Awkward array "view" attribute does not get removed on save.

[grst]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of anndata.
• (optional) I have confirmed this bug exists on the master branch of anndata.

Report

Saving a view of anndata turns it into a copy. However, the "view" attributes of an awkward array do not get removed on save, which leads to some side effects described in these discourse posts:
https://discourse.scverse.org/t/notimplementederror-cannot-create-a-view-of-an-awkward-array-with-array-parameter/3305
https://discourse.scverse.org/t/ir-tl-chain-qc-adata-error-message-with-scirpy-0-18-0/3304/4

Code:

import scirpy as ir
import anndata as ad
adata = ir.datasets.wu2020_3k()["airr"]
v = adata[:200]
v.obsm["airr"]

This awkward array now has the "_view_args" added as intended:

[...]
}, parameters={"_view_args": ["target-137048116381552", "obsm", ["airr"]], "__list__": "AwkwardArrayView"}]

v.write_h5ad("/tmp/airr.h5ad")
v2 = ad.read_h5ad("/tmp/airr.h5ad')
v2.obsm["airr"]

Now v2 is not a view anymore, but the awkward array still has the same parameters (and target-137048116381552 is a weakref to an object that does not exist anymore)

[...]
}, parameters={"_view_args": ["target-137048116381552", "obsm", ["airr"]], "__list__": "AwkwardArrayView"}]

Possible fix:

On save, send the awkward array through ak.without_parameters().

Versions

anndata             0.10.8
scirpy              0.18.1.dev7+g2157800c
session_info        1.0.0
-----
Levenshtein         0.26.0
PIL                 11.0.0
adjustText          1.2.0
asciitree           NA
asttokens           NA
awkward             2.6.9
awkward_cpp         NA
cairo               1.27.0
charset_normalizer  3.4.0
comm                0.2.2
cycler              0.12.1
cython_runtime      NA
dateutil            2.9.0.post0
debugpy             1.8.7
decorator           5.1.1
defusedxml          0.7.1
distutils           3.12.7
executing           2.1.0
fsspec              2024.9.0
h5py                3.12.1
...
Python 3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC 13.3.0]
Linux-6.11.4-arch1-1-x86_64-with-glibc2.40
-----
Session information updated at 2024-10-20 14:01