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default object_codec_class -> JSON #173

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default object_codec_class -> JSON #173

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8958fc7
default object_codec_class -> JSON
magland Mar 5, 2024
3994017
update CHANGELOG.md
magland Mar 5, 2024
b8300e8
change default object_codec_class to numcodecs.JSON
magland Mar 5, 2024
2ac5a3f
resort to Pickle codec for complex cases
magland Mar 6, 2024
29adcca
update CHANGELOG.md
magland Mar 6, 2024
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2 changes: 1 addition & 1 deletion src/hdmf_zarr/backend.py
View file
Original file line number Diff line number Diff line change
@@ -94,7 +94,7 @@ def can_read(path):
'default': None},
{'name': 'object_codec_class', 'type': None,
'doc': 'Set the numcodec object codec class to be used to encode objects.'
'Use numcodecs.pickles.Pickle by default.',
'Use numcodecs.JSON by default.',
'default': None},
{'name': 'storage_options', 'type': dict,
'doc': 'Zarr storage options to read remote folders',
8 changes: 5 additions & 3 deletions src/hdmf_zarr/nwb.py
View file
Original file line number Diff line number Diff line change
@@ -27,9 +27,10 @@ class NWBZarrIO(ZarrIO):
'doc': 'a path to a namespace, a TypeMap, or a list consisting paths to namespaces and TypeMaps',
'default': None})
def __init__(self, **kwargs):
path, mode, manager, extensions, load_namespaces, synchronizer, storage_options = \
path, mode, manager, extensions, load_namespaces, synchronizer, storage_options, object_codec_class = \
popargs('path', 'mode', 'manager', 'extensions',
'load_namespaces', 'synchronizer', 'storage_options', kwargs)
'load_namespaces', 'synchronizer', 'storage_options',
'object_codec_class', kwargs)
if load_namespaces:
if manager is not None:
warn("loading namespaces from file - ignoring 'manager'")
@@ -53,7 +54,8 @@ def __init__(self, **kwargs):
manager=manager,
mode=mode,
synchronizer=synchronizer,
storage_options=storage_options)
storage_options=storage_options,
object_codec_class=object_codec_class)

@docval({'name': 'src_io', 'type': HDMFIO, 'doc': 'the HDMFIO object for reading the data to export'},
{'name': 'nwbfile', 'type': 'NWBFile',
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