`.write` does not save `None` values

Description

When saving an AnnData object to disk, keys of a dictionary whose value is None seem not to be saved.

import numpy as np
import scanpy as sc
from anndata import AnnData

adata = AnnData(X=np.eye(3), uns={'key_1': 0, 'key_2': None})
adata.write('adata.h5ad')

_adata = sc.read('adata.h5ad')

gives

>>> _adata
AnnData object with n_obs × n_vars = 3 × 3
    uns: 'key_1'

[LustigePerson]

Just for the sake of documenting this somewhere: I ran into this issue when I used the log1p function, which as a default writes {"base": None} to uns. However after saving and reloading the object, an error was thrown with rank_genes_groups (code), because it is looking for the base key which is not present anymore.

[WeilerP]

BTW, this is also an issue if you have None in one of your columns:

import numpy as np
import scanpy as sc
from anndata import AnnData

adata = AnnData(X=np.eye(3), uns={'key_1': 0, 'key_2': None, 'key_3': pd.DataFrame({'col_0': ['string', None]})})
# Alternative failure
# adata = AnnData(X=np.eye(3), uns={'key_1': 0, 'key_2': None}, obs={'col_0': [None]})
adata.write('adata.h5ad')

Traceback

Traceback (most recent call last):
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/utils.py", line 209, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 270, in write_series
    group.create_dataset(
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/h5py/_hl/group.py", line 148, in create_dataset
    dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/h5py/_hl/dataset.py", line 140, in make_new_dset
    dset_id.write(h5s.ALL, h5s.ALL, data)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5d.pyx", line 232, in h5py.h5d.DatasetID.write
  File "h5py/_proxy.pyx", line 145, in h5py._proxy.dset_rw
  File "h5py/_conv.pyx", line 444, in h5py._conv.str2vlen
  File "h5py/_conv.pyx", line 95, in h5py._conv.generic_converter
  File "h5py/_conv.pyx", line 249, in h5py._conv.conv_str2vlen
TypeError: Can't implicitly convert non-string objects to strings

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/utils.py", line 209, in func_wrapper
    return func(elem, key, val, *args, **kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 263, in write_dataframe
    write_series(group, col_name, series, dataset_kwargs=dataset_kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
    raise type(e)(
TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'col_0' of <class 'h5py._hl.group.Group'> from /.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1912, in write_h5ad
    _write_h5ad(
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 118, in write_h5ad
    write_attribute(f, "uns", adata.uns, dataset_kwargs=dataset_kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/functools.py", line 875, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 130, in write_attribute_h5ad
    _write_method(type(value))(f, key, value, *args, **kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 294, in write_mapping
    write_attribute(f, f"{key}/{sub_key}", sub_value, dataset_kwargs=dataset_kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/functools.py", line 875, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/h5ad.py", line 130, in write_attribute_h5ad
    _write_method(type(value))(f, key, value, *args, **kwargs)
  File "/miniconda3/envs/anndata_bug/lib/python3.8/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
    raise type(e)(
TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'col_0' of <class 'h5py._hl.group.Group'> from /.

Above error raised while writing key 'uns/key_3' of <class 'h5py._hl.files.File'> from /.

Though it does work for

adata = AnnData(X=np.eye(3), uns={'key_1': 0, 'key_2': None}, obs={'col_0': ['string', 'string', None]})