[MRG] Bump to pybv 0.7.3 (#1011)

doc/install.rst

@@ -20,7 +20,7 @@ Required:
 Optional:
 
 * ``nibabel`` (>=2.5, for processing MRI data)
-* ``pybv`` (>=0.6, for writing BrainVision data)
+* ``pybv`` (>=0.7.3, for writing BrainVision data)
 * ``pymatreader`` (>=0.0.29 , for operations with EEGLAB data)
 * ``matplotlib`` (>=3.1.0, for using the interactive data inspector)
 * ``pandas`` (>=0.24.0, for generating event statistics)

doc/whats_new.rst

@@ -50,12 +50,12 @@ Detailed list of 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`)
+- 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
 ^^^^^^^^^^^^^^^
 
-- ...
+- Writing BrainVision files now requires ``pybv`` version ``0.7.3``, by `Stefan Appelhoff`_ (:gh:`1011`)
 
 🪲 Bug fixes
 ^^^^^^^^^^^^

examples/anonymize_dataset.py

@@ -16,7 +16,7 @@
 
 MNE-BIDS provides a dedicated function, :func:`mne_bids.anonymize_dataset`,
 to do the heavy lifting for you, automatically.
-"""
+"""  # noqa: D400 D205
 
 # Authors: Richard Höchenberger <[email protected]>
 # License: BSD-3-Clause

examples/convert_mne_sample.py

@@ -10,8 +10,7 @@
 In this example we will use MNE-BIDS to organize the MNE sample data according
 to the BIDS standard.
 In a second step we will read the organized dataset using MNE-BIDS.
-
-"""
+"""  # noqa: D400 D205
 
 # Authors: Mainak Jas <[email protected]>
 #          Alexandre Gramfort <[email protected]>

examples/mark_bad_channels.py

@@ -13,7 +13,7 @@
 segments as "bad".
 
 .. _MNE-Python Annotations tutorial: https://mne.tools/stable/auto_tutorials/raw/30_annotate_raw.html#annotating-raw-objects-interactively
-"""  # noqa:E501
+"""  # noqa: E501 D400 D205
 
 # Authors: Richard Höchenberger <[email protected]>
 #

examples/rename_brainvision_files.py

@@ -93,7 +93,7 @@
 # -------------------
 #
 # For converting data files, or writing new data to the BrainVision format, you
-# can use the `pybv`_ Python package.
+# can use :mod:`mne.export` or have a look at the `pybv`_ Python package.
 #
 # There is node JS tool to check the integrity of your BrainVision files.
 # For that, see the `BrainVision Validator <bv-validator_>`_

mne_bids/commands/tests/test_cli.py

@@ -109,7 +109,6 @@ def test_cp(tmp_path):
 
 def test_mark_bad_chanels_single_file(tmp_path):
     """Test mne_bids mark_channels."""
-
     # Check that help is printed
     check_usage(mne_bids_mark_channels)
 
@@ -162,7 +161,6 @@ def test_mark_bad_chanels_single_file(tmp_path):
 
 def test_mark_bad_chanels_multiple_files(tmp_path):
     """Test mne_bids mark_channels."""
-
     # Check that help is printed
     check_usage(mne_bids_mark_channels)
 
@@ -204,7 +202,6 @@ def test_mark_bad_chanels_multiple_files(tmp_path):
 
 def test_calibration_to_bids(tmp_path):
     """Test mne_bids calibration_to_bids."""
-
     # Check that help is printed
     check_usage(mne_bids_calibration_to_bids)
 
@@ -224,7 +221,6 @@ def test_calibration_to_bids(tmp_path):
 
 def test_crosstalk_to_bids(tmp_path):
     """Test mne_bids crosstalk_to_bids."""
-
     # Check that help is printed
     check_usage(mne_bids_crosstalk_to_bids)
 
@@ -245,7 +241,6 @@ def test_crosstalk_to_bids(tmp_path):
 @requires_pandas
 def test_count_events(tmp_path):
     """Test mne_bids count_events."""
-
     # Check that help is printed
     check_usage(mne_bids_count_events)
 
@@ -290,7 +285,6 @@ def test_count_events(tmp_path):
 @requires_version('mne', '0.22')
 def test_inspect(tmp_path):
     """Test mne_bids inspect."""
-
     # Check that help is printed
     check_usage(mne_bids_inspect)
 

mne_bids/config.py

@@ -5,6 +5,8 @@
 
 BIDS_VERSION = "1.7.0"
 
