Merge branch 'main' into add_emg_support

Author: drammock

.github/workflows/unit_tests.yml

@@ -51,7 +51,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
+        python-version: ["3.11", "3.13"]  # Oldest and newest supported versions
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
@@ -129,22 +129,22 @@ jobs:
     #
     # 8 checks:
     # for each machine type (ubuntu, macos, windows):
-    # 3.10 / mne-stable / full / validator-stable
+    # 3.11 / mne-stable / full / validator-stable
     # 3.13 / mne-stable / full / validator-stable
     #
     # 4 additional checks with alternative MNE-Python and BIDS validator versions:
     # ubuntu / 3.13 / mne-main / full / validator-main -->  to test cutting edge of everything
-    # ubuntu / 3.10 / mne-prev / full / validator-stable --> to test last supported of everything
+    # ubuntu / 3.11 / mne-prev / full / validator-stable --> to test last supported of everything
     # ubuntu / 3.13 / mne-stable / minimal / validator-stable --> to test a minimal installation
-    # ubuntu / 3.12 / mne-stable / full / validator-main-schema --> to test next-gen BIDS validator
+    # ubuntu / 3.13 / mne-stable / full / validator-main-schema --> to test next-gen BIDS validator
     # macos-15-intel / 3.13 / mne-stable / full / validator-stable --> to test macos x86_64
     timeout-minutes: 60
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.13"]  # Oldest and newest supported versions
+        python-version: ["3.11", "3.13"]  # Oldest and newest supported versions
         mne-version: [mne-stable]
         mne-bids-install: [full]
         bids-validator-version: [validator-stable]
@@ -159,7 +159,7 @@ jobs:
             bids-validator-version: validator-main
           # Test previous MNE stable version
           - os: ubuntu-latest
-            python-version: "3.10"
+            python-version: "3.11"
             mne-version: mne-prev-stable
             mne-bids-install: full
             bids-validator-version: validator-stable
@@ -171,7 +171,7 @@ jobs:
             bids-validator-version: validator-stable
           # Test next gen BIDS schema validator
           - os: ubuntu-latest
-            python-version: "3.12"
+            python-version: "3.13"
             mne-version: mne-stable
             mne-bids-install: full
             bids-validator-version: validator-main-schema

doc/install.rst

@@ -25,13 +25,14 @@ Optional:
 * ``matplotlib`` (>=3.6, for using the interactive data inspector)
 * ``pandas`` (>=1.3.2, for generating event statistics)
 * ``edfio`` (>=0.4.10, for writing EDF data)
+* ``curryreader`` (>=0.1.2, for reading Curry data)
 * ``defusedxml`` (for writing reading EGI MFF data and BrainVision montages)
 * ``filelock`` (for atomic file writing, and parallel processing support)
 
 We recommend installing ``mne-bids`` into an isolated Python environment,
 for example created via ``conda``
 (may be obtained through `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
-We require that you **use Python 3.10 or higher**.
+We require that you **use Python 3.11 or higher**.
 You may choose to install ``mne-bids`` into your isolated Python environment
 `via pip <#installation-via-pip>`_ or
 `via conda <#installation-via-conda>`_.

doc/whats_new.rst

@@ -27,6 +27,7 @@ The following authors contributed for the first time. Thank you so much! 🤩
 The following authors had contributed before. Thank you for sticking around! 🤘
 
 * `Stefan Appelhoff`_
+* `Daniel McCloy`_
 
 
 Detailed list of changes
@@ -44,11 +45,13 @@ Detailed list of changes
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
--  `tracksys` accepted as argument in :class:`mne_bids.BIDSPath()` by `Julius Welzel`_ (:gh:`1430`)
+-  ``tracksys`` accepted as argument in :class:`mne_bids.BIDSPath()` by `Julius Welzel`_ (:gh:`1430`)
 - :func:`mne_bids.read_raw_bids()` has a new parameter ``on_ch_mismatch`` that controls behaviour when there is a mismatch between channel names in ``channels.tsv`` and the raw data; accepted values are ``'raise'`` (default), ``'reorder'``, and ``'rename'``, by `Kalle Mäkelä`_.
+- Column names read from ``.tsv`` are now converted from :class:`numpy.str_` class to built-in :class:`str` class, by `Daniel McCloy`_ (:gh:`1475`).
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^
+- MNE-BIDS now requires Python 3.11 or higher.
 - Including ``filelock`` as a dependency to handle atomic file writing and parallel processing support by `Bruno Aristimunha`_ (:gh:`1451`)
 
