TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices'.

[cnwokolo24]

TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices' when I try to run scv.pp.moments or scv.pp.neighbors on adata. I'm a beginner with RNA velocity analysis, so please advise in detail. Many thanks in advance ...

import scanpy as sc #import scanpy
import pandas as pd #pandas
import scvelo as scv

adata = scv.read(path/to/file.loom, cache=True)
scv.pl.proportions(adata)
scv.pp.filter_genes(adata, min_shared_counts=20)
scv.pp.normalize_per_cell(adata)
scv.pp.filter_genes_dispersion(adata, n_top_genes=2000)
scv.pp.log1p(adata)
scv.pp.filter_and_normalize(adata, min_shared_counts=20, n_top_genes=2000)
scv.pp.pca(adata)
scv.pp.moments(adata,n_pcs=30, n_neighbors=30 )

Error output

```pytb # paste the error output here, if applicable computing neighbors /usr/local/lib/python3.10/dist-packages/ipykernel/ipkernel.py:283: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above. and should_run_async(code) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) [](https://localhost:8080/#) in () ----> 1 scv.pp.moments(adata,n_pcs=30, n_neighbors=30 ) 2 frames [/usr/local/lib/python3.10/dist-packages/scvelo/preprocessing/neighbors.py](https://localhost:8080/#) in _get_scanpy_neighbors(adata, **kwargs) 38 warnings.simplefilter("ignore") 39 neighbors = Neighbors(adata) ---> 40 neighbors.compute_neighbors(write_knn_indices=True, **kwargs) 41 logg.switch_verbosity("on", module="scanpy") 42 TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices' ```

Versions

```pytb # paste the ouput of scv.logging.print_versions() here scvelo==0.3.2 scanpy==1.10.1 anndata==0.10.7 loompy==3.0.7 numpy==1.25.2 scipy==1.11.4 matplotlib==3.7.1 sklearn==1.2.2 pandas==2.0.3 [ ] scv.pp.moments(adata, ) [Colab paid products ](https://colab.research.google.com/signup?utm_source=footer&utm_medium=link&utm_campaign=footer_links)- [Cancel contracts here](https://colab.research.google.com/cancel-subscription) 19202122232425262728293031323334353637383940414243444546474849505152 ```

[WeilerP]

Duplicate of #1212; please check existing issues before opening a new one.

[kulansam]

Duplicate of #1212; please check existing issues before opening a new one.

I am facing the same issue. https://github.com/theislab/scvelo/issues/1212; is not working.

[cnwokolo24]

Duplicate of #1212; please check existing issues before opening a new one.

I am facing the same issue. https://github.com/theislab/scvelo/issues/1212; is not working.

I didn't notice at first but #1212, switches from using scv to scanpy for pp.moments & pp.neighbor. Did you try that?

[kulansam]

Duplicate of #1212; please check existing issues before opening a new one.

I am facing the same issue. #1212; is not working.

I didn't notice at first but #1212, switches from using scv to scanpy for pp.moments & pp.neighbor. Did you try that?

yes, I have finally resolved by "https://github.com/theislab/scvelo/issues/449".

thanks