How to use the h5py.version function in h5py
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HDFGroup / hdf5-json / testall.py View on Github 
# Utilities. The full HDF5 REST Server copyright notice, including s #
# terms governing use, modification, and redistribution, is contained in #
# the file COPYING, which can be found at the root of the source code #
# distribution tree. If you do not have access to this file, you may #
# request a copy from help@hdfgroup.org. #
##############################################################################
import os
import sys
import h5py
unit_tests = ( 'hdf5dtypeTest', 'hdf5dbTest' )
integ_tests = ( 'h5tojson_test', 'jsontoh5_test' )
print(h5py.version.info)
# verify the hdf5 lib version is recent
hdf5_version = h5py.version.hdf5_version_tuple
if hdf5_version[1] < 8:
sys.exit("Need hdf5 lib 1.8 or later")
if hdf5_version[1] == 8 and hdf5_version[2] < 4:
sys.exit("Need hdf5 lib 1.8.4 or later")
# verify we have a recent version of h5py
h5py_version = h5py.version.version_tuple
if h5py_version[0] != 2 or h5py_version[1] < 5:
sys.exit("Need h5py version 2.5 or later")
#
#
# Run all hdf5-json tests
# Run this script before running any integ tests
#
os.chdir('test/unit')# #
# This file is part of H5Serv (HDF5 REST Server) Service, Libraries and #
# Utilities. The full HDF5 REST Server copyright notice, including s #
# terms governing use, modification, and redistribution, is contained in #
# the file COPYING, which can be found at the root of the source code #
# distribution tree. If you do not have access to this file, you may #
# request a copy from help@hdfgroup.org. #
##############################################################################
import os
import sys
import h5py
unit_tests = ( 'hdf5dtypeTest', 'hdf5dbTest' )
integ_tests = ( 'h5tojson_test', 'jsontoh5_test' )
print(h5py.version.info)
# verify the hdf5 lib version is recent
hdf5_version = h5py.version.hdf5_version_tuple
if hdf5_version[1] < 8:
sys.exit("Need hdf5 lib 1.8 or later")
if hdf5_version[1] == 8 and hdf5_version[2] < 4:
sys.exit("Need hdf5 lib 1.8.4 or later")
# verify we have a recent version of h5py
h5py_version = h5py.version.version_tuple
if h5py_version[0] != 2 or h5py_version[1] < 5:
sys.exit("Need h5py version 2.5 or later")
#
#
# Run all hdf5-json tests
# Run this script before running any integ testsself.history[-1] = (entry[0], ms_since_epoch()) + entry[2:]
else:
self.history.resize((1+len(self.history),))
def getversion(name):
if hasattr(sys.modules[name], '__version__'):
return getattr(sys.modules[name], '__version__')
else:
return 'unknown'
self.history[-1] = (ms_since_epoch(), 0,
sys.platform,
socket.getfqdn(),
getpass.getuser(),
activepapers.__version__,
sys.version.split()[0],
np.__version__,
h5py.version.version,
h5py.version.hdf5_version) \
+ tuple(getversion(m) for m in self.dependencies)def nxRootInit(h5group):
"""
Initialize NXroot instance
:param h5py.Group h5group:
:raises ValueError: not root
:raises RuntimeError: wrong Nexus class
"""
if h5group.name != '/':
raise ValueError('Group should be the root')
if nxClassNeedsInit(h5group, None, u'NXroot'):
h5group.attrs['file_time'] = timestamp()
h5group.attrs['file_name'] = asNxChar(h5group.file.filename)
h5group.attrs['HDF5_Version'] = asNxChar(h5py.version.hdf5_version)
h5group.attrs['h5py_version'] = asNxChar(h5py.version.version)
h5group.attrs['creator'] = PROGRAM_NAME
h5group.attrs['NX_class'] = u'NXroot'
updated(h5group)raise RuntimeError(
'lock must be a context manager, providing __enter__ and '
'__exit__ methods'
)
self._plock = lock
self._sorted = None
self.sorted_with(sorted_with)
if self.mode != 'r' and len(self) == 0:
if 'file_name' not in self.attrs:
self.attrs['file_name'] = name
if 'file_time' not in self.attrs:
self.attrs['file_time'] = getLocalTime()
if 'HDF5_version' not in self.attrs:
self.attrs['HDF5_version'] = h5py.version.hdf5_version
if 'HDF5_API_version' not in self.attrs:
self.attrs['HDF5_API_version'] = h5py.version.api_version
if 'HDF5_version' not in self.attrs:
self.attrs['h5py_version'] = h5py.version.version
if 'creator' not in self.attrs:
self.attrs['creator'] = 'phynx'
if 'format_version' not in self.attrs and len(self) == 0:
self.attrs['format_version'] = __format_version__sorted_with is a callable function like python's builtin sorted, or
None.
