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Update to use upcoming HDMF 2.5.1 #1355

Merged
merged 17 commits into from
Apr 23, 2021
Merged

Update to use upcoming HDMF 2.5.1 #1355

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1747826
Update test to account for new namespace in hdmf 2.5.0
rly Mar 24, 2021
5111de1
Update get_class call
rly Apr 13, 2021
dbcaa55
Remove redundant merge
rly Apr 13, 2021
91d0a61
Update get_class call
rly Apr 13, 2021
36ab7ed
Move TestCatchDuplicateSpec test to HDMF
rly Apr 13, 2021
de88fe3
Merge branch 'dev' into hdmf_2.5.0
rly Apr 13, 2021
1161a16
Replace print validation errors with assert
rly Apr 21, 2021
267b150
Update legal
rly Apr 21, 2021
919a9cd
Update hdmf requirements
rly Apr 22, 2021
716b0ef
Delete test file
rly Apr 22, 2021
e062dab
Update tox settings
rly Apr 22, 2021
0001f55
Revert get_container_cls changes and use HDMF 2.5.1
rly Apr 23, 2021
81cf151
Update reqs
rly Apr 23, 2021
888196d
Merge branch 'dev' into hdmf_2.5.0
rly Apr 23, 2021
07fddfd
Don't pin HDMF again
rly Apr 23, 2021
7803faf
Set max version on python-dateutil just in case
rly Apr 23, 2021
7220940
Return requirements
rly Apr 23, 2021
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13 changes: 7 additions & 6 deletions requirements-min.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# these minimum requirements specify '==' for testing; setup.py replaces '==' with '>='
h5py==2.9 # support for setting attrs to lists of utf-8 added in 2.9
hdmf==2.5
numpy==1.16
pandas==0.23
python-dateutil==2.7
# package dependencies and their minimum versions for installing PyNWB (note that HDMF has a range of requirements)
# the requirements here specify '==' for testing; setup.py replaces '==' with '>='
h5py==2.9,<3 # support for setting attrs to lists of utf-8 added in 2.9
hdmf==2.5.1,<3
numpy==1.16,<1.21
pandas==0.23,<2
python-dateutil==2.7,<3
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
h5py==2.10.0
hdmf==2.5.0
hdmf==2.5.1
numpy==1.18.5
pandas==0.25.3
python-dateutil==2.8.1
2 changes: 1 addition & 1 deletion src/pynwb/__init__.py
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Expand Up @@ -183,7 +183,7 @@ def get_sum(self, a, b):

"""
neurodata_type, namespace = getargs('neurodata_type', 'namespace', kwargs)
return __TYPE_MAP.get_container_cls(neurodata_type, namespace)
return __TYPE_MAP.get_dt_container_cls(neurodata_type, namespace)


@docval({'name': 'io', 'type': HDMFIO, 'doc': 'the HDMFIO object to read from'},
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4 changes: 2 additions & 2 deletions tests/unit/test_extension.py
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Expand Up @@ -49,7 +49,7 @@ def test_load_namespace(self):
def test_get_class(self):
self.test_export()
type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
type_map.get_container_cls('TetrodeSeries', self.prefix)
type_map.get_dt_container_cls('TetrodeSeries', self.prefix)

def test_load_namespace_with_reftype_attribute(self):
ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix, version='0.1.0')
Expand All @@ -74,7 +74,7 @@ def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
ns_builder.add_spec(self.ext_source, test_ds_ext)
ns_builder.export(self.ns_path, outdir=self.tempdir)
type_map = get_type_map(extensions=os.path.join(self.tempdir, self.ns_path))
my_new_type = type_map.get_container_cls('my_new_type', self.prefix)
my_new_type = type_map.get_dt_container_cls('my_new_type', self.prefix)
docval = None
for tmp in get_docval(my_new_type.__init__):
if tmp['name'] == 'target_ds':
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