Merge branch 'main' into mp

mne-tools · Jul 30, 2024 · 1b1ef5d · 1b1ef5d
2 parents 88c6dff + 3cbdbab
commit 1b1ef5d
Show file tree

Hide file tree

Showing 31 changed files with 107 additions and 122 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.5.5
     hooks:
       - id: ruff
         name: ruff mne_bids/

diff --git a/CITATION.cff b/CITATION.cff
@@ -183,6 +183,10 @@ authors:
       family-names: Mikkelsen
       affiliation: 'Department of Electrical and Computer Engineering, Aarhus University, Denmark'
       orcid: 'https://orcid.org/0000-0002-7360-8629'
+    - given-names: Amaia
+      family-names: Benitez
+      affiliation: 'Magnetoencephalography Core, National Institutes of Health, Bethesda, Maryland, USA'
+      orcid: 'https://orcid.org/0000-0001-6364-7272'
     - given-names: Alexandre
       family-names: Gramfort
       affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'

diff --git a/doc/authors.rst b/doc/authors.rst
@@ -47,3 +47,4 @@
 .. _Mara Wolter: https://github.com/marakw
 .. _Julius Welzel: https://github.com/JuliusWelzel
 .. _Kaare Mikkelsen: https://github.com/kaare-mikkelsen
+.. _Amaia Benitez: https://github.com/AmaiaBA
diff --git a/doc/conf.py b/doc/conf.py
@@ -7,7 +7,6 @@
 import sys
 from datetime import date
 
-import sphinx_gallery  # noqa: F401
 from sphinx.config import is_serializable
 
 import mne_bids
@@ -96,7 +95,7 @@
 # General information about the project.
 project = "MNE-BIDS"
 today = date.today().isoformat()
-copyright = f"2017, The MNE-BIDS developers. Last updated on {today}"
+copyright = f"2017, The MNE-BIDS developers. Last updated on {today}"  # noqa: A001
 
 author = "The MNE-BIDS developers"
 

diff --git a/doc/whats_new.rst b/doc/whats_new.rst
@@ -18,6 +18,7 @@ Version 0.16 (unreleased)
 The following authors contributed for the first time. Thank you so much! 🤩
 
 * `Kaare Mikkelsen`_
+* `Amaia Benitez`_
 
 The following authors had contributed before. Thank you for sticking around! 🤘
 
@@ -36,7 +37,8 @@ Detailed list of changes
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-- nothing yet
+- :func:`mne_bids.read_raw_bids` no longer warns about unit changes in channels upon reading, as that information is taken from ``channels.tsv`` and judged authorative, by `Stefan Appelhoff`_ (:gh:`1282`)
+- MEG OPM channels are now experimentally included, by `Amaia Benitez`_ (:gh:`1222`)
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
@@ -52,6 +54,7 @@ Detailed list of changes
 ^^^^^^^^^^^^^^
 
 - Keep MNE-BIDS up to date with recent changes on participant birthday date handling in MNE-Python, by `Eric Larson`_ (gh:1278:)
+- Make rules for linting more strict, make quality assessment exceptions less permissive, by `Stefan Appelhoff`_ (gh:1283:)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

diff --git a/examples/bidspath.py b/examples/bidspath.py
@@ -7,7 +7,7 @@
 
 BIDSPath is MNE-BIDS's working horse when it comes to file and folder
 operations. Learn here how to use it.
-"""
+"""  # noqa: D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_eeg_to_bids.py b/examples/convert_eeg_to_bids.py
@@ -19,8 +19,7 @@
 
 .. _BrainVision format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
 .. _CapTrak: https://www.fieldtriptoolbox.org/faq/coordsys/#details-of-the-captrak-coordinate-system
-
-"""  # noqa: E501
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_empty_room.py b/examples/convert_empty_room.py
@@ -7,7 +7,7 @@
 
