[FIX] Replace statsmodels.robust.scale.mad with scipy.stats.median_abs_deviation to avoid enabling the GIL and remove statsmodels from dependencies

Author: pvlov

.github/workflows/testing.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.14t"]
 
     steps:
     - uses: actions/checkout@v7

meegkit/asr.py

@@ -4,8 +4,7 @@
 import numpy as np
 import pyriemann
 from pyriemann.geometry.mean import gmean as mean_covariance
-from scipy import linalg, signal
-from statsmodels.robust.scale import mad
+from scipy import linalg, signal, stats
 
 from .utils import block_covariance, nonlinear_eigenspace
 from .utils.asr import (
@@ -407,7 +406,7 @@ def clean_windows(X, sfreq, max_bad_chans=0.2, zthresholds=[-3.5, 5],
 
     # extra meegkit-specific criterion: drop windows whose across-channel
     # z-scores are nearly flat (very low MAD or std)
-    bad_by_mad = mad(wz, c=1, axis=0) < .1
+    bad_by_mad = stats.median_abs_deviation(wz, axis=0) < .1
     bad_by_std = np.std(wz, axis=0) < .1
     mask3 = np.logical_or(bad_by_mad, bad_by_std)
 

requirements.txt

@@ -5,5 +5,4 @@ scikit-learn
 pandas
 joblib
 tqdm
-statsmodels
 pyriemann>=0.12

tests/test_freethreading.py

@@ -0,0 +1,26 @@
+import subprocess
+import sys
+import sysconfig
+
+import pytest
+
+pytestmark = pytest.mark.skipif(
+    not sysconfig.get_config_var("Py_GIL_DISABLED"),
+    reason="requires a free-threaded CPython build",
+)
+
+
+def test_import_does_not_reenable_gil():
+    # test dependencies (such as pytest extensions) could re-enable the GIL
+    # without making the library non-freethreaded so we need to run this in
+    # its own subprocess.
+    proc = subprocess.run(
+        [
+            sys.executable,
+            "-c",
+            "import sys, meegkit; raise SystemExit(int(sys._is_gil_enabled()))",
+        ],
+        capture_output=True,
+        text=True,
+    )
+    assert proc.returncode == 0, f"stdout:\n{proc.stdout}\nstderr:\n{proc.stderr}"