Merge remote-tracking branch 'upstream/main' into base-GED

Author: Genuster

.github/workflows/autofix.yml

@@ -21,4 +21,4 @@ jobs:
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
-      - uses: autofix-ci/action@551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef
+      - uses: autofix-ci/action@635ffb0c9798bd160680f18fd73371e355b85f27

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.11.13
     hooks:
       - id: ruff
         name: ruff lint mne

doc/changes/devel/13280.bugfix.rst

@@ -0,0 +1 @@
+Fixed bug where :func:`mne.preprocessing.maxwell_filter_prepare_emptyroom` would not reliably identify meg channel types for matching bads across emptyroom and task, by `Harrison Ritz`_.

mne/preprocessing/maxwell.py

@@ -172,7 +172,12 @@ def maxwell_filter_prepare_emptyroom(
     elif bads == "keep":
         bads = raw_er_prepared.info["bads"]
 
-    bads = [ch_name for ch_name in bads if ch_name.startswith("MEG")]
+    # Filter to only include MEG channels
+    meg_ch_names = [
+        raw_er_prepared.ch_names[pick]
+        for pick in pick_types(raw_er_prepared.info, meg=True, exclude=[])
+    ]
+    bads = [ch_name for ch_name in bads if ch_name in meg_ch_names]
     raw_er_prepared.info["bads"] = bads
 
     # handle dev_head_t

mne/preprocessing/tests/test_fine_cal.py

@@ -231,7 +231,7 @@ def test_fine_cal_systems(system, tmp_path):
         err_limit = 12600
         n_ref = 28
         corrs = (0.19, 0.41, 0.49)
-        sfs = [0.5, 0.7, 0.9, 1.55]
+        sfs = [0.5, 0.7, 0.9, 1.65]
         corr_tol = 0.55
     elif system == "fil":
         raw = read_raw_fil(fil_fname, verbose="error")