Correctly prune channel-specific annotations when creating Epochs (mne-tools#12010)

Author: Mathieu Scheltienne

doc/changes/devel.rst

@@ -55,6 +55,7 @@ Bugs
 - Fix bug with ``subject_info`` when loading data from and exporting to EDF file (:gh:`11952` by `Paul Roujansky`_)
 - Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` by `Paul Roujansky`_)
 - Add missing ``overwrite`` and ``verbose`` parameters to :meth:`Transform.save() <mne.transforms.Transform.save>` (:gh:`12004` by `Marijn van Vliet`_)
+- Correctly prune channel-specific :class:`~mne.Annotations` when creating :class:`~mne.Epochs` without the channel(s) included in the channel specific annotations (:gh:`12010` by `Mathieu Scheltienne`_)
 
 API changes
 ~~~~~~~~~~~

mne/annotations.py

@@ -817,7 +817,7 @@ def set_annotations(self, annotations, on_missing="raise", *, verbose=None):
                     "disk) before 1.0 will yield incorrect results if "
                     "decimation or resampling was performed on the instance, "
                     "we recommend regenerating the Epochs and re-saving them "
-                    "to disk"
+                    "to disk."
                 )
             new_annotations = annotations.copy()
             new_annotations._prune_ch_names(self.info, on_missing)

mne/epochs.py

@@ -691,7 +691,7 @@ def __init__(
             raw_sfreq = self.info["sfreq"]
         self._raw_sfreq = raw_sfreq
         self._check_consistency()
-        self.set_annotations(annotations)
+        self.set_annotations(annotations, on_missing="ignore")
 
     def _check_consistency(self):
         """Check invariants of epochs object."""