scanpy
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sc.tl.paga ValueError: mismatching number of index arrays for shape; got 0, expected 2
Please make sure these conditions are met
- [x] I have checked that this issue has not already been reported.
- [x] 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 think it's related to the same error that shows up in scvelo (and over there, more users seem to encounter) https://github.com/theislab/scvelo/issues/1241.
Not entirely sure though if this is unexpected user input causing this error. In that case, a more instructive message might also help at the scvelo issue..
Minimal code sample
import scanpy as sc
adata = sc.datasets.blobs()
sc.pp.neighbors(adata)
sc.tl.leiden(adata)
sc.tl.paga(adata)
Error output
168 def compute_connectivities(self):
169 if self._model == "v1.2":
...
206 f'got {len(self.coords)}, expected {self.ndim}')
208 # index arrays should have integer data types
209 for i, idx in enumerate(self.coords):
ValueError: mismatching number of index arrays for shape; got 0, expected 2
Versions
Package Version
----------------------- -----------
anndata 0.12.2
appnope 0.1.4
array-api-compat 1.12.0
asttokens 3.0.0
comm 0.2.3
contourpy 1.3.3
crc32c 2.7.1
cycler 0.12.1
debugpy 1.8.16
decorator 5.2.1
donfig 0.8.1.post1
exceptiongroup 1.3.0
executing 2.2.1
fonttools 4.60.0
h5py 3.14.0
igraph 0.11.9
importlib_metadata 8.7.0
ipykernel 6.30.1
ipython 9.5.0
ipython_pygments_lexers 1.1.1
jedi 0.19.2
joblib 1.5.2
jupyter_client 8.6.3
jupyter_core 5.8.1
kiwisolver 1.4.9
legacy-api-wrap 1.4.1
leidenalg 0.10.2
llvmlite 0.45.0
matplotlib 3.10.6
matplotlib-inline 0.1.7
natsort 8.4.0
nest_asyncio 1.6.0
networkx 3.5
numba 0.62.0
numcodecs 0.16.3
numpy 2.3.3
packaging 25.0
pandas 2.3.2
parso 0.8.5
patsy 1.0.1
pexpect 4.9.0
pickleshare 0.7.5
pillow 11.3.0
pip 25.2
platformdirs 4.4.0
prompt_toolkit 3.0.52
psutil 7.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
Pygments 2.19.2
pynndescent 0.5.13
pyparsing 3.2.4
python-dateutil 2.9.0.post0
pytz 2025.2
PyYAML 6.0.2
pyzmq 27.1.0
scanpy 1.11.4
scikit-learn 1.7.2
scipy 1.16.2
seaborn 0.13.2
session-info2 0.2.2
setuptools 78.1.1
six 1.17.0
stack_data 0.6.3
statsmodels 0.14.5
texttable 1.7.0
threadpoolctl 3.6.0
tornado 6.5.1
tqdm 4.67.1
traitlets 5.14.3
typing_extensions 4.15.0
tzdata 2025.2
umap-learn 0.5.9.post2
wcwidth 0.2.13
wheel 0.45.1
zarr 3.1.3
zipp 3.23.0
I solved it. I encountered this issue with version 1.9.6 before, but changing the version to scanpy==1.11.5 eliminates the problem.