A dtype error occurs in the common IO tests on macOS only. I haven't had the chance to investigate in depth yet. Traceback from one occurrence is included below.
============================= test session starts ==============================
platform darwin -- Python 3.7.2, pytest-4.1.1, py-1.7.0, pluggy-0.8.1
rootdir: /Users/achilleas/code/python-neo, inifile:
collected 1038 items / 1033 deselected
neo/test/iotest/test_nixio.py F
=================================== FAILURES ===================================
____________ CommonTests.test_assert_readed_neo_object_is_compliant ____________
self = <neo.test.iotest.test_nixio.CommonTests testMethod=test_assert_readed_neo_object_is_compliant>
def setUp(self):
'''
Set up the test fixture. This is run for every test
'''
self.files_to_test = copy(self.__class__.files_to_test)
self.higher = self.ioclass.supported_objects[0]
self.shortname = self.ioclass.__name__.lower().rstrip('io')
# these objects can both be written and read
self.io_readandwrite = list(set(self.ioclass.readable_objects) &
set(self.ioclass.writeable_objects))
# these objects can be either written or read
self.io_readorwrite = list(set(self.ioclass.readable_objects) |
set(self.ioclass.writeable_objects))
self.create_local_dir_if_not_exists()
self.download_test_files_if_not_present()
self.files_generated = []
> self.generate_files_for_io_able_to_write()
neo/test/iotest/common_io_test.py:105:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
neo/test/iotest/common_io_test.py:428: in generate_files_for_io_able_to_write
write_generic(ioobj, target=self.higher)
neo/test/iotest/tools.py:379: in write_generic
obj_writer(obj)
neo/io/nixio.py:559: in write_block
self._write_segment(seg, nixblock)
neo/io/nixio.py:661: in _write_segment
self._write_epoch(epoch, nixblock, nixgroup)
neo/io/nixio.py:872: in _write_epoch
"{}.times".format(nix_name), "neo.epoch.times", data=times
../nixpy/nixio/block.py:191: in create_data_array
dtype, shape, compression)
../nixpy/nixio/data_array.py:46: in _create_new
newentity._h5group.create_dataset("data", shape, data_type, datacompr)
../nixpy/nixio/hdf5/h5group.py:99: in create_dataset
return H5DataSet(self.group, name, dtype, shape, compression)
../nixpy/nixio/hdf5/h5dataset.py:30: in __init__
**comprargs
/usr/local/lib/python3.7/site-packages/h5py/_hl/group.py:189: in require_dataset
return self.create_dataset(name, *(shape, dtype), **kwds)
/usr/local/lib/python3.7/site-packages/h5py/_hl/group.py:136: in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
/usr/local/lib/python3.7/site-packages/h5py/_hl/dataset.py:118: in make_new_dset
tid = h5t.py_create(dtype, logical=1)
h5py/h5t.pyx:1630: in h5py.h5t.py_create
???
h5py/h5t.pyx:1652: in h5py.h5t.py_create
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: Object dtype dtype('O') has no native HDF5 equivalent
h5py/h5t.pyx:1707: TypeError
=============================== warnings summary ===============================
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/__init__.py:266
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/__init__.py:266: DeprecationWarning: invalid escape sequence \m
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/__init__.py:266: DeprecationWarning: invalid escape sequence \m
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/markup.py:113
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/markup.py:113: DeprecationWarning: invalid escape sequence \c
/usr/local/lib/python3.7/site-packages/quantities-0.12.2-py3.7.egg/quantities/markup.py:113: DeprecationWarning: invalid escape sequence \c
neo/io/tools.py:82
/Users/achilleas/code/python-neo/neo/io/tools.py:82: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
class LazyList(collections.MutableSequence):
neo/io/nixio.py:27
/Users/achilleas/code/python-neo/neo/io/nixio.py:27: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Iterable, OrderedDict
-- Docs: https://docs.pytest.org/en/latest/warnings.html
============ 1 failed, 1033 deselected, 6 warnings in 1.85 seconds =============
A dtype error occurs in the common IO tests on macOS only. I haven't had the chance to investigate in depth yet. Traceback from one occurrence is included below.