centered_pca result cannot be saved in h5ad

[MUCDK]

Description of feature

---------------------------------------------------------------------------
IORegistryError                           Traceback (most recent call last)
Cell In[138], line 3
      1 import os
----> 3 adata_train_1.write(os.path.join(output_dir, "adata_train_1.h5ad"))
      4 adata_test_1.write(os.path.join(output_dir, "adata_test_1.h5ad"))
      5 adata_ood_1.write(os.path.join(output_dir, "adata_ood_1.h5ad"))

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_core/anndata.py:1929, in AnnData.write_h5ad(self, filename, compression, compression_opts, as_dense)
   1926 if filename is None:
   1927     filename = self.filename
-> 1929 write_h5ad(
   1930     Path(filename),
   1931     self,
   1932     compression=compression,
   1933     compression_opts=compression_opts,
   1934     as_dense=as_dense,
   1935 )
   1937 if self.isbacked:
   1938     self.file.filename = filename

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/h5ad.py:107, in write_h5ad(filepath, adata, as_dense, dataset_kwargs, **kwargs)
    105 write_elem(f, "var", adata.var, dataset_kwargs=dataset_kwargs)
    106 write_elem(f, "obsm", dict(adata.obsm), dataset_kwargs=dataset_kwargs)
--> 107 write_elem(f, "varm", dict(adata.varm), dataset_kwargs=dataset_kwargs)
    108 write_elem(f, "obsp", dict(adata.obsp), dataset_kwargs=dataset_kwargs)
    109 write_elem(f, "varp", dict(adata.varp), dataset_kwargs=dataset_kwargs)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:359, in write_elem(store, k, elem, dataset_kwargs)
    335 def write_elem(
    336     store: GroupStorageType,
    337     k: str,
   (...)
    340     dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
    341 ) -> None:
    342     """
    343     Write an element to a storage group using anndata encoding.
    344 
   (...)
    357         E.g. for zarr this would be `chunks`, `compressor`.
    358     """
--> 359     Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/utils.py:243, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    241     raise ValueError("No element found in args.")
    242 try:
--> 243     return func(*args, **kwargs)
    244 except Exception as e:
    245     path = _get_display_path(store)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:309, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    303 write_func = partial(
    304     self.find_writer(dest_type, elem, modifiers),
    305     _writer=self,
    306 )
    308 if self.callback is None:
--> 309     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
    310 return self.callback(
    311     write_func,
    312     store,
   (...)
    316     iospec=self.registry.get_spec(elem),
    317 )

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:57, in write_spec.<locals>.decorator.<locals>.wrapper(g, k, *args, **kwargs)
     55 @wraps(func)
     56 def wrapper(g: GroupStorageType, k: str, *args, **kwargs):
---> 57     result = func(g, k, *args, **kwargs)
     58     g[k].attrs.setdefault("encoding-type", spec.encoding_type)
     59     g[k].attrs.setdefault("encoding-version", spec.encoding_version)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/methods.py:312, in write_mapping(f, k, v, _writer, dataset_kwargs)
    310 g = f.require_group(k)
    311 for sub_k, sub_v in v.items():
--> 312     _writer.write_elem(g, sub_k, sub_v, dataset_kwargs=dataset_kwargs)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/utils.py:243, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    241     raise ValueError("No element found in args.")
    242 try:
--> 243     return func(*args, **kwargs)
    244 except Exception as e:
    245     path = _get_display_path(store)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:304, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    300 elif k in store:
    301     del store[k]
    303 write_func = partial(
--> 304     self.find_writer(dest_type, elem, modifiers),
    305     _writer=self,
    306 )
    308 if self.callback is None:
    309     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:269, in Writer.find_writer(self, dest_type, elem, modifiers)
    267         return self.registry.get_writer(dest_type, pattern, modifiers)
    268 # Raises IORegistryError
--> 269 return self.registry.get_writer(dest_type, type(elem), modifiers)

File ~/mambaforge/envs/cfp/lib/python3.11/site-packages/anndata/_io/specs/registry.py:117, in IORegistry.get_writer(self, dest_type, src_type, modifiers)
    115     return self.write[(dest_type, src_type, modifiers)]
    116 else:
--> 117     raise IORegistryError._from_write_parts(dest_type, src_type, modifiers)

IORegistryError: No method registered for writing <class 'numpy.matrix'> into <class 'h5py._hl.group.Group'>
Error raised while writing key 'X_mean' of <class 'h5py._hl.group.Group'> to /varm

[joschif]

Should be fixed by now in #97

[joschif]

sorry my mistake, might not be fixed actually, although I believe the conversion to np.array() should have fixed it