From 805dc6e9a0bf3e6d514c17cd05ac4a8552171d81 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sep 17 2021 16:40:43 +0000 Subject: FTBFS (bug #1903956) --- diff --git a/.gitignore b/.gitignore deleted file mode 100644 index c95755f..0000000 --- a/.gitignore +++ /dev/null @@ -1,16 +0,0 @@ -/Documentation.zip -/MDAnalysis-0.14.0.tar.gz -/MDAnalysisTests-0.14.0.tar.gz -/MDAnalysis-0.16.1.tar.gz -/MDAnalysisDocs-0.16.1.tar.gz -/MDAnalysisTests-0.16.1.tar.gz -/MDAnalysis-0.16.2.tar.gz -/MDAnalysisTests-0.16.2.tar.gz -/MDAnalysisDocs-0.16.2.zip -/MDAnalysis-0.18.0.tar.gz -/MDAnalysisTests-0.18.0.tar.gz -/pypidoc.zip -/MDAnalysis-0.20.0.tar.gz -/MDAnalysisTests-0.20.0.tar.gz -/MDAnalysis-0.20.1.tar.gz -/MDAnalysisTests-0.20.1.tar.gz diff --git a/2457.patch b/2457.patch deleted file mode 100644 index be14abb..0000000 --- a/2457.patch +++ /dev/null @@ -1,113 +0,0 @@ -From dd94b4b8731e09142c08aa9422e49c7b4839d0d0 Mon Sep 17 00:00:00 2001 -From: Rocco Meli -Date: Fri, 17 Jan 2020 12:18:11 +0000 -Subject: [PATCH] remove Bio.Alphabet from align.py - -This assumes the standard gap char - ---- - MDAnalysis/analysis/align.py | 16 ++++------------ - 1 file changed, 4 insertions(+), 12 deletions(-) - -diff --git a/MDAnalysis/analysis/align.py b/MDAnalysis/analysis/align.py -index 7c94a1a..5b1c338 100644 ---- a/MDAnalysis/analysis/align.py -+++ b/MDAnalysis/analysis/align.py -@@ -197,7 +197,6 @@ import numpy as np - import Bio.SeqIO - import Bio.AlignIO - import Bio.Align.Applications --import Bio.Alphabet - import Bio.pairwise2 - - import MDAnalysis as mda -@@ -834,12 +833,11 @@ def fasta2select(fastafilename, is_aligned=False, - .. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/ - - """ -- protein_gapped = Bio.Alphabet.Gapped(Bio.Alphabet.IUPAC.protein) - if is_aligned: - logger.info("Using provided alignment {}".format(fastafilename)) - with open(fastafilename) as fasta: - alignment = Bio.AlignIO.read( -- fasta, "fasta", alphabet=protein_gapped) -+ fasta, "fasta") - else: - if alnfilename is None: - filepath, ext = os.path.splitext(fastafilename) -@@ -867,7 +865,7 @@ def fasta2select(fastafilename, is_aligned=False, - raise - with open(alnfilename) as aln: - alignment = Bio.AlignIO.read( -- aln, "clustal", alphabet=protein_gapped) -+ aln, "clustal") - logger.info( - "Using clustalw sequence alignment {0!r}".format(alnfilename)) - logger.info( -@@ -886,7 +884,7 @@ def fasta2select(fastafilename, is_aligned=False, - if orig_resids[iseq] is None: - # build default: assume consecutive numbering of all - # residues in the alignment -- GAP = a.seq.alphabet.gap_char -+ GAP = "-" - length = len(a.seq) - a.seq.count(GAP) - orig_resids[iseq] = np.arange(1, length + 1) - else: -@@ -928,7 +926,7 @@ def fasta2select(fastafilename, is_aligned=False, - nseq = len(alignment) - t = np.zeros((nseq, alignment.get_alignment_length()), dtype=int) - for iseq, a in enumerate(alignment): -- GAP = a.seq.alphabet.gap_char -+ GAP = "-" - t[iseq, :] = seq2resids[iseq][np.cumsum(np.where( - np.array(list(a.seq)) == GAP, 0, 1)) - 1] - # -1 because seq2resid is index-1 based (resids start at 1) -@@ -944,12 +942,6 @@ def fasta2select(fastafilename, is_aligned=False, - # could collect just resid and type (with/without CB) and - # then post-process and use ranges for continuous stretches, eg - # ( resid 1:35 and ( backbone or name CB ) ) or ( resid 36 and backbone ) -- -- # should