 This example demonstrates how to store empty room data "manually" in the BIDS
 format and how to retrieve them.
-"""
+"""  # noqa: E501 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_group_studies.py b/examples/convert_group_studies.py
@@ -2,13 +2,14 @@
 =====================================
 05. BIDS conversion for group studies
 =====================================
+
 Here, we show how to do BIDS conversion for group studies.
 We will use the
 `EEG Motor Movement/Imagery Dataset <https://doi.org/10.13026/C28G6P>`_
 available on the PhysioBank database.
 We recommend that you go through the more basic BIDS conversion example before
 checking out this group conversion example: :ref:`ex-convert-mne-sample`
-"""
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_ieeg_to_bids.py b/examples/convert_ieeg_to_bids.py
@@ -38,8 +38,7 @@
 .. _appendix VIII: https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html
 .. _background on FreeSurfer: https://mne.tools/dev/auto_tutorials/source-modeling/plot_background_freesurfer_mne
 .. _MNE-Python coordinate frames: https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html
-
-"""  # noqa: E501
+"""  # noqa: E501 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_mne_sample.py b/examples/convert_mne_sample.py
@@ -13,7 +13,7 @@
 
 .. _BIDS dataset_description.json definition: https://bids-specification.readthedocs.io/en/latest/modality-agnostic-files.html#dataset-description
 .. _ds000248 dataset_description.json: https://github.com/sappelhoff/bids-examples/blob/master/ds000248/dataset_description.json
-"""  # noqa: D400 D205 E501
+"""  # noqa: D400 E501
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_mri_and_trans.py b/examples/convert_mri_and_trans.py
@@ -26,8 +26,7 @@
 
 .. note:: For this example you will need to install ``matplotlib`` and
           ``nilearn`` on top of your usual ``mne-bids`` installation.
-
-"""
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/convert_nirs_to_bids.py b/examples/convert_nirs_to_bids.py
@@ -15,8 +15,7 @@
 4. Cite ``mne-bids``.
 
 .. currentmodule:: mne_bids
-
-"""  # noqa: E501
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/create_bids_folder.py b/examples/create_bids_folder.py
@@ -11,7 +11,7 @@
 
    You may automatically convert Raw objects to BIDS-compatible files with
    ``write_raw_bids``. This example is for manually creating files/folders.
-"""
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/mark_bad_channels.py b/examples/mark_bad_channels.py
@@ -5,7 +5,7 @@
 
 You can use MNE-BIDS interactively inspect your  MEG or (i)EEG data.
 Problematic channels can be marked as "bad", for example if the connected
-sensor produced mostly noise – or no signal at all. Similarly, you can declare
+sensor produced mostly noise - or no signal at all. Similarly, you can declare
 channels as "good", should you discover they were incorrectly marked as bad.
 Bad channel selection can also be performed non-interactively.
 

diff --git a/examples/read_bids_datasets.py b/examples/read_bids_datasets.py
@@ -22,8 +22,7 @@
 
 In this tutorial, we show how ``read_raw_bids`` can be used to load and
 inspect BIDS-formatted data.
-
-"""
+"""  # noqa: D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/rename_brainvision_files.py b/examples/rename_brainvision_files.py
@@ -27,7 +27,7 @@
 for the :ref:`Python Command Line Interface <python_cli>`.
 
 .. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
-"""  # noqa:E501
+"""  # noqa: E501 D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/examples/update_bids_datasets.py b/examples/update_bids_datasets.py
@@ -9,7 +9,7 @@
 
 In this tutorial, we show how ``update_sidecar_json`` can be used to update and
 modify BIDS-formatted data.
-"""
+"""  # noqa: D205 D400
 
 # Authors: The MNE-BIDS developers
 # SPDX-License-Identifier: BSD-3-Clause

diff --git a/mne_bids/config.py b/mne_bids/config.py
@@ -316,7 +316,7 @@
 ALLOWED_SPACES["anat"] = None
 ALLOWED_SPACES["beh"] = None
 
-# See: https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html#encephalography-eeg-ieeg-and-meg  # noqa
+# See: https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html#encephalography-eeg-ieeg-and-meg  # noqa: E501
 ENTITY_VALUE_TYPE = {
     "subject": "label",
     "session": "label",
@@ -340,8 +340,8 @@
     "ElektaNeuromag": "head",
     "ChietiItab": "head",
     "CapTrak": "head",
-    "ACPC": "ras",  # assumes T1 is ACPC-aligned, if not the coordinates are lost  # noqa
-    "fsaverage": "mni_tal",  # XXX: note fsaverage and MNI305 are the same  # noqa
+    "ACPC": "ras",  # assumes T1 is ACPC-aligned, if not the coordinates are lost
+    "fsaverage": "mni_tal",  # XXX: note fsaverage and MNI305 are the same
     "MNI305": "mni_tal",
 }
 

