Error in Scanpy Doublet Analysis with Scrublet on .h5ad Data Using backed="r+"

Please make sure these conditions are met

[x] I have checked that this issue has not already been reported.
[x] I have confirmed this bug exists on the latest version of scanpy.
[ ] (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

I'm encountering an issue while running Scrublet for doublet analysis on an .h5ad file loaded with backed="r+" in Scanpy. The operation throws an error, likely due to the limitations of Scrublet working with backed mode, which restricts in-memory data manipulation.

Has anyone faced this issue before? If so, do you know of any workarounds or alternative approaches to run Scrublet on such data without having to fully load it into memory? Any suggestions would be greatly appreciated!

Minimal code sample

#path to file
output_file='/home/test_folder/project1_matrix.h5ad'

#reading the h5ad file which is contains around 1 million cells
#backed="r+" do not allow the adata.obs data to be modified.
adata = sc.read_h5ad(output_file, backed="r+")

sc.pp.scrublet(adata)

Error output

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/test_env/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/test_env/lib/python3.12/site-packages/scanpy/preprocessing/_scrublet/__init__.py", line 180, in scrublet
    adata = adata.copy()
            ^^^^^^^^^^^^
  File "/home/test_env/python3.12/site-packages/anndata/_core/anndata.py", line 1447, in copy
    raise ValueError(
ValueError: To copy an AnnData object in backed mode, pass a filename: `.copy(filename='myfilename.h5ad')`. To load the object into memory, use `.to_memory()`.

Versions

``` sc.logging.print_versions() ----- anndata 0.11.1 scanpy 1.10.4 ----- PIL 11.0.0 absl NA attr 24.2.0 cffi 1.17.1 chex 0.1.87 cycler 0.12.1 cython_runtime NA dateutil 2.9.0.post0 distutils 3.12.6 docrep 0.3.2 doubletdetection 4.2 etils 1.10.0 filelock 3.16.1 flax 0.10.1 fsspec 2024.10.0 h5py 3.12.1 igraph 0.11.8 jaraco NA jax 0.4.35 jaxlib 0.4.35 joblib 1.4.2 kiwisolver 1.4.7 lazy_loader 0.4 legacy_api_wrap NA leidenalg 0.10.2 lightning 2.4.0 lightning_utilities 0.11.8 llvmlite 0.43.0 louvain 0.8.2 matplotlib 3.9.2 ml_collections 1.0.0 ml_dtypes 0.5.0 more_itertools 10.5.0 mpl_toolkits NA mpmath 1.3.0 msgpack 1.1.0 mudata 0.3.1 multipledispatch 0.6.0 natsort 8.4.0 numba 0.60.0 numexpr 2.10.1 numpy 1.26.4 numpyro 0.15.3 nvidia NA opt_einsum 3.4.0 optax 0.2.4 packaging 24.2 pandas 2.2.3 phenograph 1.5.7 pkg_resources NA platformdirs 4.3.6 psutil 6.1.0 pycparser 2.22 pygments 2.18.0 pynndescent 0.5.13 pyparsing 3.2.0 pyro 1.9.1 pytz 2024.2 rich NA scipy 1.14.1 scvi 1.2.0 session_info 1.0.0 setuptools 74.1.2 six 1.16.0 skimage 0.24.0 sklearn 1.5.2 sparse 0.15.4 sympy 1.13.1 tables 3.10.1 texttable 1.7.0 threadpoolctl 3.5.0 toolz 1.0.0 torch 2.5.1+cu124 torchgen NA torchmetrics 1.6.0 tqdm 4.67.0 triton 3.1.0 typing_extensions NA wcwidth 0.2.13 xarray 2024.10.0 yaml 6.0.2 zstandard 0.23.0 ----- Python 3.12.6 | packaged by conda-forge | (main, Sep 22 2024, 14:16:49) [GCC 13.3.0] Linux-6.8.0-48-generic-x86_64-with-glibc2.39 ----- Session information updated at 2024-11-15 11:48 ```

scverse / scanpy