be the same for both seqs -- GAP = alignment[0].seq.alphabet.gap_char -- if GAP != alignment[1].seq.alphabet.gap_char: -- raise ValueError( -- "Different gap characters in sequence 'target' and 'mobile'.") - for ipos in range(alignment.get_alignment_length()): - aligned = list(alignment[:, ipos]) - if GAP in aligned: --- -2.32.0 - -From b23e3241e89fa5dfe9fb2af994e51149a1171656 Mon Sep 17 00:00:00 2001 -From: Rocco Meli -Date: Fri, 17 Jan 2020 12:31:18 +0000 -Subject: [PATCH] remove Bio.Alphabet from topologyattrs - -use default alphabet ---- - MDAnalysis/core/topologyattrs.py | 3 +-- - 1 file changed, 1 insertion(+), 2 deletions(-) - -diff --git a/MDAnalysis/core/topologyattrs.py b/MDAnalysis/core/topologyattrs.py -index 5366bca..466d720 100644 ---- a/MDAnalysis/core/topologyattrs.py -+++ b/MDAnalysis/core/topologyattrs.py -@@ -37,7 +37,6 @@ from six.moves import zip, range - - import Bio.Seq - import Bio.SeqRecord --import Bio.Alphabet - from collections import defaultdict - import copy - import functools -@@ -1486,7 +1485,7 @@ class Resnames(ResidueAttr): - "character".format(err.message)) - if format == "string": - return sequence -- seq = Bio.Seq.Seq(sequence, alphabet=Bio.Alphabet.IUPAC.protein) -+ seq = Bio.Seq.Seq(sequence) - if format == "Seq": - return seq - return Bio.SeqRecord.SeqRecord(seq, **kwargs) --- -2.32.0 - diff --git a/2763.patch b/2763.patch deleted file mode 100644 index 00262a7..0000000 --- a/2763.patch +++ /dev/null @@ -1,42 +0,0 @@ -From d8fa7bf9d41b7a3e7a548d09be52e957cd4a55de Mon Sep 17 00:00:00 2001 -From: Oliver Beckstein -Date: Mon, 15 Jun 2020 17:31:16 -0700 -Subject: [PATCH] removed matplotlib.use('agg') from tests - -- fix #2191 -diff --git a/MDAnalysisTests-0.20.1/MDAnalysisTests/__init__.py b/MDAnalysisTests-0.20.1/MDAnalysisTests/__init__.py -index e41c7c5808..7a7fef347f 100644 ---- a/MDAnalysisTests-0.20.1/MDAnalysisTests/__init__.py -+++ b/MDAnalysisTests-0.20.1/MDAnalysisTests/__init__.py -@@ -118,14 +118,10 @@ - os.environ['DUECREDIT_ENABLE'] = 'yes' - - # Any tests that plot with matplotlib need to run with the simple agg backend --# because on Travis there is no DISPLAY set. This doesn't warn if we import --# files from the tests after loading matplotlib. This will remove unnecessary --# user warnings. --try: -- import matplotlib -- matplotlib.use('agg', warn=False) --except ImportError: -- pass -+# because on Travis there is no DISPLAY set. -+# -+# Instead of using matplotlib.use() we set MPLBACKEND=agg in the CI environment. -+# See https://matplotlib.org/3.2.1/tutorials/introductory/usage.html#backends - - from MDAnalysisTests.util import ( - block_import, -diff --git a/MDAnalysisTests-0.20.1/MDAnalysisTests/visualization/test_streamlines.py b/MDAnalysisTests-0.20.1/MDAnalysisTests/visualization/test_streamlines.py -index 8e446a0e72..333d8fda49 100644 ---- a/MDAnalysisTests-0.20.1/MDAnalysisTests/visualization/test_streamlines.py -+++ b/MDAnalysisTests-0.20.1/MDAnalysisTests/visualization/test_streamlines.py -@@ -29,8 +29,6 @@ - from MDAnalysis.coordinates.XTC import XTCWriter - from MDAnalysisTests.datafiles import Martini_membrane_gro - import pytest --import matplotlib --matplotlib.use('agg') - import matplotlib.pyplot as plt - import os - diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..c91b476 --- /dev/null +++ b/dead.package @@ -0,0 +1 @@ +FTBFS (bug #1903956) diff --git