Replace metadata eval with query (#10705)

* Replace metadata eval with query

* Reset index

* add test

* update what's new

* Adapt test

Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>

doc/changes/latest.inc

@@ -112,6 +112,8 @@ 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

@@ -2969,7 +2969,7 @@ def test_default_values():
 @requires_pandas
 def test_metadata(tmp_path):
     """Test metadata support with pandas."""
-    from pandas import DataFrame
+    from pandas import DataFrame, Series, NA
 
     data = np.random.randn(10, 2, 2000)
     chs = ['a', 'b']
@@ -3154,6 +3154,23 @@ def test_metadata(tmp_path):
         assert len(epochs) == 1
         assert len(epochs.metadata) == 1
 
+    # gh-10705: support boolean columns
+    metadata = DataFrame(
+        {"A": Series([True, True, True, False, False, NA], dtype="boolean")}
+    )
+    rng = np.random.default_rng()
+    epochs = mne.EpochsArray(
+        data=rng.standard_normal(size=(6, 8, 500)),
+        info=mne.create_info(8, 250, "eeg"),
+        event_id={"A": 1},
+        metadata=metadata
+    )
+
+    assert len(epochs["A"]) == 6  # epochs of event type A
+    assert len(epochs["A == True"]) == 3  # epochs for which column A == True
+    assert len(epochs["not A"]) == 2  # epochs for which column A == False
+    assert len(epochs["A.isna()"]) == 1  # epochs for NA in column A
+
 
 def assert_metadata_equal(got, exp):
     """Assert metadata are equal."""

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 '