Accepting request 1226942 from devel:languages:python
OBS-URL: https://build.opensuse.org/request/show/1226942 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-mrcz?expand=0&rev=4
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Ana Guerrero
Git OBS Bridge
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67
new-pythons.patch
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67
new-pythons.patch
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From ce031b069262cfd1a21c76bf2d54f7bf31a178c6 Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sun, 13 Oct 2024 11:21:06 +0100
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Subject: [PATCH 1/2] Remove use of distutils, use packaging library instead
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---
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mrcz/ioMRC.py | 8 ++++----
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requirements.txt | 1 +
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utils/update_mrcz_to_0.5.0.py | 1 -
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3 files changed, 5 insertions(+), 5 deletions(-)
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diff --git a/utils/update_mrcz_to_0.5.0.py b/utils/update_mrcz_to_0.5.0.py
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index ba84d2b..515bd01 100644
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--- a/utils/update_mrcz_to_0.5.0.py
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+++ b/utils/update_mrcz_to_0.5.0.py
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@@ -1,7 +1,6 @@
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import glob, sys, os, os.path as path
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import numpy as np
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import mrcz
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-from distutils.version import StrictVersion
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import shutil
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args = sys.argv
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From 6c196f6602a50f14545c197234e0b8fdd7711e0f Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sun, 13 Oct 2024 11:57:13 +0100
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Subject: [PATCH 2/2] Fix deprecated `unittest.makeSuite` and explicitly list
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python supported version
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---
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mrcz/test_mrcz.py | 4 ++--
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setup.py | 5 +++++
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2 files changed, 7 insertions(+), 2 deletions(-)
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diff --git a/mrcz/test_mrcz.py b/mrcz/test_mrcz.py
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index d76f5fa..fe58e38 100644
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--- a/mrcz/test_mrcz.py
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+++ b/mrcz/test_mrcz.py
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@@ -573,9 +573,9 @@ def test(verbosity=2):
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theSuite = unittest.TestSuite()
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- theSuite.addTest(unittest.makeSuite(PythonMrczTests))
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+ theSuite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(PythonMrczTests))
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if cmrczProg is not None:
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- theSuite.addTest(unittest.makeSuite(PythonToCMrczTests))
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+ theSuite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(PythonToCMrczTests))
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test_result = unittest.TextTestRunner(verbosity=verbosity).run(theSuite)
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return test_result
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diff --git a/setup.py b/setup.py
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index ebda8b3..47914a7 100644
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--- a/setup.py
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+++ b/setup.py
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@@ -62,6 +62,11 @@ def exit_with_error(message):
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Programming Language :: Python :: 3.6
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Programming Language :: Python :: 3.7
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Programming Language :: Python :: 3.8
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+Programming Language :: Python :: 3.9
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+Programming Language :: Python :: 3.10
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+Programming Language :: Python :: 3.11
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+Programming Language :: Python :: 3.12
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+Programming Language :: Python :: 3.13
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Topic :: Software Development :: Libraries :: Python Modules
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Topic :: System :: Archiving :: Compression
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Operating System :: Microsoft :: Windows
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66
numpy2.patch
66
numpy2.patch
@ -1,69 +1,3 @@
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From f28e1a2b90c04ac47c586fa7398d1e694029174a Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:02:09 +0100
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Subject: [PATCH 1/5] Replace `np.product` with `np.prod` since it has been
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removed in numpy 2
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---
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mrcz/ioMRC.py | 12 ++++++------
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1 file changed, 6 insertions(+), 6 deletions(-)
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diff --git a/mrcz/ioMRC.py b/mrcz/ioMRC.py
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index b1184bb..998de75 100644
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--- a/mrcz/ioMRC.py
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+++ b/mrcz/ioMRC.py
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@@ -318,7 +318,7 @@ def readMRC(MRCfilename, idx=None, endian='le',
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header['dimensions'][0] = n
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# This offset will be applied to f.seek():
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- offset = idx * np.product(header['dimensions'][1:])*np.dtype(header['dtype']).itemsize
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+ offset = idx * np.prod(header['dimensions'][1:])*np.dtype(header['dtype']).itemsize
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else:
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offset = 0
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@@ -331,7 +331,7 @@ def readMRC(MRCfilename, idx=None, endian='le',
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else: # Load entire file into memory
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dims = header['dimensions']
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if slices > 0: # List of NumPy 2D-arrays
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- frame_size = slices * np.product(dims[1:])
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+ frame_size = slices * np.prod(dims[1:])
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n_frames = dims[0] // slices
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dtype = header['dtype']
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@@ -343,12 +343,12 @@ def readMRC(MRCfilename, idx=None, endian='le',
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image.append(buffer)
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else: # monolithic NumPy ndarray
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- image = np.fromfile(f, dtype=header['dtype'], count=np.product(dims))
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+ image = np.fromfile(f, dtype=header['dtype'], count=np.prod(dims))
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if header['MRCtype'] == 101:
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# Seems the 4-bit is interlaced ...
