get_space error when using pynapple

[bendichter]

import pynwb
import lindi
import pynapple as nap

# Load https://api.dandiarchive.org/api/assets/2b9e441b-56bc-4be2-893e-0e02d22d239d/download/
f = lindi.LindiH5pyFile.from_lindi_file("https://lindi.neurosift.org/dandi/dandisets/000582/assets/2b9e441b-56bc-4be2-893e-0e02d22d239d/nwb.lindi.json")
nwb = pynwb.NWBHDF5IO(file=f, mode='r').read()
nap_nwb = nap.NWBFile(nwb)
results = nap.compute_tuning_curves(nap_nwb["units"], nap_nwb["ElectricalSeriesLFP"], 20)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File ~/miniconda3/lib/python3.12/site-packages/numpy/lib/_histograms_impl.py:988, in histogramdd(sample, bins, range, density, weights)
    986 try:
    987     # Sample is an ND-array.
--> 988     N, D = sample.shape
    989 except (AttributeError, ValueError):
    990     # Sample is a sequence of 1D arrays.

ValueError: not enough values to unpack (expected 2, got 1)

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
Cell In[11], line 1
----> 1 results = nap.compute_tuning_curves(nap_nwb["units"], nap_nwb["ElectricalSeriesLFP"],20)

File ~/miniconda3/lib/python3.12/site-packages/pynapple/process/tuning_curves.py:253, in compute_tuning_curves(data, features, bins, range, epochs, fs, feature_names, return_pandas, return_counts)
    250     raise TypeError("return_counts should be a boolean.")
    252 # occupancy
--> 253 occupancy, bin_edges = np.histogramdd(features, bins=bins, range=range)
    255 # tuning curves
    256 keys = (
    257     data.keys()
    258     if isinstance(data, nap.TsGroup)
    259     else data.columns if isinstance(data, nap.TsdFrame) else [0]
    260 )

File ~/miniconda3/lib/python3.12/site-packages/pynapple/core/time_series.py:330, in _BaseTsd.__array_function__(self, func, types, args, kwargs)
    327     else:
    328         new_args.append(a)
--> 330 out = func._implementation(*new_args, **kwargs)
    332 if modifies_time_axis(func, new_args, kwargs):
    333     return out

File ~/miniconda3/lib/python3.12/site-packages/numpy/lib/_histograms_impl.py:991, in histogramdd(sample, bins, range, density, weights)
    988     N, D = sample.shape
    989 except (AttributeError, ValueError):
    990     # Sample is a sequence of 1D arrays.
--> 991     sample = np.atleast_2d(sample).T
    992     N, D = sample.shape
    994 nbin = np.empty(D, np.intp)

File ~/miniconda3/lib/python3.12/site-packages/numpy/_core/shape_base.py:122, in atleast_2d(*arys)
    120 res = []
    121 for ary in arys:
--> 122     ary = asanyarray(ary)
    123     if ary.ndim == 0:
    124         result = ary.reshape(1, 1)

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/dataset.py:1112, in Dataset.__array__(self, dtype, copy)
   1109 if self.size == 0:
   1110     return arr
-> 1112 self.read_direct(arr)
   1113 return arr

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/dataset.py:1054, in Dataset.read_direct(self, dest, source_sel, dest_sel)
   1046 """ Read data directly from HDF5 into an existing NumPy array.
   1047 
   1048 The destination array must be C-contiguous and writable.
   (...)
   1051 Broadcasting is supported for simple indexing.
   1052 """
   1053 with phil:
-> 1054     if self._is_empty:
   1055         raise TypeError("Empty datasets have no numpy representation")
   1056     if source_sel is None:

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/base.py:532, in cached_property.__get__(self, obj, cls)
    529 if obj is None:
    530     return self
--> 532 value = obj.__dict__[self.func.__name__] = self.func(obj)
    533 return value

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/dataset.py:666, in Dataset._is_empty(self)
    663 @cached_property
    664 def _is_empty(self):
    665     """Check if extent type is empty"""
--> 666     return self._extent_type == h5s.NULL

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/base.py:532, in cached_property.__get__(self, obj, cls)
    529 if obj is None:
    530     return self
--> 532 value = obj.__dict__[self.func.__name__] = self.func(obj)
    533 return value

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File ~/miniconda3/lib/python3.12/site-packages/h5py/_hl/dataset.py:661, in Dataset._extent_type(self)
    657 @cached_property
    658 @with_phil
    659 def _extent_type(self):
    660     """Get extent type for this dataset - SIMPLE, SCALAR or NULL"""
--> 661     return self.id.get_space().get_simple_extent_type()

AttributeError: 'str' object has no attribute 'get_space'

[bendichter]

Fixed in #121