sc.pp.pca doesn't work after importing sparrow

[csangara]

Hi guys,

I have a strange issue that I'm wondering whether you could provide some insight on. I provide a minimum example below with the PBMC dataset, but I have the same issue with any AnnData object.

import scanpy as sc
adata = sc.read_10x_mtx(
    "data/filtered_gene_bc_matrices/hg19/",  # the directory with the `.mtx` file
    var_names="gene_symbols",
    cache=True
)
sc.pp.normalize_total(adata, target_sum=1e4)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)
sc.pp.scale(adata)
sc.pp.pca(adata)

So, the code above would just instantly run PCA:

computing PCA
    with n_comps=50
    finished (0:00:00)

but if I do this:

import sparrow
sc.pp.pca(adata)

The PCA would get stuck at

computing PCA
    with n_comps=50

without any error messages. I've left it for an hour before and it just keeps running.

When I used the debugger, it seems to be stuck at the svds function, but if I "Step Into" the function, the rest of the code runs normally.

My packages are scanpy==1.10.3 anndata==0.10.9 umap==0.5.6 numpy==1.26.4 scipy==1.14.1 pandas==2.2.3 scikit-learn==1.5.2 statsmodels==0.14.4 igraph==0.11.6 pynndescent==0.5.13

However, with a fresh install of Harpy, I don't have this issue anymore. (scanpy==1.10.4 anndata==0.11.1 umap==0.5.7 numpy==1.26.4 scipy==1.12.0 pandas==2.2.3 scikit-learn==1.5.2 statsmodels==0.14.4 igraph==0.11.8 pynndescent==0.5.13)

This is probably not very reproducible, but this has plagued me for a day, so I'm wondering if you have any ideas on what the cause could be.

Thanks!
Sai

[ArneDefauw]

I could reproduce somewhat similar behaviour, but unrelated to possible imports of sparrow.

For me it looked to be related to the scipy version installed. When I install scipy version 1.12.0, sc.pp.pca took approx 1min minute to run, while for scipy version 1.14.0, it took less than a second.

But strange enough, for you scipy version 1.12.0 was faster.

Also, solving the environment.yml of harpy results in installation of scipy version 1.12.0, but I could not find a library in the environment that pins scipy to this version.