 - None yet
@@ -60,12 +63,15 @@ Detailed list of changes
 - Updated MEG/iEEG writers to satisfy the stricter checks in the latest BIDS validator releases: BTi/4D run folders now retain their ``.pdf`` suffix (falling back to the legacy naming when an older validator is detected), KIT marker files encode the run via the ``acq`` entity instead of ``run``, datasets lacking iEEG montages receive placeholder ``electrodes.tsv``/``coordsystem.json`` files, and the ``AssociatedEmptyRoom`` entry stores dataset-relative paths  by `Bruno Aristimunha`_ (:gh:`1449`)
 - Made the lock helpers skip reference counting when the optional ``filelock`` dependency is missing, preventing spurious ``AttributeError`` crashes during reads, by `Bruno Aristimunha`_ (:gh:`1469`)
 - Fixed a bug in :func:`mne_bids.read_raw_bids` that caused it to fail when reading BIDS datasets where the acquisition time was specified in local time rather than UTC only in Windows, by `Bruno Aristimunha`_ (:gh:`1452`)
+- Fixed bug in :func:`~mne_bids.write_raw_bids` where incorrect unit was sometimes written into ``channels.tsv`` file when converting data to BrainVision, EDF, or EEGLAB formats, by `Daniel McCloy`_ (:gh:`1475`)
+- Converting data to EDF format while also anonymizing it will now yield valid EDF files (with ``startdate`` set to 1985-01-01 00:00:00); the BIDS-compliant anonymized date will still be stored in ``scans.tsv`` file and restored to the in-memory Raw object when read using :func:`~mne_bids.read_raw_bids`, by `Daniel McCloy`_ (:gh:`1479`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^
 
 - Made :func:`mne_bids.copyfiles.copyfile_brainvision` output more meaningful error messages when encountering problematic files, by `Stefan Appelhoff`_ (:gh:`1444`)
 - Raised the minimum ``edfio`` requirement to ``0.4.10``,  eeglabio to ``0.1.0``  by `Bruno Aristimunha`_ (:gh:`1449`)
 - Relaxed EDF padding warnings in the test suite to accommodate upstream changes by `Bruno Aristimunha`_ (:gh:`1449`)
+- Adapt to upstream switch to new reader package for Neuroscan-Curry-format files, by `Daniel McCloy`_ (:gh:`1475`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`

examples/convert_empty_room.py

@@ -29,7 +29,7 @@
 # Let us first import mne_bids.
 
 import shutil
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 
 import mne
 from mne.datasets import sample
@@ -98,7 +98,7 @@
 for date in dates:
     er_bids_path.update(session=date)
     er_meas_date = datetime.strptime(date, "%Y%m%d")
-    er_raw.set_meas_date(er_meas_date.replace(tzinfo=timezone.utc))
+    er_raw.set_meas_date(er_meas_date.replace(tzinfo=UTC))
     write_raw_bids(er_raw, er_bids_path, overwrite=True)
 
 # %%

mne_bids/config.py

@@ -10,6 +10,7 @@
 
 PYBV_VERSION = "0.7.3"
 EEGLABIO_VERSION = "0.0.2"
+CURRYREADER_VERSION = "0.1.2"
 
 DOI = """https://doi.org/10.21105/joss.01896"""
 

mne_bids/path.py

@@ -1766,7 +1766,8 @@ def get_entities_from_fname(fname, on_error="raise", verbose=None):
 'space': None, \
 'recording': None, \
 'split': None, \
-'description': None}
+'description': None, \
+'tracking_system': None}
     """
     if on_error not in ("warn", "raise", "ignore"):
         raise ValueError(

mne_bids/read.py

@@ -6,7 +6,7 @@
 import json
 import os
 import re
-from datetime import datetime, timedelta, timezone
+from datetime import UTC, datetime, timedelta
 from difflib import get_close_matches
 from pathlib import Path
 
@@ -417,14 +417,14 @@ def _handle_scans_reading(scans_fname, raw, bids_path):
 
         if acq_time_is_utc:
             # Enforce setting timezone to UTC without additonal conversion
-            acq_time = acq_time.replace(tzinfo=timezone.utc)
+            acq_time = acq_time.replace(tzinfo=UTC)
         else:
             # Convert time offset to UTC
             if acq_time.tzinfo is None:
                 # Windows needs an explicit local tz for naive, pre-epoch times.
-                local_tz = datetime.now().astimezone().tzinfo or timezone.utc
+                local_tz = datetime.now().astimezone().tzinfo or UTC
                 acq_time = acq_time.replace(tzinfo=local_tz)
-            acq_time = acq_time.astimezone(timezone.utc)
+            acq_time = acq_time.astimezone(UTC)
 
         logger.debug(f"Loaded {scans_fname} scans file to set acq_time as {acq_time}.")
         # First set measurement date to None and then call call anonymize() to
@@ -541,14 +541,16 @@ def _handle_info_reading(sidecar_fname, raw):
     return raw
 
 
-def events_file_to_annotation_kwargs(events_fname: str | Path) -> dict:
+@verbose
+def events_file_to_annotation_kwargs(events_fname: str | Path, *, verbose=None) -> dict:
     r"""
     Read the ``events.tsv`` file and extract onset, duration, and description.
 
