Merge branch 'main' into empty/tsv

.github/workflows/unit_tests.yml

@@ -59,7 +59,7 @@ jobs:
     - uses: actions/cache@v3
       with:
         path: ${{ env.pythonLocation }}
-        key: build-0-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('test_requirements.txt') }}
+        key: build-1-${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}-${{ hashFiles('test_requirements.txt') }}
 
     - name: Install dependencies
       run: |
@@ -174,7 +174,7 @@ jobs:
     - name: Install MNE (stable)
       if: "matrix.mne-version == 'mne-stable'"
       run: |
-        git clone --depth 1 https://github.com/mne-tools/mne-python.git -b maint/0.24
+        git clone --depth 1 https://github.com/mne-tools/mne-python.git -b maint/1.0
         python -m pip install -e ./mne-python
 
     - name: Install MNE (main)

doc/install.rst

@@ -12,7 +12,7 @@ Dependencies
 
 Required:
 
-* ``mne`` (>=0.24)
+* ``mne`` (>=1.0)
 * ``numpy`` (>=1.16.0)
 * ``scipy`` (>=1.2.0, or >=1.5.0 for certain operations with EEGLAB data)
 * ``setuptools`` (>=46.4.0)

doc/whats_new.rst

@@ -65,6 +65,8 @@ Detailed list of changes
 🛠 Requirements
 ^^^^^^^^^^^^^^^
 
+- MNE-BIDS now requires MNE-Python 1.0 or newer.
+
 - Writing BrainVision files now requires ``pybv`` version ``0.7.3``, by `Stefan Appelhoff`_ (:gh:`1011`)
 
 🪲 Bug fixes
@@ -86,6 +88,8 @@ Detailed list of changes
 
 - Writing and copying CTF files now works on Windows when files already exist (``overwrite=True``), by `Stefan Appelhoff`_ (:gh:`1035`)
 
+- Instead of deleting files and raising cryptic errors, an intentional error message is now sent when calling :func:`~mne_bids.write_raw_bids` with the source file identical to the destination file, unless ``format`` is specified, by `Adam Li`_ and `Stefan Appelhoff`_ (:gh:`889`)
+
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 
 .. include:: authors.rst

examples/convert_eeg_to_bids.py

@@ -17,7 +17,7 @@
 
 .. currentmodule:: mne_bids
 
-.. _BrainVision format: https://www.brainproducts.com/productdetails.php?id=21&tab=5
+.. _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

examples/rename_brainvision_files.py

@@ -26,13 +26,7 @@
 For the command line version of this tool, see the :code:`cp` tool in the docs
 for the :ref:`Python Command Line Interface <python_cli>`.
 
-References
-----------
-.. [1] Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al. EEG-BIDS, an
-       extension to the brain imaging data structure for
-       electroencephalography. Sci Data 6, 103 (2019).
-       https://doi.org/10.1038/s41597-019-0104-8
-.. _BrainVision data format: https://www.brainproducts.com/productdetails.php?id=21&tab=5
+.. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/
 """  # noqa:E501
 
 # Authors: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
@@ -100,3 +94,10 @@
 #
 # .. _`pybv`: https://github.com/bids-standard/pybv
 # .. _`bv-validator`: https://github.com/sappelhoff/brainvision-validator
+#
+# References
+# ----------
+# .. [1] Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al. EEG-BIDS, an
+#        extension to the brain imaging data structure for
+#        electroencephalography. Sci Data 6, 103 (2019).
+#        https://doi.org/10.1038/s41597-019-0104-8

mne_bids/config.py

@@ -155,7 +155,7 @@
     ['.mrk']  # KIT/Yokogawa/Ricoh marker coil
 )
 
-# allowed BIDS path entities
+# allowed BIDSPath entities
 ALLOWED_PATH_ENTITIES = ('subject', 'session', 'task', 'run',
                          'processing', 'recording', 'space',
                          'acquisition', 'split',

mne_bids/path.py

@@ -568,7 +568,7 @@ def fpath(self):
             # else, return the relative path with the basename
             if (self.suffix is None or self.extension is None) and \
                     self.root is not None:
-                # get matching BIDS paths inside the bids root
+                # get matching BIDSPaths inside the bids root
                 matching_paths = \
                     _get_matching_bidspaths_from_filesystem(self)
 
