Merge branch 'main' into doc-ref-channel-clarification

Author: tsbinns

doc/changes/dev/13875.newfeature.rst

@@ -0,0 +1 @@
+Fix :func:`mne.preprocessing.nirs.beer_lambert_law` to support explicitly provided ``sd_distances`` during Beer-Lambert conversion. When valid source-detector distances are already present in ``raw.info``, overriding them now emits a warning, and when all inferred distances are invalid and no explicit distances are provided, a ``ValueError`` is raised instead of silently producing zero concentrations, by :newcontrib:`Kalle Makela`.

doc/changes/dev/13884.newfeature.rst

@@ -0,0 +1 @@
+Add ``overrides`` parameter to :func:`mne.io.read_raw_brainvision` for reading non-spec-compliant ``.vhdr`` files where the header contradicts the actual layout (e.g. renamed BIDS siblings, missing ``MarkerFile=``, truncated ``[Channel Infos]``). Accepts a dict with keys ``data_fname``, ``marker_fname``, ``n_channels``, ``sfreq``, ``ch_names``, ``units_fallback``, ``data_orientation``, ``data_format``, and ``binary_format``; see the function docstring for details. Missing or empty ``MarkerFile=`` is now also tolerated natively (per the BV Core Data Format spec). When ``MarkerFile=`` names a path that does not exist (common after BIDS renames), :func:`mne.io.read_raw_brainvision` now falls back to the co-located ``<stem>.vmrk`` next to the ``.vhdr`` and warns, instead of raising :class:`FileNotFoundError`, by `Bruno Aristimunha`_.

doc/changes/dev/13885.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :meth:`mne.preprocessing.ICA.plot_properties` when using ``reject`` in :meth:`mne.preprocessing.ICA.fit`, by `Eric Larson`_.

examples/preprocessing/find_ref_artifacts.py

@@ -24,7 +24,6 @@
 on the reference channels are removed.
 
 This technique is fully described and validated in :footcite:`HannaEtAl2020`
-
 """
 # Authors: Jeff Hanna <jeff.hanna@gmail.com>
 #
@@ -78,6 +77,7 @@
 ica_kwargs = dict(
     method="picard",
     fit_params=dict(tol=1e-4),  # use a high tol here for speed
+    random_state=99,
 )
 all_picks = mne.pick_types(raw_tog.info, meg=True, ref_meg=True)
 ica_tog = ICA(n_components=60, max_iter="auto", allow_ref_meg=True, **ica_kwargs)

examples/preprocessing/muscle_ica.py

@@ -48,9 +48,7 @@
 
 # %%
 # By inspection, let's select out the muscle-artifact components based on
-# :footcite:`DharmapraniEtAl2016` manually.
-#
-# The criteria are:
+# :footcite:`DharmapraniEtAl2016` manually. The criteria are:
 #
 # - Positive slope of log-log power spectrum between 7 and 75 Hz
 #   (here just flat because it's not in log-log)

mne/_fiff/pick.py

@@ -1238,7 +1238,7 @@ def _picks_to_idx(
             extra_repr = ", treated as range({n_chan})"
         else:
             picks = none  # let _picks_str_to_idx handle it
-            extra_repr = f'None, treated as "{none}"'
+            extra_repr = f', treated as "{none}"'
 
     #
     # slice