Fix one-tailed Wilcoxon p-values in compute_pvals_wilcoxon

[azrabano23]

Fixes #1176

What was wrong

compute_pvals_wilcoxon built the one-tailed p-value from SciPy's two-sided signed-rank p-value: halve it, then put it on the "pipe1 > pipe2" side if the mean paired difference is positive, else on the other side (1 - p/2). The signed-rank test does not test the mean; its direction comes from the rank sums W+/W-, which disagree with the sign of the mean whenever a few large differences point one way and many small ones the other.

Example, 7 subjects, pipeline 1 wins on 6 by 0.02 and loses on one by 0.20 (SciPy 1.15.3):

	current develop	scipy.stats.wilcoxon(x, y, alternative=...)
pvals[pipeline_1, pipeline_2]	0.8203	"greater": 0.1797
pvals[pipeline_2, pipeline_1]	0.1797	"less": 0.9453

So the matrix said pipeline 2 was better (p = 0.18) when the signed-rank test says the opposite (p = 0.18 for pipeline 1). The values feed compute_dataset_statistics (every dataset with >= perm_cutoff subjects), find_significant_differences and the summary / meta-analysis plots. When mean and rank sums agree, the halved value still differs from the exact one-sided p by the point mass at the observed statistic (0.82 vs 0.95 above).

The fix

Ask SciPy for the one-sided test directly:

p = stats.wilcoxon(df.loc[:, pipe1], df.loc[:, pipe2], alternative="greater")[1]

alternative exists since SciPy 1.5; moabb requires scipy>=1.9.3. The all-zero-differences guard (0.5) and the (0, 1) clipping from #1134 are unchanged. In the common case where mean and rank sums agree and the exact method is used, results change only by the point-mass term; with the normal approximation used for larger n, the two agree whenever the rank sums and the mean point the same way.

Verification (CPU only, Python 3.12, macOS arm64)

python -m pytest moabb/tests/test_analysis.py -k "TestStats or Corrected"   # 36 passed
# the new test test_wilcoxon_tail_follows_rank_sums_not_mean fails on develop:
#   assert np.isclose(pvals[0, 1], expected_greater)  ->  0.8203 vs 0.1797
ruff check / ruff format --check on the two changed files                  # clean

Also added a "Bugs" entry to docs/source/whats_new.rst.

🤖 Generated with Claude Code

[bruAristimunha]

@qbarthelemy, i was wondering, can you please review once you have time please 🙏🏽

[Copilot]

🟢 Approval recommended

The change directly aligns implementation with SciPy’s one-sided Wilcoxon API and is backed by a focused regression test reproducing the reported failure mode.

Pull request overview

This PR fixes the computation of one-tailed Wilcoxon signed-rank p-values in compute_pvals_wilcoxon by using SciPy’s native one-sided test (alternative="greater") instead of deriving a one-sided value from the two-sided p-value and the mean paired difference (which can disagree with the signed-rank statistic’s direction).

Changes:

• Update compute_pvals_wilcoxon to call scipy.stats.wilcoxon(..., alternative="greater") directly for the “pipe1 > pipe2” direction.
• Add a regression test covering the case where mean difference and signed-rank direction disagree (issue #1176 reproducer).
• Add a changelog entry documenting the bug fix.

File summaries

File	Description
moabb/tests/test_analysis.py	Adds a regression test validating that one-tailed p-values follow the signed-rank statistic direction (via SciPy alternatives), not the mean difference.
moabb/analysis/meta_analysis.py	Fixes one-tailed Wilcoxon p-value computation by delegating tail selection to SciPy’s alternative="greater" logic.
docs/source/whats_new.rst	Documents the Wilcoxon one-tailed p-value fix in the Bugs section.

Review details

• Files reviewed: 3/3 changed files
• Comments generated: 0
• Review effort level: Lite

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