a/python-MDAnalysis-32bit.patch b/python-MDAnalysis-32bit.patch deleted file mode 100644 index c6b42f6..0000000 --- a/python-MDAnalysis-32bit.patch +++ /dev/null @@ -1,78 +0,0 @@ -diff -up MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/affinityprop.pyx.32bit MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/affinityprop.pyx ---- MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/affinityprop.pyx.32bit 2018-07-02 15:40:27.495006418 +0200 -+++ MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2018-07-02 15:43:47.016901634 +0200 -@@ -30,9 +30,10 @@ import logging - import numpy - cimport numpy - cimport cython -+from libc.stdint cimport int64_t - - cdef extern from "ap.h": -- int CAffinityPropagation(float*, int, float, int, int, bint, long*) -+ int CAffinityPropagation(float*, int, float, int, int, bint, int64_t*) - - @cython.boundscheck(False) - @cython.wraparound(False) -@@ -96,10 +97,10 @@ def AffinityPropagation(s, preference, f - - # Prepare input and ouput arrays - cdef numpy.ndarray[numpy.float32_t, ndim=1] matndarray = numpy.ascontiguousarray(s._elements, dtype=numpy.float32) -- cdef numpy.ndarray[long, ndim=1] clusters = numpy.zeros((s.size),dtype=long) -+ cdef numpy.ndarray[numpy.int64_t, ndim=1] clusters = numpy.zeros((s.size),dtype=numpy.int64) - - # run C module Affinity Propagation -- iterations = CAffinityPropagation(matndarray.data, cn, lam, max_iterations, convergence, noise, clusters.data) -+ iterations = CAffinityPropagation(matndarray.data, cn, lam, max_iterations, convergence, noise, clusters.data) - - # Provide warning in case of lack of convergence - if iterations == 0: -diff -up MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/include/ap.h.32bit MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/include/ap.h ---- MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/include/ap.h.32bit 2018-04-15 21:56:44.000000000 +0200 -+++ MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/include/ap.h 2018-07-02 15:41:51.358803074 +0200 -@@ -19,6 +19,8 @@ - MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. - J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 - */ -+#include -+ - int trmIndex(int, int); - - int sqmIndex(int, int, int); -@@ -27,4 +29,4 @@ float min(float*, int); - #endif - - --int CAffinityPropagation(float*, int, float, int, int, int, long*); -+int CAffinityPropagation(float*, int, float, int, int, int, int64_t*); -diff -up MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/src/ap.c.32bit MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/src/ap.c ---- MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/src/ap.c.32bit 2018-04-15 21:56:44.000000000 +0200 -+++ MDAnalysis-0.18.0/MDAnalysis/analysis/encore/clustering/src/ap.c 2018-07-02 15:41:51.359803083 +0200 -@@ -22,6 +22,7 @@ - #include - #include - #include -+#include - - /* Helper functions */ - -@@ -80,7 +81,7 @@ void printtrmatrix(float* array, int len - } - } - --int CAffinityPropagation(float *s, int n, float lambda, int max_iterations, int convergence, int noise, long* clusters) { // Affinity Propagation clustering algorithm -+int CAffinityPropagation(float *s, int n, float lambda, int max_iterations, int convergence, int noise, int64_t* clusters) { // Affinity Propagation clustering algorithm - - /* n: number of elements - s: similarity matrix -diff -up MDAnalysis-0.18.0/MDAnalysisTests-0.18.0/MDAnalysisTests/analysis/test_encore.py.32bit