     Parameters
     ----------
     events_fname : str
         The file path to the ``events.tsv`` file.
+    %(verbose)s
 
     Returns
     -------
@@ -592,8 +594,8 @@ def events_file_to_annotation_kwargs(events_fname: str | Path) -> dict:
     ...     'duration': [0.1, 0.1, 0.1],
     ...     'trial_type': ['event1', 'event2', 'event1'],
     ...     'value': [1, 2, 1],
-    ...     'sample': [10, 20, 30]
-            'foo': ['a', 'b', 'c'],
+    ...     'sample': [10, 20, 30],
+    ...     'foo': ['a', 'b', 'c'],
     ... }
     >>> df = pd.DataFrame(data)
     >>>
@@ -603,15 +605,11 @@ def events_file_to_annotation_kwargs(events_fname: str | Path) -> dict:
     >>> df.to_csv(events_file, sep='\t', index=False)
     >>>
     >>> # Read the events file using the function
-    >>> events_dict = events_file_to_annotation_kwargs(events_file)
+    >>> events_dict = events_file_to_annotation_kwargs(events_file, verbose=False)
     >>> events_dict
-    {'onset': array([0.1, 0.2, 0.3]),
-    'duration': array([0.1, 0.1, 0.1]),
-    'description': array(['event1', 'event2', 'event1'], dtype='<U6'),
-    'event_id': {'event1': 1, 'event2': 2},
-    'extras': [{'foo': 'a'}, {'foo': 'b'}, {'foo': 'c'}]}
+    {'onset': array([0.1, 0.2, 0.3]), 'duration': array([0.1, 0.1, 0.1]), 'description': array(['event1', 'event2', 'event1'], dtype='<U6'), 'event_id': {'event1': 1, 'event2': 2}, 'extras': [{'foo': 'a'}, {'foo': 'b'}, {'foo': 'c'}]}
 
-    """
+    """  # noqa E501
     logger.info(f"Reading events from {events_fname}.")
     events_dict = _from_tsv(events_fname)
 
@@ -677,9 +675,11 @@ def events_file_to_annotation_kwargs(events_fname: str | Path) -> dict:
                     culled_vals = culled_vals.astype(int)
                 except ValueError:  # numeric, but has some non-integer values
                     pass
+            # purge any np.str_, np.int_, or np.float_ types
+            culled_vals = np.asarray(culled_vals).tolist()
             event_id = dict(zip(culled[trial_type_col_name], culled_vals))
         else:
-            event_id = dict(zip(trial_types, np.arange(len(trial_types))))
+            event_id = dict(zip(trial_types, list(range(len(trial_types)))))
         descrs = np.asarray(trial_types, dtype=str)
 
     # convert onsets & durations to floats ("n/a" onsets were already dropped)

mne_bids/tests/test_path.py

@@ -8,7 +8,7 @@
 import shutil
 import shutil as sh
 import timeit
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from pathlib import Path
 
 import mne
@@ -1435,7 +1435,7 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     for date in dates:
         er_bids_path.update(session=date)
         er_meas_date = datetime.strptime(date, "%Y%m%d")
-        er_meas_date = er_meas_date.replace(tzinfo=timezone.utc)
+        er_meas_date = er_meas_date.replace(tzinfo=UTC)
         er_raw.set_meas_date(er_meas_date)
         write_raw_bids(er_raw, er_bids_path, verbose=False)
 
@@ -1460,8 +1460,8 @@ def test_find_empty_room(return_bids_test_dir, tmp_path):
     bids_root = tmp_path / "associated-empty-room"
     bids_root.mkdir()
     raw = _read_raw_fif(raw_fname)
-    meas_date = datetime(year=2020, month=1, day=10, tzinfo=timezone.utc)
-    er_date = datetime(year=2010, month=1, day=1, tzinfo=timezone.utc)
+    meas_date = datetime(year=2020, month=1, day=10, tzinfo=UTC)
+    er_date = datetime(year=2010, month=1, day=1, tzinfo=UTC)
     raw.set_meas_date(meas_date)
 
     er_raw_matching_date = er_raw.copy().set_meas_date(meas_date)
@@ -1543,7 +1543,7 @@ def test_find_emptyroom_ties(tmp_path):
     )
     er_dir = er_dir_path.mkdir().directory
 
