Decision/Extra trees & missing values: split ignored when NaNs + single unique value in feature #32272
Description
Describe the bug
When feature values consist of only NaNs and another value, the feature is considered as constant by this if:
if (
# All values for this feature are missing, or
end_non_missing == start or
# This feature is considered constant (max - min <= FEATURE_THRESHOLD)
feature_values[end_non_missing - 1] <= feature_values[start] + FEATURE_THRESHOLD
):and not considered for the split. This if considers [0 0 0 NaN NaN] as constant (which is false, you can make a split between NaNs and non-NaNs and such a split might make a lot of sense in some datasets).
Same problem in the node_split_random for Extra trees.
Steps/Code to Reproduce
import numpy as np
from sklearn.tree import DecisionTreeClassifier
X = [0, 0, 0, np.nan, np.nan]
y = [0, 0, 0, 1 , 1 ]
X = np.array(X).reshape(-1, 1)
tree = DecisionTreeClassifier().fit(X, y)
print(tree.predict(X))
# prints: [0 0 0 0 0]
print(tree.tree_.node_count)
# prints: 1Expected Results
A split is made, the tree has 3 nodes (2 leaves) and predicts [0 0 0 1 1].
Actual Results
No split was made, the tree is a single node.
Versions
System:
python: 3.12.11 (main, Aug 18 2025, 19:19:11) [Clang 20.1.4 ]
executable: /home/arthur/dev-perso/scikit-learn/sklearn-env/bin/python
machine: Linux-6.14.0-29-generic-x86_64-with-glibc2.39
Python dependencies:
sklearn: 1.8.dev0
pip: None
setuptools: 80.9.0
numpy: 2.3.3
scipy: 1.16.2
Cython: 3.1.4
pandas: 2.3.2
matplotlib: 3.10.6
joblib: 1.5.2
threadpoolctl: 3.6.0
Built with OpenMP: True
threadpoolctl info:
user_api: blas
internal_api: openblas
num_threads: 16
prefix: libscipy_openblas
filepath: /home/arthur/dev-perso/scikit-learn/sklearn-env/lib/python3.12/site-packages/numpy.libs/libscipy_openblas64_-8fb3d286.so
version: 0.3.30
threading_layer: pthreads
architecture: Haswell
user_api: blas
internal_api: openblas
num_threads: 16
prefix: libscipy_openblas
filepath: /home/arthur/dev-perso/scikit-learn/sklearn-env/lib/python3.12/site-packages/scipy.libs/libscipy_openblas-b75cc656.so
version: 0.3.29.dev
threading_layer: pthreads
architecture: Haswell
user_api: openmp
internal_api: openmp
num_threads: 16
prefix: libgomp
filepath: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
version: None