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⚠️ CI failed on Linux_Nightly.pylatest_pip_scipy_dev (last failure: May 17, 2025) ⚠️ #31370

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scikit-learn-bot opened this issue May 16, 2025 · 4 comments
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⚠️ CI failed on Linux_Nightly.pylatest_pip_scipy_dev (last failure: May 17, 2025) ⚠️ #31370

scikit-learn-bot opened this issue May 16, 2025 · 4 comments

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scikit-learn-bot commented May 16, 2025 •
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CI is still failing on Linux_Nightly.pylatest_pip_scipy_dev (May 17, 2025)

  • test_r_regression[True]
  • test_f_regression[csr_matrix]
@github-actions github-actions bot added the Needs Triage Issue requires triage label May 16, 2025
@lesteve lesteve removed the Needs Triage Issue requires triage label May 16, 2025
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lesteve commented May 16, 2025

Looks like a change in scipy-dev

from scipy import sparse

m = sparse.csr_matrix([[1, 2, 3], [4, 5, 6]])
m.mean(axis=0)

scipy 1.15.2 is a numpy matrix

matrix([[2.5, 3.5, 4.5]])

scipy-dev is an numpy array

array([[2.5, 3.5, 4.5]])

Somehow we are relying on this in r_regression to flatten the result of X.mean(axis=0)

scikit-learn/sklearn/feature_selection/_univariate_selection.py

Lines 370 to 386 in 675736a

if center:
y = y - np.mean(y)
# TODO: for Scipy <= 1.10, `isspmatrix(X)` returns `True` for sparse arrays.
# Here, we check the output of the `.mean` operation that returns a `np.matrix`
# for sparse matrices while a `np.array` for dense and sparse arrays.
# We can reconsider using `isspmatrix` when the minimum version is
# SciPy >= 1.11
X_means = X.mean(axis=0)
X_means = X_means.getA1() if isinstance(X_means, np.matrix) else X_means
# Compute the scaled standard deviations via moments
X_norms = np.sqrt(row_norms(X.T, squared=True) - n_samples * X_means**2)
else:
X_norms = row_norms(X.T)
correlation_coefficient = safe_sparse_dot(y, X)
with np.errstate(divide="ignore", invalid="ignore"):
correlation_coefficient /= X_norms

@lesteve lesteve mentioned this issue May 16, 2025
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lesteve commented May 16, 2025

It seems like this is linked to #22873, I commented scipy/scipy#22873 (comment) to ask about it there.

@scikit-learn-bot scikit-learn-bot changed the title ⚠️ CI failed on Linux_Nightly.pylatest_pip_scipy_dev (last failure: May 16, 2025) ⚠️ ⚠️ CI failed on Linux_Nightly.pylatest_pip_scipy_dev (last failure: May 17, 2025) ⚠️ May 17, 2025
@dschult dschult mentioned this issue May 17, 2025
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scikit-learn-bot commented May 18, 2025 •
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CI is no longer failing! ✅

Successful run on May 19, 2025

@lesteve
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lesteve commented May 19, 2025

Looks like it was fixed by scipy/scipy#23005, let's close this one!

@lesteve lesteve closed this as completed May 19, 2025
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