MDAnalysis-0.18.0/MDAnalysisTests-0.18.0/MDAnalysisTests/analysis/test_encore.py ---- MDAnalysis-0.20.0/MDAnalysisTests-0.20.0/MDAnalysisTests/analysis/test_encore.py.32bit 2018-04-15 21:56:44.000000000 +0200 -+++ MDAnalysis-0.20.0/MDAnalysisTests-0.20.0/MDAnalysisTests/analysis/test_encore.py 2018-07-02 15:41:51.360803093 +0200 -@@ -262,7 +262,7 @@ inconsistent results") - clustering_method=encore.AffinityPropagationNative(preference = -3.0)) - result_value = results[0,1] - expected_value = 0. -- assert_almost_equal(result_value, expected_value, -+ assert_almost_equal(result_value, expected_value, decimal=2, - err_msg="ClusteringEnsemble Similarity to itself not zero: {0:f}".format(result_value)) - - def test_ces(self, ens1, ens2): diff --git a/python-MDAnalysis-cython.patch b/python-MDAnalysis-cython.patch deleted file mode 100644 index 852c5ed..0000000 --- a/python-MDAnalysis-cython.patch +++ /dev/null @@ -1,9 +0,0 @@ -diff -up MDAnalysis-0.17.0/setup.cfg.cython MDAnalysis-0.17.0/setup.cfg ---- MDAnalysis-0.17.0/setup.cfg.cython 2018-01-25 13:05:02.000000001 +0100 -+++ MDAnalysis-0.17.0/setup.cfg 2018-03-12 21:57:13.103240022 +0100 -@@ -1,4 +1,5 @@ - [options] -+use_cython = 1 - - [wheel] - universal = 1 diff --git a/python-MDAnalysis-flags.patch b/python-MDAnalysis-flags.patch deleted file mode 100644 index 8b494f0..0000000 --- a/python-MDAnalysis-flags.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -up MDAnalysis-0.17.0/setup.py.flags MDAnalysis-0.17.0/setup.py ---- MDAnalysis-0.17.0/setup.py.flags 2018-01-24 19:00:10.000000000 +0100 -+++ MDAnalysis-0.17.0/setup.py 2018-02-23 00:51:37.033514330 +0100 -@@ -253,7 +253,7 @@ def extensions(config): - use_cython = config.get('use_cython', default=not is_release) - use_openmp = config.get('use_openmp', default=True) - -- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops'] -+ extra_compile_args = ['-std=c99'] - define_macros = [] - if config.get('debug_cflags', default=False): - extra_compile_args.extend(['-Wall', '-pedantic']) diff --git a/python-MDAnalysis.spec b/python-MDAnalysis.spec deleted file mode 100644 index a149534..0000000 --- a/python-MDAnalysis.spec +++ /dev/null @@ -1,326 +0,0 @@ -%global pname MDAnalysis -%bcond_without check - -Name: python-%{pname} -Version: 0.20.1 -Release: 8%{?dist} -Summary: Analyze and manipulate molecular dynamics trajectories -License: GPLv2+ and BSD and MIT and CC-BY-ND -# BSD: -# MDAnalysis/lib/formats/*/xdrfile* -# MDAnalysis/lib/qcprot.pyx -# MDAnalysis/lib/src/transformations/transformations.c -# MDAnalysis/lib/transformations.py -# MIT: -# MDAnalysisTests-0.16.0/MDAnalysisTests/tempdir.py -# CC-BY-ND: -# doc/sphinx/source/_static/logos -# GPLv2+: -# everything else -URL: http://www.mdanalysis.org -Source0: https://files.pythonhosted.org/packages/source/M/%{pname}/%{pname}-%{version}.tar.gz -Source1: https://files.pythonhosted.org/packages/source/M/%{pname}Tests/%{pname}Tests-%{version}.tar.gz -Source2: https://github.com/%{pname}/mdanalysis/files/1935925/pypidoc.zip -# force rebuild of cythonized intermediate sources -Patch1: %{name}-cython.patch -Patch2: %{name}-flags.patch -# https://bugzilla.redhat.com/show_bug.cgi?id=1853117 -Patch3: 2763.patch -# https://bugzilla.redhat.com/show_bug.cgi?id=1903956 -# https://github.com/MDAnalysis/mdanalysis/pull/2457 -Patch4: 2457.patch -# 32-bit archs: https://github.com/MDAnalysis/mdanalysis/issues/2342 -# ppc64le, aarch64: https://github.com/MDAnalysis/mdanalysis/issues/2343 -ExcludeArch: i686 armv7hl s390x ppc64le aarch64 -# we don't want to provide private python extension libs in python3 dirs -# there are actually called lib...so, so this is needed -%global __provides_exclude_from ^%{python3_sitearch}/.