Comments (1)
ktpolanski
commented on June 2, 2024
Scanorama's nn_approx uses annoy, which is a package that has caused many a headache due to its instability. From my experience, these segfaults started showing up since 1.17.x got released, and tend to begin happening more consistently if anything is installed into the environment after annoy itself somehow. Downgrading to 1.16.3 via pip tends to make them go away.
It would be neat if there was some sort of more reliable workaround, keeping annoy stable and not bothering the user.
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Related Issues (20)
- Benchmarks: Add all from Dask tutorial
- sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency
- Different clustering results when setting metrics = "cosine", using callable cosine function and direct cos distance input.
- sc.pl.paga_path error in dimensions of array passed to ax.imshow
- AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet' HOT 2
- Unexplainable sc.pp.highly_variable_genes(subset = True) behavior HOT 1
- sc.tl.leiden with `flavor='igraph'` raises an (ignored by igraph) “ValueError: high is out of bounds for int32” HOT 6
- When importing Scanpy 1.9.1, if you're using matplotlib version below 3.7, you might encounter a metaclass error. HOT 5
- Loophole with using scaled adata for sc.tl.score_genes_cell_cycle
- will rank_genes_groups_dotplot support results from filter_rank_genes_groups? HOT 4
- More complete dataset documentation HOT 2
- Switch away from asv HOT 1
- Access to Diffusion Map methods (and other embedding methods) as Scikit-Learn style API HOT 2
- Wrongly ordered DotPlot totals in `scanpy` 1.10.1 with Pandas 1.x HOT 3
- sc.get.aggregate summary statistics
- Broken Scrublet Test
- Error in running scrublet HOT 1
- error in readwrite.py HOT 1
- Adata.raw gets modified upon log normalization of adata HOT 1
- AttributeError: 'Ingest' object has no attribute '_pca_use_hvg'
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