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MRG: Remove deprecated mark_bad_channels() #1009

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May 18, 2022
Merged

MRG: Remove deprecated mark_bad_channels() #1009

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0baced6
Remove deprecated mark_bad_channels()
hoechenberger May 18, 2022
1db195a
Style
hoechenberger May 18, 2022
23e474d
Update changelog
hoechenberger May 18, 2022
76cf4c4
Fix doc build
hoechenberger May 18, 2022
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6 changes: 4 additions & 2 deletions doc/whats_new.rst
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Expand Up @@ -43,13 +43,15 @@ Detailed list of changes
🚀 Enhancements
^^^^^^^^^^^^^^^

- You can now write raw data and an associated empty-room recording with just a single call to :func:`mne_bids.write_raw_bids`: the ``empty_room`` parameter now also accepts a :class:`mne.io.Raw` data object. The empty-room session name will be derived from the recording date automatically, by `Richard Höchenberger`_ (:gh:`xxx`)
- You can now write raw data and an associated empty-room recording with just a single call to :func:`mne_bids.write_raw_bids`: the ``empty_room`` parameter now also accepts an :class:`mne.io.Raw` data object. The empty-room session name will be derived from the recording date automatically, by `Richard Höchenberger`_ (:gh:`998`)

🧐 API and behavior changes
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- :func:`mne_bids.make_dataset_description` now accepts keyword arguments only, and can now also write the following metadata: ``HEDVersion``, ``EthicsApprovals``, ``GeneratedBy``, and ``SourceDatasets``, by `Stefan Appelhoff`_ (:gh:`406`)

- The deprecated function ```mne_bids.mark_bad_channels`` has been removed in favor of :func:`mne_bids.mark_channels`, by `Richard Höchenberger`_ (:gh:`1009`)

🛠 Requirements
^^^^^^^^^^^^^^^

Expand All @@ -64,7 +66,7 @@ Detailed list of changes

- The MNE-BIDS Inspector didn't work if ``mne-qt-browser`` was installed and used as the default plotting backend, as the Inspector currently only supports the Matplotlib backend, by `Richard Höchenberger`_ (:gh:`1007`)

- :func:`mne.copyfiles.copyfile_brainvision` can now deal with ``.dat`` file extension, by `Dominik Welke`_ (:gh:`1008`)
- :func:`~mne_bids.copyfiles.copyfile_brainvision` can now deal with ``.dat`` file extension, by `Dominik Welke`_ (:gh:`1008`)

:doc:`Find out what was new in previous releases <whats_new_previous_releases>`

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45 changes: 1 addition & 44 deletions mne_bids/write.py
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Expand Up @@ -31,7 +31,7 @@
from mne.channels.channels import _unit2human
from mne.utils import (check_version, has_nibabel, logger, warn, Bunch,
_validate_type, get_subjects_dir, verbose,
deprecated, ProgressBar)
ProgressBar)
import mne.preprocessing

from mne_bids.pick import coil_type
Expand Down Expand Up @@ -2166,49 +2166,6 @@ def write_anat(image, bids_path, landmarks=None, deface=False, overwrite=False,
return bids_path


@deprecated(extra='mark_bad_channels is deprecated in favor of mark_channels '
'and will be removed in v0.10.')
@verbose
def mark_bad_channels(ch_names, descriptions=None, *, bids_path,
overwrite=False, verbose=None):
"""Update which channels are marked as "bad" in an existing BIDS dataset.

This modifies entries in the ``channels.tsv`` file in a BIDS dataset.

Parameters
----------
ch_names : str | list of str
The names of the channel(s) to mark as bad. Pass an empty list in
combination with ``overwrite=True`` to mark all channels as good.
descriptions : None | str | list of str
Descriptions of the reasons that lead to the exclusion of the
channel(s). If a list, it must match the length of ``ch_names``.
If ``None``, no descriptions are added.
bids_path : BIDSPath
The recording to update. The :class:`mne_bids.BIDSPath` instance passed
here **must** have the ``.root`` attribute set. The ``.datatype``
attribute **may** be set. If ``.datatype`` is not set and only one data
type (e.g., only EEG or MEG data) is present in the dataset, it will be
selected automatically.
overwrite : bool
If ``False``, only update the information of the channels passed via
``ch_names``, and leave the rest untouched. If ``True``, update the
information of **all** channels: mark the channels passed via
``ch_names`` as bad, and all remaining channels as good, also
discarding their descriptions.
%(verbose)s
"""
# if overwrite, first mark all channels as good and overwrite
# their descriptions
if overwrite:
mark_channels(bids_path=bids_path, ch_names=[], status='good',
descriptions='n/a', verbose=verbose)

# now mark the channels that we want as bad
mark_channels(bids_path=bids_path, ch_names=ch_names, status='bad',
descriptions=descriptions, verbose=verbose)


@verbose
def mark_channels(bids_path, *, ch_names, status, descriptions=None,
verbose=None):
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2 changes: 0 additions & 2 deletions setup.cfg
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Expand Up @@ -85,8 +85,6 @@ filterwarnings =
ignore:numpy.ufunc size changed.*:RuntimeWarning
ignore:tostring\(\) is deprecated.*:DeprecationWarning
ignore:MEG ref channel RMSP did not.*:RuntimeWarning
# These can be deleted in v0.10.
ignore:Function mark_bad_channels is deprecated.*:DeprecationWarning
# This is for Python 3.10+ and MNE <1.0
ignore:The distutils package is deprecated.*:DeprecationWarning
# Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
Expand Down