[Bug] Kernel crush #3946
Description
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?
When I use the sc.external.pp.harmony_integrate method with vscode(ipynb), it causes a kernel crash every time.
Minimal code sample
import scanpy as sc
concat = sc.read_10x_mtx(item, var_names='gene_symbols', make_unique=True)
sc.pp.normalize_total(concat, target_sum=1e4)
sc.pp.log1p(concat)
sc.pp.highly_variable_genes(concat, n_top_genes=3000, flavor='seurat_v3')
concat.raw = concat
concat = concat[:, concat.var.highly_variable]
sc.pp.scale(concat, max_value=10)
sc.tl.pca(concat, n_comps=50)
sc.external.pp.harmony_integrate(concat, key='Sample')
concat.obsm['X_pca'] = concat.obsm['X_pca_harmony']
sc.tl.umap(concat, random_state=random)
sc.tl.leiden(concat, flavor='igraph', n_iterations=2, random_state=random)Error output
11:28:23.758 [error] Disposing session as kernel process died ExitCode: undefined, Reason:
11:33:38.342 [error] Error in execution (get message for cell) Error: 内核 "venv (Python 3.10.12)" 已终止。有关详细信息，请单击[此处](https://aka.ms/vscodeJupyterKernelCrash)。有关更多详细信息，请查看 Jupyter [log](command:jupyter.viewOutput)。
> Kernel Id = .jvsc74a57bd0aac885d2aded06390ba2db5cdef13a285a5b547fccc0faf8e7c60f0ffa1268b4./work/users/<username>/xinjiang/venv/python./work/users/<username>/xinjiang/venv/python.-m#ipykernel_launcher
> Interpreter Id = /work/users/<username>/xinjiang/venv/bin/python
> at n.verifyKernelState (~/.vscode-server/extensions/ms-toolsai.jupyter-2025.9.1-linux-x64/dist/extension.node.js:309:81661)
> originalException = undefinedVersions
scanpy==1.11.5
anndata==0.11.4
Details
| Dependency | Version |
| ------------------ | ----------- |
| prompt_toolkit | 3.0.51 |
| python-dateutil | 2.9.0.post0 |
| numba | 0.61.2 |
| pillow | 11.3.0 |
| executing | 2.2.0 |
| charset-normalizer | 3.4.2 |
| PyYAML | 6.0.2 |
| setuptools | 80.9.0 |
| texttable | 1.7.0 |
| joblib | 1.5.1 |
| leidenalg | 0.10.2 |
| igraph | 0.11.9 |
| kiwisolver | 1.4.8 |
| pytz | 2025.2 |
| debugpy | 1.8.14 |
| six | 1.17.0 |
| statsmodels | 0.14.5 |
| cycler | 0.12.1 |
| pure_eval | 0.2.3 |
| natsort | 8.4.0 |
| Cython | 3.2.4 |
| patsy | 1.0.1 |
| parso | 0.8.4 |
| pyarrow | 20.0.0 |
| jedi | 0.19.2 |
| tornado | 6.5.1 |
| decorator | 5.2.1 |
| stack-data | 0.6.3 |
| h5py | 3.14.0 |
| wcwidth | 0.2.13 |
| asttokens | 3.0.0 |
| ipython | 8.37.0 |
| llvmlite | 0.44.0 |
| psutil | 7.0.0 |
| Component | Info |
| --------- | -------------------------------------------------- |
| Python | 3.10.12 (main, May 27 2025, 17:12:29) [GCC 11.4.0] |
| OS | Linux-5.15.0-143-generic-x86_64-with-glibc2.35 |
| CPU | 144 logical CPU cores, x86_64 |
| GPU | No GPU found |
| Updated | 2026-01-16 03:34 |