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scverse / anndata

Annotated data.
http://anndata.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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IO support for pandas datetime format #1708

Open le-ander opened 20 hours ago

le-ander commented 20 hours ago

Please make sure these conditions are met

Report

Code:

adata.write("file.h5ad")

Traceback:

---------------------------------------------------------------------------
IORegistryError                           Traceback (most recent call last)
Cell In[13], line 1
----> 1 adata.write("data[/microbiome_layered.h5ad](http://localhost:8888/microbiome_layered.h5ad)")

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_core/anndata.py:1863](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_core/anndata.py#line=1862), in AnnData.write_h5ad(self, filename, compression, compression_opts, as_dense)
   1860 if filename is None:
   1861     filename = self.filename
-> 1863 write_h5ad(
   1864     Path(filename),
   1865     self,
   1866     compression=compression,
   1867     compression_opts=compression_opts,
   1868     as_dense=as_dense,
   1869 )
   1871 if self.isbacked:
   1872     self.file.filename = filename

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/h5ad.py:101](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/h5ad.py#line=100), in write_h5ad(filepath, adata, as_dense, dataset_kwargs, **kwargs)
     99 elif adata.raw is not None:
    100     write_elem(f, "raw", adata.raw, dataset_kwargs=dataset_kwargs)
--> 101 write_elem(f, "obs", adata.obs, dataset_kwargs=dataset_kwargs)
    102 write_elem(f, "var", adata.var, dataset_kwargs=dataset_kwargs)
    103 write_elem(f, "obsm", dict(adata.obsm), dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:378](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=377), in write_elem(store, k, elem, dataset_kwargs)
    354 def write_elem(
    355     store: GroupStorageType,
    356     k: str,
   (...)
    359     dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
    360 ) -> None:
    361     """
    362     Write an element to a storage group using anndata encoding.
    363 
   (...)
    376         E.g. for zarr this would be `chunks`, `compressor`.
    377     """
--> 378     Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/utils.py:247](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/utils.py#line=246), in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    245     raise ValueError("No element found in args.")
    246 try:
--> 247     return func(*args, **kwargs)
    248 except Exception as e:
    249     path = _get_display_path(store)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:328](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=327), in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    325 write_func = self.find_write_func(dest_type, elem, modifiers)
    327 if self.callback is None:
--> 328     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
    329 return self.callback(
    330     write_func,
    331     store,
   (...)
    335     iospec=self.registry.get_spec(elem),
    336 )

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:71](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=70), in write_spec.<locals>.decorator.<locals>.wrapper(g, k, *args, **kwargs)
     69 @wraps(func)
     70 def wrapper(g: GroupStorageType, k: str, *args, **kwargs):
---> 71     result = func(g, k, *args, **kwargs)
     72     g[k].attrs.setdefault("encoding-type", spec.encoding_type)
     73     g[k].attrs.setdefault("encoding-version", spec.encoding_version)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/methods.py:830](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/methods.py#line=829), in write_dataframe(f, key, df, _writer, dataset_kwargs)
    825 _writer.write_elem(
    826     group, index_name, df.index._values, dataset_kwargs=dataset_kwargs
    827 )
    828 for colname, series in df.items():
    829     # TODO: this should write the "true" representation of the series (i.e. the underlying array or ndarray depending)
--> 830     _writer.write_elem(
    831         group, colname, series._values, dataset_kwargs=dataset_kwargs
    832     )

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/utils.py:247](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/utils.py#line=246), in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    245     raise ValueError("No element found in args.")
    246 try:
--> 247     return func(*args, **kwargs)
    248 except Exception as e:
    249     path = _get_display_path(store)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:325](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=324), in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    322 elif k in store:
    323     del store[k]
--> 325 write_func = self.find_write_func(dest_type, elem, modifiers)
    327 if self.callback is None:
    328     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:292](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=291), in Writer.find_write_func(self, dest_type, elem, modifiers)
    288         return self.registry.get_write(
    289             dest_type, pattern, modifiers, writer=self
    290         )
    291 # Raises IORegistryError
--> 292 return self.registry.get_write(dest_type, type(elem), modifiers, writer=self)

File [~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py:131](http://localhost:8888/lab/tree/work/projects/hackathon_ehrapy/~/.pyenv/versions/3.12.3/envs/ehrapy-3.12.3/lib/python3.12/site-packages/anndata/_io/specs/registry.py#line=130), in IORegistry.get_write(self, dest_type, src_type, modifiers, writer)
    128     dest_type = h5py.Group
    130 if (dest_type, src_type, modifiers) not in self.write:
--> 131     raise IORegistryError._from_write_parts(dest_type, src_type, modifiers)
    132 internal = self.write[(dest_type, src_type, modifiers)]
    133 return partial(internal, _writer=writer)

IORegistryError: No method registered for writing <class 'pandas.core.arrays.datetimes.DatetimeArray'> into <class 'h5py._hl.group.Group'>
Error raised while writing key 'rounded_birthdate' of <class 'h5py._hl.group.Group'> to /obs

Versions

anndata             0.10.9
session_info        1.0.0
-----
cython_runtime      NA
dateutil            2.9.0.post0
h5py                3.12.1
natsort             8.4.0
numpy               1.26.4
packaging           24.1
pandas              2.2.3
pyarrow             17.0.0
pytz                2024.2
scipy               1.14.1
six                 1.16.0
-----
Python 3.12.3 (main, Oct  7 2024, 17:13:37) [Clang 14.0.0 (clang-1400.0.29.202)]
macOS-12.7.6-x86_64-i386-64bit
-----
Session information updated at 2024-10-09 12:10
flying-sheep commented 18 hours ago

Comment by @ilan-gold: xarray probably has something here