@@ -645,7 +645,7 @@ def update(self, *, check=None, **kwargs):
             the existing ``.check`` attribute instead, which is set upon
             `mne_bids.BIDSPath` instantiation. Defaults to ``None``.
         **kwargs : dict
-            It can contain updates for valid BIDS path entities:
+            It can contain updates for valid BIDSPath entities:
             'subject', 'session', 'task', 'acquisition', 'processing', 'run',
             'recording', 'space', 'suffix', 'split', 'extension',
             or updates for 'root' or 'datatype'.
@@ -981,7 +981,7 @@ def meg_crosstalk_fpath(self):
 
 
 def _get_matching_bidspaths_from_filesystem(bids_path):
-    """Get matching file paths for a BIDS path.
+    """Get matching file paths for a BIDSPath.
 
     Assumes suffix and/or extension is not provided.
     """
@@ -1264,7 +1264,7 @@ def get_bids_path_from_fname(fname, check=True, verbose=None):
     Returns
     -------
     bids_path : BIDSPath
-        The BIDS path object.
+        The BIDSPath object.
     """
     fpath = Path(fname)
     fname = fpath.name

mne_bids/read.py

@@ -10,15 +10,14 @@
 from pathlib import Path
 import json
 import re
-import warnings
 from datetime import datetime, timezone
 
 import numpy as np
 import mne
 from mne import io, read_events, events_from_annotations
 from mne.io.pick import pick_channels_regexp
 from mne.utils import (
-    has_nibabel, logger, warn, get_subjects_dir, check_version
+    has_nibabel, logger, warn, get_subjects_dir
 )
 from mne.coreg import fit_matched_points
 from mne.transforms import apply_trans
@@ -57,13 +56,6 @@ def _read_raw(raw_path, electrode=None, hsp=None, hpi=None,
         raw = reader[ext](raw_path, allow_maxshield, **kwargs)
 
     elif ext in ['.ds', '.vhdr', '.set', '.edf', '.bdf', '.EDF', '.snirf']:
-        if (
-            ext == '.snirf' and
-            not check_version('mne', '1.0')
-        ):  # pragma: no cover
-            raise RuntimeError(
-                'fNIRS support in MNE-BIDS requires MNE-Python version 1.0'
-            )
         raw_path = Path(raw_path)
         raw = reader[ext](raw_path, **kwargs)
 
@@ -286,17 +278,7 @@ def _handle_scans_reading(scans_fname, raw, bids_path):
         # by the MNE documentation, and in fact we cannot load e.g. OpenNeuro
         # ds003392 without this combination.
         raw.set_meas_date(None)
-        with warnings.catch_warnings():
-            # This is to silence a warning emitted by MNE-Python < 0.24. The
-            # warnings filter can be safely removed once we drop support for
-            # MNE-Python 0.23 and older.
-            warnings.filterwarnings(
-                action='ignore',
-                message="Input info has 'meas_date' set to None",
-                category=RuntimeWarning,
-                module='mne'
-            )
-            raw.anonymize(daysback=None, keep_his=True)
+        raw.anonymize(daysback=None, keep_his=True)
         raw.set_meas_date(acq_time)
 
     return raw

mne_bids/report/_report.py

@@ -315,7 +315,7 @@ def _summarize_sidecar_json(root, scans_fpaths):
 
             n_scans += 1
 
-            # convert to BIDS Path
+            # convert to BIDSPath
             if not isinstance(bids_path, BIDSPath):
                 bids_path = get_bids_path_from_fname(bids_path)
             bids_path.root = root
@@ -401,7 +401,7 @@ def _summarize_channels_tsv(root, scans_fpaths):
             if datatype not in ['meg', 'eeg', 'ieeg']:
                 continue
 
