Leiden clustering returns different results for Scanpy `1.10.4` and `1.9.3`

[alam-shahul]

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 scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

I am doing some data analysis that depends on Scanpy, and for reproducibility reasons it is important that the results from Scanpy's implementation of Leiden clustering are consistent.

It seems that the changes to the sc.tl.leiden implementation in v1.10 change the clustering results, although they are not supposed to (there is a warning that the defaults will change in the future, but that they have not yet).

Can this be patched?

Minimal code sample

import numpy as np
import anndata as ad
import scanpy as sc

print(sc.__version__)

def cluster(dataset, use_rep, random_state: int = 0, resolution: float = 1.0, n_neighbors: int = 20, method="leiden", **kwargs):
    """Test clustering."""
    clustering_function = getattr(sc.tl, method)
    sc.pp.neighbors(dataset, use_rep=use_rep, random_state=random_state, n_neighbors=n_neighbors)
    clustering_function(dataset, resolution=resolution, random_state=random_state, key_added=method, **kwargs)


normalized_X = np.array([[-0.0153584372512808719352106479050235066097229719161987304687500000,
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random_subset = ad.AnnData(
    X=np.zeros_like(normalized_X),
    obsm={
        "normalized_X": normalized_X,
    }
)

cluster(random_subset, use_rep="normalized_X")

Error output

Versions

[flying-sheep]

Hm, I need to take a closer look at that. I didn‘t try to reproduce it, but logically, it seems impossible, the code’s behavior looks identical to me:

git diff 1.9.3:scanpy/tools/_leiden.py 1.10.4:src/scanpy/tools/_leiden.py

[alam-shahul]

@flying-sheep I just tested it again and it still seems to be inconsistent between 1.9.3 and 1.10.4... again, this seems like a problematic input, since it doesn't seem to be inconsistent for other mock data.

Another possibility is that the implementation of sc.pp.neighbors has changed...?