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interlaced_image = image
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- image = np.empty(np.product(dims), dtype=header['dtype'])
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+ image = np.empty(np.prod(dims), dtype=header['dtype'])
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image[0::2] = np.left_shift(interlaced_image,4) / 15
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image[1::2] = np.right_shift(interlaced_image,4)
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@@ -429,7 +429,7 @@ def __MRCZImport(f, header, slices, endian='le', fileConvention='ccpem',
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raise NotImplementedError('MRC type 101 (uint4) not supported with return as `list`')
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interlaced_image = image
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- image = np.empty(np.product(header['dimensions']), dtype=dtype)
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+ image = np.empty(np.prod(header['dimensions']), dtype=dtype)
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# Bit-shift and Bit-and to seperate decimated pixels
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image[0::2] = np.left_shift(interlaced_image, 4) / 15
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image[1::2] = np.right_shift(interlaced_image, 4)
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@@ -872,7 +872,7 @@ def writeMRC(input_image, MRCfilename, meta=None, endian='le', dtype=None,
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header['dimensions'] = np.array([idx + input_image.shape[0], header['dimensions'][1], header['dimensions'][2]])
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# This offset will be applied to f.seek():
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- offset = idx * np.product(header['dimensions'][1:]) * np.dtype(header['dtype']).itemsize
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+ offset = idx * np.prod(header['dimensions'][1:]) * np.dtype(header['dtype']).itemsize
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else:
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offset = 0
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From 07c01ce360fd3bad884f2a3c03c5f33c0f8348cf Mon Sep 17 00:00:00 2001
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From: Eric Prestat <eric.prestat@gmail.com>
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Date: Sat, 22 Jun 2024 20:05:46 +0100
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:8568a9d9fbf3fa8d1097f4b00edd0ed7ab9dcfda97fe236e05076e67b62fae13
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size 56897
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3
python-mrcz-0.5.7.tar.gz
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3
python-mrcz-0.5.7.tar.gz
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version https://git-lfs.github.com/spec/v1
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oid sha256:dfb729604436942e912d5034ea2df72ba0055e00b31ec403b113222b827f4fa4
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size 56956
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@ -1,3 +1,11 @@
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-------------------------------------------------------------------
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Wed Nov 27 11:40:39 UTC 2024 - Markéta Machová <mmachova@suse.com>
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- Update to 0.5.7
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* Renamed np.product to np.prod as the old name is deprecated in NumPy 2.0.
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- Add patch new-pythons.patch to fix build with Python 3.13
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- Python 2 can be finally gone
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-------------------------------------------------------------------
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Mon Sep 9 13:39:13 UTC 2024 - Markéta Machová <mmachova@suse.com>
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@ -18,7 +18,7 @@
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%{?sle15_python_module_pythons}
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Name: python-mrcz
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Version: 0.5.6
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Version: 0.5.7
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Release: 0
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Summary: MRCZ meta-compressed image file-format library
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License: BSD-3-Clause
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@ -26,6 +26,8 @@ URL: https://github.com/em-MRCZ/python-mrcz
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Source: https://github.com/em-MRCZ/python-mrcz/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz
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# PATCH-FIX-UPSTREAM https://github.com/em-MRCZ/python-mrcz/pull/15 Numpy 2.0 and deprecation fixes
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Patch: numpy2.patch
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# PATCH-FIX-UPSTREAM https://github.com/em-MRCZ/python-mrcz/pull/16 Remove distutils / support python >=3.12
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Patch: new-pythons.patch
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BuildRequires: %{python_module blosc}
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BuildRequires: %{python_module numpy}
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BuildRequires: %{python_module pytest}
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@ -36,14 +38,6 @@ BuildRequires: python-rpm-macros
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Requires: python-numpy
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Recommends: python-blosc
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BuildArch: noarch
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%if %{with python2}
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BuildRequires: python-enum34
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BuildRequires: python-futures
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%endif
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%ifpython2
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Requires: python-enum34
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Requires: python-futures
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%endif
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%python_subpackages
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%description
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