Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Cannot query an index constructed from sparse matrix

See original GitHub issue

I have a sparse matrix X on which I can successfully run UMAP:

<100000x9630 sparse matrix of type '<class 'numpy.float64'>'
	with 266398 stored elements in List of Lists format>

I can construct an index like this, and it works fine:

nn = NNDescent(X, metric='cosine')

However, querying this index does not seem to work. nn.query(X[:5,:], k=15) returns the following error:

~/anaconda3/lib/python3.7/site-packages/pynndescent/pynndescent_.py in query(self, query_data, k, epsilon)
   1263 
   1264         if self._distance_correction is not None:
-> 1265             dists = self._distance_correction(dists)
   1266 
   1267         return indices, dists

~/anaconda3/lib/python3.7/site-packages/numba/npyufunc/dufunc.py in _compile_for_args(self, *args, **kws)
    164                     argty = argty.dtype
    165                 argtys.append(argty)
--> 166         return self._compile_for_argtys(tuple(argtys))
    167 
    168     def _compile_for_argtys(self, argtys, return_type=None):

~/anaconda3/lib/python3.7/site-packages/numba/npyufunc/dufunc.py in _compile_for_argtys(self, argtys, return_type)
    184             self._dispatcher, self.targetoptions, sig)
    185         actual_sig = ufuncbuilder._finalize_ufunc_signature(
--> 186             cres, argtys, return_type)
    187         dtypenums, ptr, env = ufuncbuilder._build_element_wise_ufunc_wrapper(
    188             cres, actual_sig)

~/anaconda3/lib/python3.7/site-packages/numba/npyufunc/ufuncbuilder.py in _finalize_ufunc_signature(cres, args, return_type)
    140         if cres.objectmode:
    141             # Object mode is used and return type is not specified
--> 142             raise TypeError("return type must be specified for object mode")
    143         else:
    144             return_type = cres.signature.return_type

TypeError: return type must be specified for object mode

Versions:

UMAP 0.3.10
pynndescent 0.4.5
numba 0.46.0

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:7 (5 by maintainers)

Top GitHub Comments

2reactions

lmcinnescommented, Mar 14, 2020

Nope, but that should be fixed now. Sorry was away from dealing with github for a while and lost track of these.

1reaction

lmcinnescommented, Mar 13, 2020

Found it – it was the added checks of near zero distances that were unsupported by numba. Resolved easily enough. It should work now, and there should be a 0.4.6 release with it fixed available on PyPi (and conda-forge) shortly.