sc.tl.paga ValueError: mismatching number of index arrays for shape; got 0, expected 2

[eroell]

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 think it's related to the same error that shows up in scvelo (and over there, more users seem to encounter) theislab/scvelo#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