*\\.so$ - -%global desc \ -MDAnalysis is a python framework to analyze molecular dynamics trajectories\ -generated by CHARMM, NAMD, LAMMPS, or Gromacs. It is mainly useful for geometric\ -analyses, as there is no implemented potential model. \ -\ -It is inspired by the Schulten Group's MDtools for python, and the source for\ -the DCD reading code is derived from VMD. MDAnalysis isGPL licensed, except for\ -the dcd reading code (UIUC Open Source Licence) which comes from VMD (and is\ -GPL-compatible). Gromacs trajectories are utilizing the Gromacs libxdrfile\ -library (GPL). MDAnalysis exposes trajectory data transparently as NumPy arrays\ -and as such it is easily extensible. - -%description -%{desc} - -%package -n python3-%{pname} -Summary: %{summary} -Requires: python3-biopython -Requires: python3-GridDataFormats >= 0.4.0 -Requires: python3-gsd -Requires: python3-joblib -Requires: python3-matplotlib -Requires: python3-mmtf -Requires: python3-networkx -Requires: python3-numpy -Requires: python3-scipy -# optional deps -# this should also include matplotlib and scipy, -# but their lack is not handled gracefully -# https://github.com/MDAnalysis/mdanalysis/issues/1361 -Recommends: python3-netcdf4 -Recommends: python3-scikit-learn -Recommends: python3-seaborn -BuildRequires: python3-Cython -BuildRequires: python3-devel -BuildRequires: python3-gsd -BuildRequires: python3-numpy -BuildRequires: python3-setuptools -%if %{with check} -BuildRequires: python3-biopython -BuildRequires: python3-GridDataFormats >= 0.4.0 -BuildRequires: python3-hypothesis -BuildRequires: python3-joblib -BuildRequires: python3-matplotlib -BuildRequires: python3-mmtf -BuildRequires: python3-mock -BuildRequires: python3-netcdf4 -BuildRequires: python3-networkx -BuildRequires: python3-psutil -BuildRequires: python3-pytest-xdist -BuildRequires: python3-scikit-learn -BuildRequires: python3-tempdir -%endif -BuildRequires: gcc-c++ -# MDAnalysis/coordinates/xdrfile/src -Provides: bundled(xdrfile) = 0.7.7 -%{?python_provide:%python_provide python3-%{pname}} - -%description -n python3-%{pname} -%{desc} - -%package doc -Summary: Documentation for MDAnalysis -BuildArch: noarch -License: CC-BY-ND and GPLv2+ - -%description doc -MDAnalysis is a python framework to analyze molecular dynamics trajectories -generated by CHARMM, NAMD, LAMMPS, or Gromacs. It is mainly useful for geometric -analyses, as there is no implemented potential model. - -This package contains the documentation - -%prep -%setup -q -n %{pname}-%{version} -a 1 -%patch1 -p1 -b .cython -%patch2 -p1 -b .flags -%patch3 -p1 -%patch4 -p1 -# force rebuild of Egg Metadata -rm -r %{pname}.egg-info -rm -r %{pname}Tests-%{version}/%{pname}Tests.egg-info -chmod -x %{pname}Tests-%{version}/%{pname}Tests/data/dlpoly/CONFIG* - -%build -%{py3_build} - -pushd %{pname}Tests-%{version} -%{py3_build} -popd - -mkdir -p doc/html -unzip -qq -o %{SOURCE2} -d doc/html -find doc/html -type d |xargs chmod 755 - -%install -%{py3_install} -find %{buildroot}%{python3_sitearch}/%{pname} -type f -name "*.so" | xargs