29 |
|
|
|
497a5c7 |
* Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.20.1-2
|
|
|
497a5c7 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
|
|
|
497a5c7 |
|
|
|
6f231a2 |
* Wed Sep 11 2019 Christoph Junghans <junghans@votca.org> - 0.20.1-1
|
|
|
6f231a2 |
- Version bump to 0.20.1
|
|
|
6f231a2 |
|
|
|
a273212 |
* Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.18.0-4
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.18.0-3
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Fri Aug 24 2018 Miro HronĨok <mhroncok@redhat.com> - 0.18.0-2
|
|
|
a273212 |
- Switch to Python 3
|
|
|
a273212 |
|
|
|
a273212 |
* Mon Jul 02 2018 Dominik Mierzejewski <rpm@greysector.net> - 0.18.0-1
|
|
|
a273212 |
- update to 0.18.0
|
|
|
a273212 |
- drop obsolete patches
|
|
|
a273212 |
- fix analysis tests on 32bit
|
|
|
a273212 |
- new dependency: python-gsd
|
|
|
a273212 |
- upstream switched from nose to pytest for testing
|
|
|
a273212 |
- use standard bcond to enable/disable tests
|
|
|
a273212 |
- use pytest options to skip some tests instead of patching them out
|
|
|
a273212 |
|
|
|
a273212 |
* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.16.2-4
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.16.2-3
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.16.2-2
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Fri Jun 30 2017 Dominik Mierzejewski <rpm@greysector.net> - 0.16.2-1
|
|
|
a273212 |
- update to 0.16.2
|
|
|
a273212 |
- update doc tarball URL and handling
|
|
|
a273212 |
- drop obsolete patch
|
|
|
a273212 |
|
|
|
a273212 |
* Thu Jun 22 2017 Dominik Mierzejewski <rpm@greysector.net> - 0.16.1-3
|
|
|
a273212 |
- fix endianness issues on BE arches (ppc64, s390x)
|
|
|
a273212 |
- increase test process timeout (was timing out on aarch64)
|
|
|
a273212 |
|
|
|
a273212 |
* Sat Jun 17 2017 Dominik Mierzejewski <rpm@greysector.net> - 0.16.1-2
|
|
|
a273212 |
- backport more fixes from git
|
|
|
a273212 |
|
|
|
a273212 |
* Thu Jun 08 2017 Dominik Mierzejewski <rpm@greysector.net> - 0.16.1-1
|
|
|
a273212 |
- update to 0.16.1
|
|
|
a273212 |
- fix test failures on 32bit
|
|
|
a273212 |
|
|
|
a273212 |
* Thu May 18 2017 Dominik Mierzejewski <rpm@greysector.net> - 0.16.0-1
|
|
|
a273212 |
- update to 0.16.0
|
|
|
a273212 |
- drop obsolete patches
|
|
|
a273212 |
- add new dependencies (joblib, mmtf, mock, psutil)
|
|
|
a273212 |
- fix netcdf4-python dependencies (need python2-netcdf4, actually)
|
|
|
a273212 |
- switch to nosetests while strange test failures are investigated
|
|
|
a273212 |
(https://github.com/MDAnalysis/mdanalysis/issues/1360)
|
|
|
a273212 |
- add a link to upstream-recommended way of running tests
|
|
|
a273212 |
- modernize python module dependencies
|
|
|
a273212 |
|
|
|
a273212 |
* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.14.0-5
|
|
|
a273212 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
|
|
|
a273212 |
|
|
|
a273212 |
* Mon Sep 26 2016 Dominik Mierzejewski <rpm@greysector.net> - 0.14.0-4
|
|
|
a273212 |
- rebuilt for matplotlib-2.0.0
|
|
|
a273212 |
|
|
|
a273212 |
* Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.14.0-3
|
|
|
a273212 |
- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages
|
|
|
a273212 |
|
|
|
a273212 |
* Tue Mar 15 2016 Dominik Mierzejewski <rpm@greysector.net> 0.14.0-2
|
|
|
a273212 |
- fix non-standard-dir-perm in doc subpackage
|
|
|
a273212 |
- move python2 build to python2-MDAnalysis subpackage
|
|
|
a273212 |
- exclude private libmdaxdr.so from Provides:
|
|
|
a273212 |
|
|
|
a273212 |
* Fri Mar 11 2016 Dominik Mierzejewski <rpm@greysector.net> 0.14.0-1
|
|
|
a273212 |
- update to 0.14.0
|
|
|
a273212 |
- don't build docs for now, upstream published them in a zip file
|
|
|
a273212 |
- drop obsolete patch
|
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a273212 |
- fix tests with numpy 1.11
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a273212 |
- fix license field for docs subpackage
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a273212 |
- install LICENSE with the doc subpackage as well
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a273212 |
- move building of docs to the build section
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a273212 |
- use some python-related convenience macros
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a273212 |
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a273212 |
* Tue Feb 09 2016 Dominik Mierzejewski <rpm@greysector.net> 0.13.0-2
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a273212 |
- build docs
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a273212 |
- new dependency: seaborn
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a273212 |
- omit failing tests on f24 for now
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a273212 |
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a273212 |
* Mon Feb 08 2016 Dominik Mierzejewski <rpm@greysector.net> 0.13.0-1
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a273212 |
- update to 0.13.0
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a273212 |
- fix running tests
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a273212 |
- add Provides for bundled xdrfile
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a273212 |
- docs not included and failing to build, so disable for now
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a273212 |
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a273212 |
* Wed Oct 14 2015 Dominik Mierzejewski <rpm@greysector.net> 0.12.1-1
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a273212 |
- update to 0.12.1
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a273212 |
- drop obsolete patch
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a273212 |
- use the new mda_nosetests script for running tests
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a273212 |
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a273212 |
* Mon May 18 2015 Dominik Mierzejewski <rpm@greysector.net> 0.9.2-4
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a273212 |
- relax Improper Torsion topology test check on i686
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a273212 |
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a273212 |
* Mon May 11 2015 Dominik Mierzejewski <rpm@greysector.net> 0.9.2-3
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a273212 |
- document licensing breakdown
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a273212 |
- package docs
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a273212 |
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a273212 |
* Fri May 08 2015 Dominik Mierzejewski <rpm@greysector.net> 0.9.2-2
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a273212 |
- call the testsuite per upstream docs
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a273212 |
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a273212 |
* Wed May 06 2015 Dominik Mierzejewski <rpm@greysector.net> 0.9.2-1
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a273212 |
- update to 0.9.2
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a273212 |
- update upstream URL
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a273212 |
- drop obsolete patch
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a273212 |
- fix testsuite invocation
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a273212 |
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a273212 |
* Wed Feb 04 2015 Dominik Mierzejewski <rpm@greysector.net> 0.8.1-1
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a273212 |
- initial build
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