diff --git a/mne_bids/path.py b/mne_bids/path.py
@@ -1869,13 +1869,13 @@ def get_datatypes(root, verbose=None):
     """
     # Take all possible data types from "entity" table
     # (Appendix in BIDS spec)
-    # https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html  # noqa
+    # https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html
     datatype_list = ("anat", "func", "dwi", "fmap", "beh", "meg", "eeg", "ieeg", "nirs")
     datatypes = list()
     for root, dirs, files in os.walk(root):
-        for dir in dirs:
-            if dir in datatype_list and dir not in datatypes:
-                datatypes.append(dir)
+        for _dir in dirs:
+            if _dir in datatype_list and _dir not in datatypes:
+                datatypes.append(_dir)
 
     return datatypes
 

diff --git a/mne_bids/pick.py b/mne_bids/pick.py
@@ -46,6 +46,11 @@ def get_coil_types():
             FIFF.FIFFV_COIL_NM_122,
             FIFF.FIFFV_COIL_MAGNES_MAG,
             FIFF.FIFFV_COIL_BABY_MAG,
+            # support for OPM data
+            FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG,  # QuSpin v1
+            FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG2,  # QuSpin v2
+            FIFF.FIFFV_COIL_FIELDLINE_OPM_MAG_GEN1,  # FieldLine v1
+            FIFF.FIFFV_COIL_KERNEL_OPM_MAG_GEN1,  # Kernel
         ),
         megrefmag=(
             FIFF.FIFFV_COIL_KIT_REF_MAG,

diff --git a/mne_bids/read.py b/mne_bids/read.py
@@ -622,7 +622,7 @@ def _handle_channels_reading(channels_fname, raw):
 
         if updated_ch_type is None:
             # XXX Try again with uppercase spelling – this should be removed
-            # XXX once https://github.com/bids-standard/bids-validator/issues/1018  # noqa:E501
+            # XXX once https://github.com/bids-standard/bids-validator/issues/1018
             # XXX has been resolved.
             # XXX x-ref https://github.com/mne-tools/mne-bids/issues/481
             updated_ch_type = bids_to_mne_ch_types.get(ch_type.upper(), None)
@@ -683,7 +683,9 @@ def _handle_channels_reading(channels_fname, raw):
             f"Cannot set channel type for the following channels, as they "
             f'are missing in the raw data: {", ".join(sorted(ch_diff))}'
         )
-    raw.set_channel_types(channel_type_bids_mne_map_available_channels)
+    raw.set_channel_types(
+        channel_type_bids_mne_map_available_channels, on_unit_change="ignore"
+    )
 
     # Set bad channels based on _channels.tsv sidecar
     if "status" in channels_dict:

diff --git a/mne_bids/report/_report.py b/mne_bids/report/_report.py
@@ -41,12 +41,12 @@ def _pretty_str(listed):
     return "{}, and {}".format(", ".join(listed[:-1]), listed[-1])
 
 
-def _range_str(minval, maxval, meanval, stdval, n_unknown, type):
+def _range_str(minval, maxval, meanval, stdval, n_unknown, typ):
     if minval == "n/a":
         return "ages all unknown"
 
     if n_unknown > 0:
-        unknown_str = f"; {n_unknown} with unknown {type}"
+        unknown_str = f"; {n_unknown} with unknown {typ}"
     else:
         unknown_str = ""
     return (

diff --git a/mne_bids/tests/test_path.py b/mne_bids/tests/test_path.py
@@ -354,7 +354,7 @@ def test_parse_ext():
     [
         "sub-01_ses-02_task-test_run-3_split-1_meg.fif",
         "sub-01_ses-02_task-test_run-3_split-1",
-        "/bids_root/sub-01/ses-02/meg/sub-01_ses-02_task-test_run-3_split-1_meg.fif",  # noqa: E501
+        "/bids_root/sub-01/ses-02/meg/sub-01_ses-02_task-test_run-3_split-1_meg.fif",
         "sub-01/ses-02/meg/sub-01_ses-02_task-test_run-3_split-1_meg.fif",
     ],
 )
@@ -898,7 +898,7 @@ def test_make_filenames():
     assert (
         basename.basename
         == "sub-one_ses-two_task-three_acq-four_run-1_proc-six_rec-seven_ieeg.h5"
-    )  # noqa
+    )
 
     # what happens with scans.tsv file
     with pytest.raises(ValueError, match="scans.tsv file name can only contain"):