chmod 755 - -pushd %{pname}Tests-%{version} -%{py3_install} -popd - -%if %{with check} -%check -# https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests#recommended -# skip some tests for now -# https://github.com/MDAnalysis/mdanalysis/issues/1969 -# https://github.com/MDAnalysis/mdanalysis/issues/1970 -# GSD test needs a native-endian sample, so skip on big-endian for now -# https://github.com/MDAnalysis/mdanalysis/issues/1829 -cd %{pname}Tests-%{version}/%{pname}Tests -PYTHONPATH=%{buildroot}%{python3_sitelib}:%{buildroot}%{python3_sitearch} \ - pytest-%{python3_version} \ - -v \ - --disable-pytest-warnings \ - --numprocesses=auto \ - -k "not test_hes \ - and not test_clustering_KMeans_direct \ - and not test_clustering_method_w_no_distance_matrix \ -%ifarch s390x - and not test_clustering_three_ensembles_two_identical \ - and not test_rmsd \ - and not (test_rms and test_custom_weighted) \ - and not (test_rms and test_mass_weighted) \ - and not (test_chainreader and test_time) \ - and not test_dcd \ - and not (test_lammps and test_Timestep_time) \ - and not (test_lammps and test_dt) \ - and not test_rename_aux \ - and not test_iter_as_aux_lowf \ - and not test_iter_as_aux_highf \ -%endif -%ifarch ppc64 s390x - and not test_gsd \ -%endif - and not test_clustering_two_methods_one_w_no_distance_matrix" \ - -%endif - -%files -n python3-%{pname} -%license LICENSE -%doc AUTHORS CHANGELOG README SUMMARY.txt -%{python3_sitearch}/%{pname}-%{version}-py%{python3_version}.egg-info -%{python3_sitearch}/%{pname} -%exclude %{python3_sitelib}/%{pname}Tests-%{version}-py%{python3_version}.egg-info -%exclude %{python3_sitelib}/%{pname}Tests - -%files doc -%license LICENSE -%doc doc/html/* - -%changelog -* Fri Jul 23 2021 Fedora Release Engineering - 0.20.1-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild - -* Fri Jun 04 2021 Python Maint - 0.20.1-7 -- Rebuilt for Python 3.10 - -* Wed Jan 27 2021 Fedora Release Engineering - 0.20.1-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Tue Jul 28 2020 Fedora Release Engineering - 0.20.1-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Thu Jul 02 2020 Christoph Junghans - 0.20.1-4 -- Fix build with matplotlib 3.3.0rc1 (bug #1853117) - -* Tue May 26 2020 Miro Hrončok - 0.20.1-3 -- Rebuilt for Python 3.9 - -* Thu Jan 30 2020 Fedora Release Engineering - 0.20.1-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Wed Sep 11 2019 Christoph Junghans - 0.20.1-1 -- Version bump to 0.20.1 - -* Fri Jul 26 2019 Fedora Release Engineering - 0.18.0-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - -* Sat Feb 02 2019 Fedora Release Engineering - 0.18.0-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Fri Aug 24 2018 Miro Hrončok - 0.18.0-2 -- Switch to Python 3 - -* Mon Jul 02 2018 Dominik Mierzejewski - 0.18.0-1 -- update to 0.18.0 -- drop obsolete patches -- fix analysis tests on 32bit -- new dependency: python-gsd -- upstream switched from nose to pytest for testing -- use standard bcond to enable/disable tests -- use pytest options to skip some tests instead of patching them out - -* Fri Feb 09 2018 Fedora Release Engineering - 0.16.2-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Aug 03 2017 Fedora Release Engineering - 0.16.2-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Thu Jul 27 2017 Fedora Release Engineering - 0.16.2-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Fri