Writing to H5AD fails if AnnData contains datetime64 objects #455
Description
Writing an AnnData object to disk fails if it contains numpy datetime64 objects. Example:
import anndata
import numpy as np
ad = anndata.AnnData()
ad.uns['now'] = np.datetime64('now')
ad.write("test_h5py.h5ad")ERROR MESSAGE
Traceback (most recent call last):
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/utils.py", line 188, in func_wrapper
return func(elem, key, val, *args, **kwargs)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 144, in write_not_implemented
raise NotImplementedError(
NotImplementedError: Failed to write value for uns/now, since a writer for type <class 'numpy.datetime64'> has not been implemented yet.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/luke.zappia/Desktop/test_h5py.py", line 8, in <module>
ad.write("test_h5py.h5ad")
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_core/anndata.py", line 1846, in write_h5ad
_write_h5ad(
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 112, in write_h5ad
write_attribute(f, "uns", adata.uns, dataset_kwargs=dataset_kwargs)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/functools.py", line 877, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 126, in write_attribute_h5ad
_write_method(type(value))(f, key, value, *args, **kwargs)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 286, in write_mapping
write_attribute(f, f"{key}/{sub_key}", sub_value, dataset_kwargs=dataset_kwargs)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/functools.py", line 877, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/h5ad.py", line 126, in write_attribute_h5ad
_write_method(type(value))(f, key, value, *args, **kwargs)
File "/Users/luke.zappia/miniconda3/envs/test-h5py/lib/python3.9/site-packages/anndata/_io/utils.py", line 191, in func_wrapper
raise type(e)(
NotImplementedError: Failed to write value for uns/now, since a writer for type <class 'numpy.datetime64'> has not been implemented yet.
Above error raised while writing key 'uns/now' of <class 'h5py._hl.files.File'> from /.
This behaviour is from h5py rather than anndata. From v3.0.0 they suggest storing these values using opaque dtypes https://docs.h5py.org/en/stable/special.html#opaque-dtypes.
Not sure how big a problem this is but it came up here theislab/zellkonverter#24 so I just wanted to raise it. Would be nice if anndata could handle this (at least with a nicer error) but maybe not a priority.