FutureWarning raised when constructing lil_matrix

[leriomaggio]

Description

Constructing a scipy.sparse.lil_matrix in UMAP.inverse_transform raises a FutureWarning

Versions

OS: macOS
Python 3.7.7 (default, Mar 26 2020, 10:32:53)
NumPy 1.17.5
SciPy 1.2.1
umap 0.4

Steps/Code to Reproduce

I put the code to reproduce the issue in this gist

Cause

This issue is caused by a backward incompatibility of scipy < 1.3 with the latest updates of Numpy (numpy>=1.17) APIs for broadcast_arrays.

scipy 1.3.1 fixes this issue: scipy/scipy#10379

Proposed solution

Looking at UMAP requirements.txt this is a perfectly valid combination of packages versions.

Due to the recent API changes in Numpy I would suggest to updates the requirements with most recent and non-conflicting numpy and scipy versions:

numpy>=1.17
scipy>=1.3.1

[lmcinnes]

Thanks -- good catch. I am not great at keeping up with the changing requirements.