Numba warnings

First I want to thank you for sharing this great work. It is very useful for me. The first time I execute UMAP fit and transform I get some numba warnings. They do not seem to be critical, but they are somewhat disturbing.

numba.__version__ '0.44.0'

sys.version '3.7.3 (default, Mar 27 2019, 22:11:17) \n[GCC 7.3.0]'

reducer = umap.UMAP(random_state=42)
reducer.fit(X)
Y = reducer.transform(X)

/home/mbr085/anaconda3/envs/divisivegater/lib/python3.7/site-packages/umap/umap_.py:349: NumbaWarning: 
Compilation is falling back to object mode WITH looplifting enabled because Function "fuzzy_simplicial_set" failed type inference due to: Untyped global name 'nearest_neighbors': cannot determine Numba type of <class 'function'>

File "../../../../../anaconda3/envs/divisivegater/lib/python3.7/site-packages/umap/umap_.py", line 467:
def fuzzy_simplicial_set(
    <source elided>
    if knn_indices is None or knn_dists is None:
        knn_indices, knn_dists, _ = nearest_neighbors(
        ^

  @numba.jit()
/home/mbr085/anaconda3/envs/divisivegater/lib/python3.7/site-packages/numba/compiler.py:725: NumbaWarning: Function "fuzzy_simplicial_set" was compiled in object mode without forceobj=True.

File "../../../../../anaconda3/envs/divisivegater/lib/python3.7/site-packages/umap/umap_.py", line 350:
@numba.jit()
def fuzzy_simplicial_set(
^

  self.func_ir.loc))
/home/mbr085/anaconda3/envs/divisivegater/lib/python3.7/site-packages/numba/compiler.py:734: NumbaDeprecationWarning: 
Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

File "../../../../../anaconda3/envs/divisivegater/lib/python3.7/site-packages/umap/umap_.py", line 350:
@numba.jit()
def fuzzy_simplicial_set(
^

  warnings.warn(errors.NumbaDeprecationWarning(msg, self.func_ir.loc))

[lmcinnes]

These are, indeed, non-critical – numba has just gotten a little more verbose about it’s warnings, and umap continues to be somewhat optimistic about how well numba can compile things. In this case numba is just letting you know that umap was a little over-optimistic and not as much could be as completely compiled as one might have hoped. I’ll try to fix this up in an upcoming release. Thanks for the heads up, it is appreciated.

[00krishna]

I was getting the same warnings. I added the following code to my notebooks and it solved it.

import warnings
warnings.filterwarnings('ignore')

This was based upon the StackExchange Post https://stackoverflow.com/questions/9031783/hide-all-warnings-in-ipython