Replace metadata eval with query

doc/changes/latest.inc

@@ -110,6 +110,8 @@ Bugs
 
 - Retain epochs metadata when using :func:`mne.channels.combine_channels` (:gh:`10504` by `Clemens Brunner`_)
 
+- Fix epochs indexing with metadata containing boolean type and missing values (:gh:`10705` by `Clemens Brunner`_ and `Alex Gramfort`_)
+
 - Fix reading of fiducial locations in :func:`mne.io.read_raw_eeglab` (:gh:`10521` by `Alex Gramfort`_)
 
 - Prevent creation of montage with invalid ``[x, y, z]`` coordinates with :func:`mne.channels.make_dig_montage` (:gh:`10547` by `Mathieu Scheltienne`_)

mne/tests/test_epochs.py

@@ -3155,6 +3155,30 @@ def test_metadata(tmp_path):
         assert len(epochs.metadata) == 1
 
 
+@requires_pandas
+def test_metadata_query_bool():
+    """Test metadata query with boolean indexing and NaNs gh #10705."""
+    import mne
+    import numpy as np
+    import pandas as pd
+    from random import choices
+
+    n_epochs, n_chans, n_samples = 40, 3, 101
+    correct = pd.Series(choices([True, False, None], k=n_epochs),
+                        dtype="boolean")
+    metadata = pd.DataFrame({"correct": correct})
+    rng = np.random.default_rng()
+    epochs = mne.EpochsArray(
+        data=rng.standard_normal(size=(n_epochs, n_chans, n_samples)),
+        info=mne.create_info(n_chans, 500, "eeg"),
+        metadata=metadata
+    )
+
+    assert len(epochs) > metadata.sum()["correct"]
+    epochs = epochs["correct"]
+    assert len(epochs) == metadata.sum()["correct"]
+
+
 def assert_metadata_equal(got, exp):
     """Assert metadata are equal."""
     if exp is None:

mne/utils/mixin.py

@@ -254,12 +254,15 @@ def _keys_to_idx(self, keys):
                 self._check_metadata(metadata=md)
                 try:
                     # Try metadata
-                    mask = self.metadata.eval(keys[0], engine='python').values
+                    vals = self.metadata.reset_index().query(
+                        keys[0],
+                        engine='python'
+                    ).index.values
                 except Exception as exp:
                     msg += (' The epochs.metadata Pandas query did not '
                             'yield any results: %s' % (exp.args[0],))
                 else:
-                    return np.where(mask)[0]
+                    return vals
             else:
                 # If not, warn this might be a problem
                 msg += (' The epochs.metadata Pandas query could not '