numba 0.57.0 raises NumbaDeprecationWarning regarding 'nopython' kwarg

[dpoznik]

Importing umap 0.5.3 with numba 0.57.0 (released today) elicits the following NumbaDeprecationWarning:

In [1]: import umap
/usr/local/lib/python3.11/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/usr/local/lib/python3.11/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/usr/local/lib/python3.11/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/usr/local/lib/python3.11/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()

In [2]: umap.__version__
Out[2]: '0.5.3'

In [3]: umap.numba.__version__
Out[3]: '0.57.0'

Not a big deal, but figured I'd mention.

Here is that numba link:
https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

[lmcinnes]

Thanks; I'll try to get around to updating those soon.

[buhrmann]

FWIW, I'm also getting segmentation faults at runtime which I don't get with the same code and numba<0.57

[gmarkall]

@buhrmann I believe the segfaults were due to a patch not being applied to LLVM in conda-forge. conda-forge/llvmdev-feedstock#209 is now merged and new packages are uploaded - if you update libllvm14 (e.g. with conda update libllvm14 and run again, are the segfaults now resolved?

[l8l]

I still get this error as of August 2nd 2023. It seems that it is very simple to fix as one only needs to add nopython=True in all numba.jit() code fragments. Is it already clear when this will be implemented?

[hoondy]

try reinstalling the latest from the master branch. warnings gone after they switched calls to numba.njit

pip install --upgrade --force-reinstall git+https://github.com/lmcinnes/umap@master

[dpoznik]

Resolved in 0.5.4. Thanks!