lmcinnes / lmcinnes/umap

Issue with numba and umap

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Description

Hi there

I have an error I'm having trouble resolving. I can't seem to get
numba==0.45.0 and umap-learn<=0.3.8 to work together.

I keep getting the following error:

numba.errors.LoweringError: Failed in nopython mode pipeline (step: nopython mode backend)
Type of #4 arg mismatch: i1 != i32

File "../../miniconda3/envs/solo-sc/lib/python3.7/site-packages/umap/utils.py", line 131:
def make_heap(n_points, size):
    <source elided>
    """
    result = np.zeros((3, int(n_points), int(size)), dtype=np.float64)
    ^

Which seems to be similar to this issue:
https://github.com/lmcinnes/umap/issues/225

I've tried python 3.6.1, 3.6.7, and 3.7 none of which have helped the issue.
Any ideas about troubleshooting would be great. Other versions of Numba and umap-learn woork together for me but for a variety of other dependencies I'd really like the versions mentioned above to work together.

Please let me know if you have any thoughts

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the traceback location in umap/utils.py at line 131 and the linked issue #225. Reproduce the failure using Python 3.6 or 3.7 with numba==0.45.0 and umap-learn<=0.3.8, then compare the behavior with the other versions mentioned. Done means identifying whether this version combination is supported and documenting a confirmed resolution or incompatibility.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
18/100

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