+PYBV_VERSION = "0.7.3"
+
 DOI = """https://doi.org/10.21105/joss.01896"""
 
 EPHY_ALLOWED_DATATYPES = ['meg', 'eeg', 'ieeg', 'nirs']

mne_bids/tests/conftest.py

@@ -1,3 +1,4 @@
+"""Configure tests."""
 import os
 import platform
 

mne_bids/tests/test_write.py

@@ -48,7 +48,8 @@
 from mne_bids.sidecar_updates import _update_sidecar, update_sidecar_json
 from mne_bids.path import _find_matching_sidecar, _parse_ext
 from mne_bids.pick import coil_type
-from mne_bids.config import REFERENCES, BIDS_COORD_FRAME_DESCRIPTIONS
+from mne_bids.config import (REFERENCES, BIDS_COORD_FRAME_DESCRIPTIONS,
+                             PYBV_VERSION)
 
 base_path = op.join(op.dirname(mne.__file__), 'io')
 subject_id = '01'
@@ -456,7 +457,7 @@ def test_line_freq(line_freq, _bids_validate, tmp_path):
         assert eeg_json['PowerLineFrequency'] == 'n/a'
 
 
-@requires_version('pybv', '0.6')
+@requires_version('pybv', PYBV_VERSION)
 @pytest.mark.filterwarnings(warning_str['channel_unit_changed'])
 @pytest.mark.filterwarnings(warning_str['maxshield'])
 def test_fif(_bids_validate, tmp_path):
@@ -515,12 +516,6 @@ def test_fif(_bids_validate, tmp_path):
     events = mne.find_events(raw2)
     event_id = {'auditory/left': 1, 'auditory/right': 2, 'visual/left': 3,
                 'visual/right': 4, 'smiley': 5, 'button': 32}
-    # XXX: Need to remove "Status" channel until pybv supports
-    # channels that are non-Volt
-    idxs = mne.pick_types(raw.info, meg=False, stim=True)
-    stim_ch_names = np.array(raw.ch_names)[idxs]
-    raw2.drop_channels(stim_ch_names)
-    raw.drop_channels(stim_ch_names)
 
     epochs = mne.Epochs(raw2, events, event_id=event_id, tmin=-0.2, tmax=0.5,
                         preload=True)
@@ -1136,7 +1131,7 @@ def test_vhdr(_bids_validate, tmp_path):
     assert op.exists(events_tsv_fname)
 
     # test anonymize and convert
-    if check_version('pybv', '0.6'):
+    if check_version('pybv', PYBV_VERSION):
         raw = _read_raw_brainvision(raw_fname)
         output_path = _test_anonymize(tmp_path / 'tmp', raw, bids_path)
         _bids_validate(output_path)
@@ -1404,7 +1399,7 @@ def test_eegieeg(dir_name, fname, reader, _bids_validate, tmp_path):
     assert len(list(data.values())[0]) == 2
 
     # check that scans list is properly converted to brainvision
-    if check_version('pybv', '0.6') or dir_name == 'EDF':
+    if check_version('pybv', PYBV_VERSION) or dir_name == 'EDF':
         if raw.info['meas_date'] is not None:
             daysback_min, daysback_max = _get_anonymization_daysback(raw)
             daysback = (daysback_min + daysback_max) // 2
@@ -1597,7 +1592,7 @@ def test_eegieeg(dir_name, fname, reader, _bids_validate, tmp_path):
         write_raw_bids(**kwargs)
 
     # test anonymize and convert
-    if check_version('pybv', '0.6') or dir_name == 'EDF':
+    if check_version('pybv', PYBV_VERSION) or dir_name == 'EDF':
         raw = reader(raw_fname)
         bids_path.update(root=bids_root, datatype='eeg')
         kwargs = dict(raw=raw, bids_path=bids_path, overwrite=True)
@@ -1635,7 +1630,6 @@ def test_eegieeg(dir_name, fname, reader, _bids_validate, tmp_path):
 )
 def test_snirf(_bids_validate, tmp_path):
     """Test write_raw_bids conversion for SNIRF data."""
-
     raw_fname = op.join(testing.data_path(), 'SNIRF', 'MNE-NIRS', '20220217',
                         '20220217_nirx_15_3_recording.snirf')
     bids_path = _bids_path.copy().update(root=tmp_path, datatype='nirs')
@@ -1790,7 +1784,7 @@ def test_set(_bids_validate, tmp_path):
     _bids_validate(bids_root)
 