"""
h5file = h5py.File(name, mode, **kwargs)
if h5file.mode != 'r' and len(h5file) == 0:
if 'file_name' not in h5file.attrs:
h5file.attrs.create('file_name', to_h5py_utf8(name))
if 'file_time' not in h5file.attrs:
h5file.attrs.create('file_time', to_h5py_utf8(getDate()))
if 'HDF5_version' not in h5file.attrs:
txt = "%s" % h5py.version.hdf5_version
h5file.attrs.create('HDF5_version', to_h5py_utf8(txt))
if 'HDF5_API_version' not in h5file.attrs:
txt = "%s" % h5py.version.api_version
h5file.attrs.create('HDF5_API_version', to_h5py_utf8(txt))
if 'h5py_version' not in h5file.attrs:
txt = "%s" % h5py.version.version
h5file.attrs.create('h5py_version', to_h5py_utf8(txt))
if 'creator' not in h5file.attrs:
h5file.attrs.create('creator', to_h5py_utf8('PyMca'))
# if 'format_version' not in self.attrs and len(h5file) == 0:
# h5file.attrs['format_version'] = __format_version__
return h5fileimport math
import types
import ctypes
import numpy
import h5py
from threading import Thread
from multiprocessing import Queue, Process
try:
from concurrent.futures import ThreadPoolExecutor
except ImportError:
ThreadPoolExecutor = None
from pyscf.lib import param
from pyscf import __config__
if h5py.version.version[:4] == '2.2.':
sys.stderr.write('h5py-%s is found in your environment. '
'h5py-%s has bug in threading mode.\n'
'Async-IO is disabled.\n' % ((h5py.version.version,)*2))
if h5py.version.version[:2] == '3.':
h5py.get_config().default_file_mode = 'a'
c_double_p = ctypes.POINTER(ctypes.c_double)
c_int_p = ctypes.POINTER(ctypes.c_int)
c_null_ptr = ctypes.POINTER(ctypes.c_void_p)
def load_library(libname):
# numpy 1.6 has bug in ctypeslib.load_library, see numpy/distutils/misc_util.py
if '1.6' in numpy.__version__:
if (sys.platform.startswith('linux') or
sys.platform.startswith('gnukfreebsd')):
so_ext = '.so''__exit__ methods'
)
self._plock = lock
self._sorted = None
self.sorted_with(sorted_with)
if self.mode != 'r' and len(self) == 0:
if 'file_name' not in self.attrs:
self.attrs['file_name'] = name
if 'file_time' not in self.attrs:
self.attrs['file_time'] = getLocalTime()
if 'HDF5_version' not in self.attrs:
self.attrs['HDF5_version'] = h5py.version.hdf5_version
if 'HDF5_API_version' not in self.attrs:
self.attrs['HDF5_API_version'] = h5py.version.api_version
if 'HDF5_version' not in self.attrs:
self.attrs['h5py_version'] = h5py.version.version
if 'creator' not in self.attrs:
self.attrs['creator'] = 'phynx'
if 'format_version' not in self.attrs and len(self) == 0:
self.attrs['format_version'] = __format_version__def get_version_stack():
import numpy, matplotlib, h5py
version_info = {}
version_info['yt'] = get_yt_version()
version_info['numpy'] = numpy.version.version
version_info['matplotlib'] = matplotlib.__version__
version_info['h5py'] = h5py.version.version
return version_infof.create_group("history")
gg = f["history"]
gg.create_group("intensities")
gg.create_group("error")
gg.create_group("angle")
gg.create_group("mutual_info")
gg.create_group("quaternion")
gg.create_group("time")
c = numpy.array([gen.qmax, gen.qmax, gen.qmax])
f.create_dataset("data/center", data=c)
f.create_dataset("misc/qmax", data=gen.qmax)
f.create_dataset("misc/detector", data=gen.detector)
f.create_dataset("misc/beamstop", data=gen.beamstop)
f.create_dataset("version", data=h5py.version.hdf5_version)
f.close()
else:
f = h5py.File(outFile, 'r')
offset_iter = len(f["/history/intensities"].keys())
f.close()
msg = "Output will be appended to the results of %d iterations before this."%offset_iter
_print_to_log(msg=msg, log_file=self._outputLog)
###############################################################
# Iterate EMC
###############################################################
intensL = 2*gen.qmax + 1
iter_num = 1
currQuat = initial_number_of_quaternions
try:
