scvelo: scanpy 1.4.2 breaks pp.moments
The new version of scanpy released today appears to break scvelo.pp.moments (and presumably much of scanpy itself). This is reproducible with the Dentate Gyrus example data. Full error (following the example vignette):
>>> scv.pp.moments(adata, n_pcs=30, n_neighbors=30)
computing neighbors
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/scvelo/preprocessing/moments.py", line 45, in moments
neighbors(adata, n_neighbors=n_neighbors, use_rep=use_rep, n_pcs=n_pcs, method=method, metric=metric)
File "/usr/local/lib/python3.7/site-packages/scvelo/preprocessing/neighbors.py", line 82, in neighbors
neighbors = Neighbors(adata)
File "/usr/local/lib/python3.7/site-packages/scanpy/neighbors/__init__.py", line 466, in __init__
self.n_neighbors = int(self._distances.count_nonzero() / self._distances.shape[0])
AttributeError: 'NoneType' object has no attribute 'count_nonzero'
Rolling back to scanpy 1.4.1 solves the problem. @theislab - Filing this issue here rather than in the scanpy repo as I don’t have a reproducible upstream example.
About this issue
- Original URL
- State: closed
- Created 5 years ago
- Comments: 15 (9 by maintainers)
Commits related to this issue
- fix https://github.com/theislab/scvelo/issues/58 — committed to Marius1311/scvelo by VolkerBergen 5 years ago
OK! We should make 1.4.3 asap in this case.