Gist code to reproduce UMAP Issue #400 - https://github.com/lmcinnes/umap/issues/400

umap_inverse_transform_future_warning.py

import umap
import numpy as np
import scipy as sp

print('umap: ', umap.__version__)
print('Numpy: ', np.__version__)
print('Scipy: ', sp.__version__)

# umap:  0.4.0
# Numpy:  1.17.5
# Scipy:  1.2.1

from sklearn.datasets import load_digits
X, _ = load_digits(return_X_y=True)

trans = umap.UMAP(n_neighbors=10, random_state=42, 
                  metric="euclidean", output_metric="euclidean", 
                  init="spectral").fit(X)

inverse_trans = trans.inverse_transform(trans.embedding_[:10, :])