Fix nightly build failure
Closed this issue · 0 comments
sgratiy commented
Describe the bug
TypeError: No conversion path for dtype: dtype('<U12')
tmpdir_factory = TempdirFactory(_tmppath_factory=TempPathFactory(_given_basetemp=None, _trace=<pluggy._tracing.TagTracerSub object at 0x7ff65d4d0e10>, _basetemp=PosixPath('/tmp/pytest-of-root/pytest-0')))
nwbfile = root pynwb.file.NWBFile at 0x140698916992560
Fields:
acquisition: {
a current clamp <class 'pynwb.icephys.Curren...ep_table: sweep_table <class 'pynwb.icephys.SweepTable'>
timestamps_reference_time: 2020-10-31 05:03:18.242359+00:00
name = 'session_id', value = '12345', sweep_id = None
getter = <function <lambda> at 0x7ff7163a68c8>, expected = '12345'
@pytest.mark.parametrize("name, value, sweep_id, getter, expected", [
["subject_id", "mouse01", None, lambda f: f.subject.subject_id, "mouse01"],
["institution", "aibs", None, lambda f: f.institution, "aibs"],
["session_id", "12345", None, lambda f: f.session_id, "12345"],
["age", "P56D", None, lambda f: f.subject.age, "P56D"],
["date_of_birth", "2019-05-12 17:00:00 -0700", None,
lambda f: f.subject.date_of_birth, datetime(
2019, 5, 12, 17, 0, tzinfo=timezone(timedelta(hours=-7))
)
],
["genotype", "Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt", None,
lambda f: f.subject.genotype, "Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt"
],
["sex", "F", None, lambda f: f.subject.sex, "F"],
["species", "Mus musculus", None, lambda f: f.subject.species,
"Mus musculus"
],
])
def test_register(
tmpdir_factory, nwbfile, name, value, sweep_id, getter, expected
):
tmpdir = tmpdir_factory.mktemp("test_register")
path = os.path.join(str(tmpdir), "test.nwb")
sink = nwb2_sink.Nwb2Sink(None)
sink.nwbfile = nwbfile
sink.register(name, value, sweep_id)
with pynwb.NWBHDF5IO(path, "w") as writer:
> writer.write(nwbfile)
tests/attach_metadata/test_nwb2_sink.py:163:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:323: in write
call_docval_func(super().write, kwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:405: in call_docval_func
return func(*fargs, **fkwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/io.py:45: in write
self.write_builder(f_builder, **kwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:716: in write_builder
self.write_group(self.__file, gbldr, **kwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:896: in write_group
self.write_group(group, sub_builder, **kwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:896: in write_group
self.write_group(group, sub_builder, **kwargs)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:908: in write_group
self.set_attributes(group, attributes)
/usr/local/lib/python3.6/site-packages/hdmf/utils.py:561: in func_call
return func(args[0], **pargs)
/usr/local/lib/python3.6/site-packages/hdmf/backends/hdf5/h5tools.py:849: in set_attributes
obj.attrs[key] = value
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
/usr/local/lib/python3.6/site-packages/h5py/_hl/attrs.py:103: in __setitem__
self.create(name, data=value)
/usr/local/lib/python3.6/site-packages/h5py/_hl/attrs.py:180: in create
htype = h5t.py_create(original_dtype, logical=True)
h5py/h5t.pyx:1629: in h5py.h5t.py_create
???
h5py/h5t.pyx:1653: in h5py.h5t.py_create
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: No conversion path for dtype: dtype('<U12')
h5py/h5t.pyx:1719: TypeError