[python] Avoid two warnings on ingest

[johnkerl]

Drive-by finding on ingest.

Repro at the AnnData level:

>>> import anndata as ad

>>> adata = ad.read_h5ad('/var/s/a/white-matter-astrocytes.h5ad', 'r')

>>> adata.X.format
'csr'

>>> adata.X.format_str
/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/anndata/_core/sparse_dataset.py:311: FutureWarning: The attribute .format_str is deprecated and will be removed in the anndata 0.11.0. Please use .format instead.
  warnings.warn(
'csr'

As noted below there is another warning:

/usr/lib/python3.10/abc.py:119: FutureWarning: SparseDataset is deprecated and will be removed in late 2024. It has been replaced by the public classes CSRDataset and CSCDataset.

but we can't get rid of this in Python 3.8 which we still support (#2141)

[johnkerl]

Garg; from anndata._core.sparse_dataset import CSCDataset is not supported in Python 3.8 apparently ...

[johnkerl]

Confirmed:

# ================================================================
ubuntu@anzo[prod][][~]$ alias dreb
alias dreb='docker run --rm -it --entrypoint=/bin/bash'

# ================================================================
ubuntu@anzo[prod][][~]$ dreb python:3.11

root@43acc809a778:/# pip install -q anndata

root@43acc809a778:/# python
Python 3.11.8 (main, Mar 12 2024, 11:41:52) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from anndata._core.sparse_dataset import CSCDataset

# ================================================================
ubuntu@anzo[prod][][~]$ dreb python:3.10

root@de3e2090a4f5:/# pip install -q anndata

root@de3e2090a4f5:/# python
Python 3.10.13 (main, Mar 12 2024, 12:16:25) [GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from anndata._core.sparse_dataset import CSCDataset

# ================================================================
ubuntu@anzo[prod][][~]$ dreb python:3.9

root@05008e9a6e51:/# pip install -q anndata

root@05008e9a6e51:/# python
Python 3.9.18 (main, Mar 12 2024, 12:36:48)
[GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from anndata._core.sparse_dataset import CSCDataset

# ================================================================
ubuntu@anzo[prod][][~]$ dreb python:3.8

root@6684c0f109fe:/# pip install -q anndata

root@6684c0f109fe:/# python
Python 3.8.18 (default, Mar 12 2024, 12:46:23)
[GCC 12.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from anndata._core.sparse_dataset import CSCDataset
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'CSCDataset' from 'anndata._core.sparse_dataset' (/usr/local/lib/python3.8/site-packages/anndata/_core/sparse_dataset.py)

[johnkerl]

Garg. We can't fix either one on Python 3.8 :(

FAILED apis/python/tests/test_basic_anndata_io.py::test_named_X_layers[None] - AttributeError: 'SparseDataset' object has no attribute 'format'