non_zero_dists might be size 0
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0.4
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Description
This does not seem to be an issue when the function is annotated with
@numba.njit(
fastmath=True
)
But when removing it, it will sometimes throw:
rho[i] = interpolation * non_zero_dists[0]
IndexError: index 0 is out of bounds for axis 0 with size 0
This happens when non_zero_dists = ith_distances[ith_distances > 0.0] will return no indices for numpy to select.
Example: 2 points, n=2, local_connectivity=0.0
https://github.com/lmcinnes/umap/blob/d5d995625b5cfe55430771e4ec2f044533da7b4c/umap/umap_.py#L118
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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Research direction
Open umap/umap_.py around line 118 and inspect how ith_distances is filtered before non_zero_dists[0] is accessed. Reproduce the failure with 2 points, n=2, and local_connectivity=0.0. Done means this input no longer raises IndexError while existing behavior remains intact.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100