Untyped global name 'nearest_neighbors'

With the most recent version of scanpy, I’m getting the above mentioned warning, which causes the dynverse/ti_paga builds to fail.

The problem can be replicated by building the dynverse/ti_paga container manually and trying to run it. For the sake of simplicity, I have built the container for you and pushed it to dynverse/ti_paga_issue.

Minimum reproducible example

Inside terminal:

# fetch newest dynverse/ti_paga container in which this problem occurs
docker pull dynverse/ti_paga_issue

# enter the container 
docker run --entrypoint bash -it dynverse/ti_paga_issue

# create an example dataset and save it at /input.h5
/code/example.sh /input.h5

# enter python
python

Inside python

import dynclipy
task = dynclipy.main(["--dataset", "/input.h5", "--output", "/output.h5"])

import scanpy.api as sc
import anndata

counts = task["counts"]

adata = anndata.AnnData(counts)
sc.pp.recipe_zheng17(adata, n_top_genes=101)
sc.tl.pca(adata, n_comps=50)
sc.pp.neighbors(adata, n_neighbors=15)

Which generates the following warning:

/usr/local/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 "usr/local/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()
/usr/local/lib/python3.7/site-packages/numba/compiler.py:725: NumbaWarning: Function "fuzzy_simplicial_set" was compiled in object mode without forceobj=True.

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

  self.func_ir.loc))
/usr/local/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 "usr/local/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))

[rcannood]

Thanks @flying-sheep! I will suppress the warning this way.

[rcannood]

Makes sense, thanks for clarifying. This issue is then related to lmcinnes/umap#252.

@flying-sheep @lmcinnes Is there any way I can turn these specific warnings off?