-    meas_date = datetime.strptime(session, "%Y%m%d").replace(tzinfo=timezone.utc)
+    meas_date = datetime.strptime(session, "%Y%m%d").replace(tzinfo=UTC)
 
     raw = _read_raw_fif(raw_fname)
 

mne_bids/tests/test_read.py

@@ -13,7 +13,7 @@
 import shutil as sh
 from collections import OrderedDict
 from contextlib import nullcontext
-from datetime import date, datetime, timezone
+from datetime import UTC, date, datetime
 from pathlib import Path
 
 import mne
@@ -108,7 +108,7 @@ def _make_parallel_raw(subject, *, seed=None):
     info = mne.create_info(["MEG0113"], 100, ch_types="mag")
     data = rng.standard_normal((1, 100)) * 1e-12
     raw = mne.io.RawArray(data, info)
-    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=timezone.utc))
+    raw.set_meas_date(datetime(2020, 1, 1, tzinfo=UTC))
     raw.info["line_freq"] = 60
     raw.info["subject_info"] = {
         "his_id": subject,
@@ -635,7 +635,7 @@ def test_handle_events_reading(tmp_path, with_extras):
             match=re.escape(
                 "The version of MNE-Python you are using (<1.10) "
                 "does not support the extras argument in mne.Annotations. "
-                "The extra column(s) [np.str_('foo')] will be ignored."
+                "The extra column(s) ['foo'] will be ignored."
             ),
         )
         if with_extras and not check_version("mne", "1.10")
@@ -802,7 +802,7 @@ def test_handle_scans_reading(tmp_path):
     scans_tsv = _from_tsv(scans_path)
     acq_time_str = scans_tsv["acq_time"][0]
     acq_time = datetime.strptime(acq_time_str, "%Y-%m-%dT%H:%M:%S.%fZ")
-    acq_time = acq_time.replace(tzinfo=timezone.utc)
+    acq_time = acq_time.replace(tzinfo=UTC)
     new_acq_time = acq_time_str.split(".")[0] + "Z"
     assert acq_time == raw_01.info["meas_date"]
     scans_tsv["acq_time"][0] = new_acq_time
@@ -813,7 +813,7 @@ def test_handle_scans_reading(tmp_path):
     raw_02 = read_raw_bids(bids_path)
     new_acq_time = new_acq_time.replace("Z", ".0Z")
     new_acq_time = datetime.strptime(new_acq_time, "%Y-%m-%dT%H:%M:%S.%fZ")
-    new_acq_time = new_acq_time.replace(tzinfo=timezone.utc)
+    new_acq_time = new_acq_time.replace(tzinfo=UTC)
     assert raw_02.info["meas_date"] == new_acq_time
     assert new_acq_time != raw_01.info["meas_date"]
 
@@ -833,7 +833,7 @@ def test_handle_scans_reading(tmp_path):
         # from the original date and the same as the newly altered date
         raw_03 = read_raw_bids(bids_path)
         new_acq_time = datetime.strptime(new_acq_time_str, date_format)
-        assert raw_03.info["meas_date"] == new_acq_time.astimezone(timezone.utc)
+        assert raw_03.info["meas_date"] == new_acq_time.astimezone(UTC)
 
     # Regression for naive, pre-epoch acquisition times (Windows bug GH-1399)
     pre_epoch_str = "1950-06-15T13:45:30"
@@ -842,10 +842,8 @@ def test_handle_scans_reading(tmp_path):
 
     raw_pre_epoch = read_raw_bids(bids_path)
     pre_epoch_naive = datetime.strptime(pre_epoch_str, "%Y-%m-%dT%H:%M:%S")
-    local_tz = datetime.now().astimezone().tzinfo or timezone.utc
-    expected_pre_epoch = pre_epoch_naive.replace(tzinfo=local_tz).astimezone(
-        timezone.utc
-    )
+    local_tz = datetime.now().astimezone().tzinfo or UTC
+    expected_pre_epoch = pre_epoch_naive.replace(tzinfo=local_tz).astimezone(UTC)
     assert raw_pre_epoch.info["meas_date"] == expected_pre_epoch
     if raw_pre_epoch.annotations.orig_time is not None:
         assert raw_pre_epoch.annotations.orig_time == expected_pre_epoch