     # test anonymize and convert
-    if check_version('pybv', '0.6'):
+    if check_version('pybv', PYBV_VERSION):
         with pytest.warns(RuntimeWarning,
                           match='Encountered data in "double" format'):
             output_path = _test_anonymize(tmp_path / 'tmp', raw, bids_path)
@@ -2078,6 +2072,7 @@ def test_write_anat(_bids_validate, tmp_path):
 
 
 def test_write_raw_pathlike(tmp_path):
+    """Ensure writing pathlib.Path works."""
     data_path = Path(testing.data_path())
     raw_fname = op.join(data_path, 'MEG', 'sample',
                         'sample_audvis_trunc_raw.fif')
@@ -2100,6 +2095,7 @@ def test_write_raw_pathlike(tmp_path):
 
 
 def test_write_raw_no_dig(tmp_path):
+    """Test writing without dig."""
     data_path = testing.data_path()
     raw_fname = op.join(data_path, 'MEG', 'sample',
                         'sample_audvis_trunc_raw.fif')
@@ -2955,7 +2951,7 @@ def test_sidecar_encoding(_bids_validate, tmp_path):
 
 
 @requires_version('mne', '0.24')
-@requires_version('pybv', '0.6')
+@requires_version('pybv', PYBV_VERSION)
 @pytest.mark.parametrize(
     'dir_name, format, fname, reader', test_converteeg_data)
 @pytest.mark.filterwarnings(
@@ -3031,7 +3027,7 @@ def test_convert_eeg_formats(dir_name, format, fname, reader, tmp_path):
 
 
 @requires_version('mne', '0.24')
-@requires_version('pybv', '0.6')
+@requires_version('pybv', PYBV_VERSION)
 @pytest.mark.parametrize(
     'dir_name, format, fname, reader', test_converteeg_data)
 @pytest.mark.filterwarnings(
@@ -3325,7 +3321,7 @@ def test_write_associated_emptyroom(
 
 
 def test_preload(_bids_validate, tmp_path):
-    """Test writing custom preloaded raw objects"""
+    """Test writing custom preloaded raw objects."""
     bids_root = tmp_path / 'bids'
     bids_path = _bids_path.copy().update(root=bids_root)
     sfreq, n_points = 1024., int(1e6)

mne_bids/write.py

@@ -55,7 +55,7 @@
                              IGNORED_CHANNELS, ALLOWED_DATATYPE_EXTENSIONS,
                              BIDS_VERSION, REFERENCES, _map_options, reader,
                              ALLOWED_INPUT_EXTENSIONS, CONVERT_FORMATS,
-                             ANONYMIZED_JSON_KEY_WHITELIST,
+                             ANONYMIZED_JSON_KEY_WHITELIST, PYBV_VERSION,
                              BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS)
 
 
@@ -975,9 +975,9 @@ def _write_raw_brainvision(raw, bids_fname, events, overwrite):
     overwrite : bool
         Whether or not to overwrite existing files.
     """
-    if not check_version('pybv', '0.6'):  # pragma: no cover
-        raise ImportError('pybv >=0.6 is required for converting '
-                          'file to BrainVision format')
+    if not check_version('pybv', PYBV_VERSION):  # pragma: no cover
+        raise ImportError(f'pybv >= {PYBV_VERSION} is required for converting'
+                          ' file to BrainVision format')
     from pybv import write_brainvision
     # Subtract raw.first_samp because brainvision marks events starting from
     # the first available data point and ignores the raw.first_samp

setup.cfg

@@ -45,7 +45,7 @@ include_package_data = True
 [options.extras_require]
 full =
   nibabel >= 2.5
-  pybv >= 0.6
+  pybv >= 0.7.3
   matplotlib >= 3.1.0
   pandas >= 0.24.0
   EDFlib-Python >= 1.0.6
@@ -110,3 +110,6 @@ exclude_lines =
 
     # Don't complain if non-runnable code isn't run:
     if __name__ == .__main__.:
+
+[isort]
+skip_glob = */*

test_requirements.txt

@@ -4,7 +4,7 @@ mne>=0.24
 matplotlib>=3.1
 pandas>=0.24.0
 nibabel>=2.5
-pybv>=0.6
+pybv>=0.7.3
 openneuro-py>=2022.1
 EDFlib-Python>=1.0.6
 pymatreader>=0.0.29