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Adapt to API change of h5py version 3.0 #893

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Merged
merged 2 commits into from
Nov 4, 2020
Merged

Adapt to API change of h5py version 3.0 #893

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4a75a84
Fix API change of h5py version 3.0
JuliaSprenger Nov 3, 2020
b717865
Add version check for h5py
JuliaSprenger Nov 3, 2020
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15 changes: 10 additions & 5 deletions neo/io/hdf5io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@


import logging
from distutils.version import LooseVersion
import pickle
import numpy as np
import quantities as pq
Expand All @@ -23,7 +24,7 @@
from neo.core.baseneo import MergeError

logger = logging.getLogger('Neo')

min_h5py_version = LooseVersion('2.6.0')

def disjoint_groups(groups):
"""`groups` should be a list of sets"""
Expand Down Expand Up @@ -55,6 +56,10 @@ class NeoHdf5IO(BaseIO):
def __init__(self, filename):
if not HAVE_H5PY:
raise ImportError("h5py is not available")
if HAVE_H5PY:
if LooseVersion(h5py.__version__) < min_h5py_version:
raise ImportError('h5py version {} is too old. Minimal required version is {}'
''.format(h5py.__version__, min_h5py_version))
BaseIO.__init__(self, filename=filename)
self._data = h5py.File(filename, 'r')
self.object_refs = {}
Expand Down Expand Up @@ -213,7 +218,7 @@ def _read_epocharray(self, node, parent):
attributes = self._get_standard_attributes(node)
times = self._get_quantity(node["times"])
durations = self._get_quantity(node["durations"])
labels = node["labels"].value.astype('U')
labels = node["labels"][()].astype('U')
epoch = Epoch(times=times, durations=durations, labels=labels, **attributes)
epoch.segment = parent
return epoch
Expand All @@ -224,7 +229,7 @@ def _read_epoch(self, node, parent):
def _read_eventarray(self, node, parent):
attributes = self._get_standard_attributes(node)
times = self._get_quantity(node["times"])
labels = node["labels"].value.astype('U')
labels = node["labels"][()].astype('U')
event = Event(times=times, labels=labels, **attributes)
event.segment = parent
return event
Expand All @@ -235,8 +240,8 @@ def _read_event(self, node, parent):
def _read_recordingchannelgroup(self, node, parent):
# todo: handle Units
attributes = self._get_standard_attributes(node)
channel_indexes = node["channel_indexes"].value
channel_names = node["channel_names"].value
channel_indexes = node["channel_indexes"][()]
channel_names = node["channel_names"][()]

if channel_indexes.size:
if len(node['recordingchannels']):
Expand Down