-            # convert to BIDS Path
+            # convert to BIDSPath
             if not isinstance(bids_path, BIDSPath):
                 bids_path = get_bids_path_from_fname(bids_path)
             bids_path.root = root

mne_bids/tests/test_path.py

@@ -1,4 +1,4 @@
-"""Test for the MNE BIDS path functions."""
+"""Test for the MNE BIDSPath functions."""
 # Authors: Adam Li <adam2392@gmail.com>
 #
 # License: BSD-3-Clause
@@ -490,7 +490,7 @@ def test_bids_path(return_bids_test_dir):
                                   f'ses-{session_id}', 'meg')
     assert str(bids_path.fpath.parent) == expected_parent_dir
 
-    # test bids path without bids_root, suffix, extension
+    # test BIDSPath without bids_root, suffix, extension
     # basename and fpath should be the same
     expected_basename = f'sub-{subject_id}_ses-{session_id}_task-{task}_run-{run}'  # noqa
     assert (op.basename(bids_path.fpath) ==
@@ -853,8 +853,6 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
                         'sample_audvis_trunc_raw.fif')
     bids_root = tmp_path / "bids"
     bids_root.mkdir()
-    tmp_dir = tmp_path / "tmp"
-    tmp_dir.mkdir()
 
     raw = _read_raw_fif(raw_fname)
     bids_path = BIDSPath(subject='01', session='01',
@@ -870,6 +868,8 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     # The testing data has no "noise" recording, so save the actual data
     # as named as if it were noise. We first need to write the FIFF file
     # before reading it back in.
+    tmp_dir = tmp_path / "tmp"
+    tmp_dir.mkdir()
     er_raw_fname = op.join(tmp_dir, 'ernoise_raw.fif')
     raw.copy().crop(0, 10).save(er_raw_fname, overwrite=True)
     er_raw = _read_raw_fif(er_raw_fname)
@@ -910,13 +910,12 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     raw = read_raw_bids(bids_path=bids_path)
     raw.set_meas_date(None)
     anonymize_info(raw.info)
-    write_raw_bids(raw, bids_path, overwrite=True)
+    write_raw_bids(raw, bids_path, overwrite=True, format="FIF")
     with pytest.raises(ValueError, match='The provided recording does not '
                                          'have a measurement date set'):
         bids_path.find_empty_room()
 
     # test that the `AssociatedEmptyRoom` key in MEG sidecar is respected
-
     bids_root = tmp_path / 'associated-empty-room'
     bids_root.mkdir()
     raw = _read_raw_fif(raw_fname)

mne_bids/tests/test_read.py

@@ -595,7 +595,7 @@ def test_handle_info_reading(tmp_path):
 
     # setting line_freq to None should produce 'n/a' in the JSON sidecar
     raw.info['line_freq'] = None
-    write_raw_bids(raw, bids_path, overwrite=True)
+    write_raw_bids(raw, bids_path, overwrite=True, format="FIF")
     raw = read_raw_bids(bids_path=bids_path)
     assert raw.info['line_freq'] is None
 
@@ -605,7 +605,7 @@ def test_handle_info_reading(tmp_path):
     # 2. if line frequency is not set in raw file, then ValueError
     del raw.info['line_freq']
     with pytest.raises(ValueError, match="PowerLineFrequency .* required"):
-        write_raw_bids(raw, bids_path, overwrite=True)
+        write_raw_bids(raw, bids_path, overwrite=True, format="FIF")
 
     # check whether there are "Extra points" in raw.info['dig'] if
     # DigitizedHeadPoints is set to True and not otherwise
@@ -636,7 +636,7 @@ def test_handle_info_reading(tmp_path):
     # in addition, it should not break the sidecar reading
     # in `read_raw_bids`
     raw.info['line_freq'] = 60
-    write_raw_bids(raw, bids_path, overwrite=True)
+    write_raw_bids(raw, bids_path, overwrite=True, format="FIF")
     deriv_dir = tmp_path / 'derivatives'
     deriv_dir.mkdir()
     sidecar_copy = deriv_dir / op.basename(sidecar_fname)

mne_bids/tests/test_write.py

@@ -539,10 +539,7 @@ def test_fif(_bids_validate, tmp_path):
         assert op.isfile(op.join(bids_dir, sidecar_basename.basename))
 
     bids_path.update(root=bids_root, datatype='eeg')
-    if check_version('mne', '0.24'):
-        with pytest.warns(RuntimeWarning, match='Not setting position'):
-            raw2 = read_raw_bids(bids_path=bids_path)
-    else:
+    with pytest.warns(RuntimeWarning, match='Not setting position'):
         raw2 = read_raw_bids(bids_path=bids_path)
     os.remove(op.join(bids_root, 'test-raw.fif'))
 