Jun 30 2017 Dominik Mierzejewski - 0.16.2-1 -- update to 0.16.2 -- update doc tarball URL and handling -- drop obsolete patch - -* Thu Jun 22 2017 Dominik Mierzejewski - 0.16.1-3 -- fix endianness issues on BE arches (ppc64, s390x) -- increase test process timeout (was timing out on aarch64) - -* Sat Jun 17 2017 Dominik Mierzejewski - 0.16.1-2 -- backport more fixes from git - -* Thu Jun 08 2017 Dominik Mierzejewski - 0.16.1-1 -- update to 0.16.1 -- fix test failures on 32bit - -* Thu May 18 2017 Dominik Mierzejewski - 0.16.0-1 -- update to 0.16.0 -- drop obsolete patches -- add new dependencies (joblib, mmtf, mock, psutil) -- fix netcdf4-python dependencies (need python2-netcdf4, actually) -- switch to nosetests while strange test failures are investigated - (https://github.com/MDAnalysis/mdanalysis/issues/1360) -- add a link to upstream-recommended way of running tests -- modernize python module dependencies - -* Sat Feb 11 2017 Fedora Release Engineering - 0.14.0-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild - -* Mon Sep 26 2016 Dominik Mierzejewski - 0.14.0-4 -- rebuilt for matplotlib-2.0.0 - -* Tue Jul 19 2016 Fedora Release Engineering - 0.14.0-3 -- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages - -* Tue Mar 15 2016 Dominik Mierzejewski 0.14.0-2 -- fix non-standard-dir-perm in doc subpackage -- move python2 build to python2-MDAnalysis subpackage -- exclude private libmdaxdr.so from Provides: - -* Fri Mar 11 2016 Dominik Mierzejewski 0.14.0-1 -- update to 0.14.0 -- don't build docs for now, upstream published them in a zip file -- drop obsolete patch -- fix tests with numpy 1.11 -- fix license field for docs subpackage -- install LICENSE with the doc subpackage as well -- move building of docs to the build section -- use some python-related convenience macros - -* Tue Feb 09 2016 Dominik Mierzejewski 0.13.0-2 -- build docs -- new dependency: seaborn -- omit failing tests on f24 for now - -* Mon Feb 08 2016 Dominik Mierzejewski 0.13.0-1 -- update to 0.13.0 -- fix running tests -- add Provides for bundled xdrfile -- docs not included and failing to build, so disable for now - -* Wed Oct 14 2015 Dominik Mierzejewski 0.12.1-1 -- update to 0.12.1 -- drop obsolete patch -- use the new mda_nosetests script for running tests - -* Mon May 18 2015 Dominik Mierzejewski 0.9.2-4 -- relax Improper Torsion topology test check on i686 - -* Mon May 11 2015 Dominik Mierzejewski 0.9.2-3 -- document licensing breakdown -- package docs - -* Fri May 08 2015 Dominik Mierzejewski 0.9.2-2 -- call the testsuite per upstream docs - -* Wed May 06 2015 Dominik Mierzejewski 0.9.2-1 -- update to 0.9.2 -- update upstream URL -- drop obsolete patch -- fix testsuite invocation - -* Wed Feb 04 2015 Dominik Mierzejewski 0.8.1-1 -- initial build diff --git a/sources b/sources deleted file mode 100644 index 402b4a8..0000000 --- a/sources +++ /dev/null @@ -1,3 +0,0 @@ -SHA512 (MDAnalysis-0.20.1.tar.gz) = 9b3e5b5e600a9250923952d329052fbefa699a3b24acfc34b6157714e3797641c0de229be5322e8c954d2a45fb5556e0fe30a60958022c24199173d3345a2152 -SHA512 (MDAnalysisTests-0.20.1.tar.gz) = afdd1f063a600075dd8554a37d48acaccd9540fdfc5909d57bcf1be46acbadb9b376c2a57b2b2877ee5bad43f4bb8e53df3f9d8a3492b133e954335fa4527c79 -SHA512 (pypidoc.zip) = 574506cad8f3935e6d5bf7b2bd4e9a7d298a8c29f35e70c3ac4d51c9f33c073f2ad8fa824f2d62121b8745318c967b1cef06965c155a66cece9f37e0b662abc5