@@ -1216,7 +1213,7 @@ def test_eegieeg(dir_name, fname, reader, _bids_validate, tmp_path):
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
 
     raw = reader(raw_fname)
@@ -1724,10 +1721,6 @@ def test_eegieeg(dir_name, fname, reader, _bids_validate, tmp_path):
     os.environ.get('BIDS_VALIDATOR_BRANCH') != 'NIRS',
     reason="requires Rob's NIRS branch of bids-validator"
 )
-@pytest.mark.skipif(
-    not check_version('mne', '1.0'),
-    reason='requires MNE-Python 1.0'
-)
 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',
@@ -2751,7 +2744,7 @@ def test_coordsystem_json_compliance(
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root,
                                          datatype=datatype)
 
@@ -3067,7 +3060,7 @@ def test_convert_eeg_formats(dir_name, format, fname, reader, tmp_path):
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
 
     raw = reader(raw_fname)
@@ -3144,7 +3137,7 @@ def test_format_conversion_overwrite(dir_name, format, fname, reader,
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
 
     raw = reader(raw_fname)
@@ -3200,7 +3193,7 @@ def test_convert_meg_formats(dir_name, format, fname, reader, tmp_path):
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root, datatype='meg')
 
     raw = reader(raw_fname)
@@ -3239,7 +3232,7 @@ def test_convert_raw_errors(dir_name, fname, reader, tmp_path):
     data_path = op.join(testing.data_path(), dir_name)
     raw_fname = op.join(data_path, fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
 
     # test conversion to BrainVision/FIF
@@ -3300,7 +3293,7 @@ def test_write_extension_case_insensitive(_bids_validate, tmp_path, datatype):
     new_raw_fname = op.join(data_path, new_fname)
     os.rename(raw_fname, new_raw_fname)
 
-    # the BIDS path for test datasets to get written to
+    # the BIDSPath for test datasets to get written to
     raw = reader(new_raw_fname)
     bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
     write_raw_bids(raw, bids_path)
@@ -3764,3 +3757,22 @@ def test_anonymize_dataset_daysback(tmpdir):
         rng=np.random.default_rng(),
         show_progress_thresh=20
     )
+
+
+def test_repeat_write_location(tmpdir):
+    """Test error writing BIDS dataset to the same location."""
+    # Get test data
+    raw_fname = testing.data_path() / "EDF" / "test_reduced.edf"
+    raw = _read_raw_edf(raw_fname)
+
+    # Write as BIDS
+    bids_root = tmpdir.mkdir('bids2')
+    bids_path = _bids_path.copy().update(root=bids_root)
+    bids_path = write_raw_bids(raw, bids_path, verbose=False)
+
+    # Read back in
+    raw = read_raw_bids(bids_path, verbose=False)
+
+    # Re-writing with src == dest should error
+    with pytest.raises(FileExistsError, match='Desired output BIDSPath'):
+        write_raw_bids(raw, bids_path, overwrite=True, verbose=False)

mne_bids/utils.py

@@ -17,7 +17,7 @@
 from mne.channels import make_standard_montage
 from mne.io.kit.kit import get_kit_info
 from mne.io.pick import pick_types
-from mne.utils import warn, logger, verbose, check_version
+from mne.utils import warn, logger, verbose
 
 from mne_bids.tsv_handler import _to_tsv
 
@@ -128,10 +128,6 @@ def _handle_datatype(raw, datatype):
         if 'eeg' in raw:
             datatypes.append('eeg')
         if 'fnirs_cw_amplitude' in raw:
-            if not check_version('mne', '1.0'):  # pragma: no cover
-                raise RuntimeError(
-                    'fNIRS support in MNE-BIDS requires MNE-Python version 1.0'
-                )
             datatypes.append('nirs')
         if len(datatypes) == 0:
             raise ValueError('No MEG, EEG or iEEG channels found in data. '