MAINT: Compat with MNE 1.8 birthday date (#1278)

* MAINT: Compat with MNE 1.8 birthday date

* FIX: Write, too

* Update whats_new.rst

---------

Co-authored-by: Stefan Appelhoff <[email protected]>

.circleci/config.yml

@@ -48,7 +48,13 @@ jobs:
             name: Build the documentation
             no_output_timeout: 30m
             command: |
-              make build-doc
+              make build-doc 2>&1 | tee sphinx_log.txt
+
+        - run:
+            name: Check sphinx log for warnings (which are treated as errors)
+            when: always
+            command: |
+              ! grep "^.*WARNING: .*$" sphinx_log.txt
 
         - persist_to_workspace:
             root: doc/_build

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
       - id: ruff
         name: ruff mne_bids/
         files: ^mne_bids/
+        args: ["--fix"]
       - id: ruff
         name: ruff examples/
         # D103: missing docstring in public function

doc/whats_new.rst

@@ -22,6 +22,7 @@ The following authors contributed for the first time. Thank you so much! 🤩
 The following authors had contributed before. Thank you for sticking around! 🤘
 
 * `Daniel McCloy`_
+* `Eric Larson`_
 * `Stefan Appelhoff`_
 
 Detailed list of changes
@@ -45,12 +46,12 @@ Detailed list of changes
 🪲 Bug fixes
 ^^^^^^^^^^^^
 
-- When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``. By `Daniel McCloy`_ (:gh:`1270`)
+- When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^
 
-- nothing yet
+- Keep MNE-BIDS up to date with recent changes on participant birthday date handling in MNE-Python, by `Eric Larson`_ (gh:1278:)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

doc/whats_new_previous_releases.rst

@@ -536,7 +536,7 @@ API and behavior changes
 
 - Reading BIDS data with ``"HeadCoilFrequency"`` and ``"PowerLineFrequency"`` data specified in JSON sidecars will only "warn" in case of mismatches between Raw and JSON data, by `Franziska von Albedyll`_ (:gh:`855`)
 
-- Accessing :attr:`mne_bids.BIDSPath.fpath` emit a warning anymore if the path does not exist. This behavior was unreliable and yielded confusing error messages in certain use cases. Use `mne_bids.BIDSPath.fpath.exists()` to check whether the path exists in the file system, by `Richard Höchenberger`_ (:gh:`904`)
+- Accessing :attr:`mne_bids.BIDSPath.fpath` emit a warning anymore if the path does not exist. This behavior was unreliable and yielded confusing error messages in certain use cases. Use ``mne_bids.BIDSPath.fpath.exists()`` to check whether the path exists in the file system, by `Richard Höchenberger`_ (:gh:`904`)
 
 - :func:`mne_bids.get_entity_vals` gained a new parameter, ``ignore_dirs``, to exclude directories from the search, by `Adam Li`_ and `Richard Höchenberger`_ (:gh:`899`, :gh:`908`)
 
@@ -587,13 +587,13 @@ Notable changes
 - You can now write preloaded and potentially modified data with
   :func:`mne_bids.write_raw_bids` by passing ``allow_preload=True``. This is
   a first step towards supporting derivative files.
-- `mne_bids.BIDSPath` now has property getters and setters for all BIDS
+- :func:`mne_bids.BIDSPath` now has property getters and setters for all BIDS
   entities. What this means is that you can now do things like
   ``bids_path.subject = '01'`` instead of ``bids_path.update(subject='01')``.
 - We now support Deep Brain Stimulation (DBS) data.
 - The way we handle anatomical landmarks was greatly revamped to ensure we're
   always using the correct coordinate systems. A new function,
-  `mne_bids.get_anat_landmarks`, helps with extracting fiducial points from
+  :func:`mne_bids.get_anat_landmarks`, helps with extracting fiducial points from
   anatomical scans.
 - When creating a BIDS dataset from FIFF files on macOS and Linux, MNE-BIDS
   can now optionally generate symbolic links to the original files instead of
@@ -859,7 +859,7 @@ been cooking for you!
 
 Notable changes
 ~~~~~~~~~~~~~~~
-- We introduce `mne_bids.BIDSPath`, a new class for all BIDS file and folder
+- We introduce :func:`mne_bids.BIDSPath`, a new class for all BIDS file and folder
   operations. All functions in MNE-BIDS that previously accepted filenames
   and folder locations (e.g. ``bids_root``) have been updated to work with
   ``BIDSPath``. Others have been removed.
@@ -956,7 +956,7 @@ Bug fixes
 API changes
 ^^^^^^^^^^^
 
-In the transition to using `mne_bids.BIDSPath`, the following functions have been updated:
+In the transition to using :func:`mne_bids.BIDSPath`, the following functions have been updated:
 
 - :func:`mne_bids.write_anat` now accepts a :class:`mne_bids.BIDSPath` instead of entities as keyword arguments, by `Adam Li`_ (:gh:`575`)
 - In :func:`mne_bids.write_raw_bids`, :func:`mne_bids.read_raw_bids`, and :func:`mne_bids.get_head_mri_trans`, the ``bids_basename`` and ``bids_root`` keyword arguments have been removed. The functions now expect ``bids_path``, an instance of :class:`mne_bids.BIDSPath`, by `Adam Li`_ (:gh:`525`)
@@ -1110,7 +1110,7 @@ Bug
 API
 ~~~
 
-- :func:`make_dataset_description` is now available from `mne_bids` main namespace, all copyfile functions are available from `mne_bids.copyfiles` namespace, by `Stefan Appelhoff`_ (:gh:`196`)
+- :func:`make_dataset_description` is now available from `mne_bids` main namespace, all copyfile functions are available from :func:`mne_bids.copyfiles` namespace, by `Stefan Appelhoff`_ (:gh:`196`)
 - Add support for non maxfiltered .fif files, by `Maximilien Chaumon`_ (:gh:`171`)
 - Remove support for Neuroscan ``.cnt`` data because its support is no longer planned in BIDS, by `Stefan Appelhoff`_ (:gh:`142`)
 - Remove support for Python 2 because it is no longer supported in MNE-Python, by `Teon Brooks`_ (:gh:`141`)

examples/bidspath.py

@@ -81,7 +81,7 @@
 # **data type**, i.e., ``meg`` for MEG data, ``eeg`` and ``ieeg`` for EEG and
 # iEEG data, or ``anat`` for anatomical MRI scans. Typically, MNE-BIDS will
 # infer the data type of your data automatically, for example when writing data
-# using `mne_bids.write_raw_bids`. For the sake of this example, however, we
+# using :func:`mne_bids.write_raw_bids`. For the sake of this example, however, we
 # are going to specify the data type explicitly.
 
 datatype = "eeg"

examples/read_bids_datasets.py

@@ -78,7 +78,7 @@
 #
 # We can use MNE-BIDS to print a tree of all
 # included files and folders. We pass the ``max_depth`` parameter to
-# `mne_bids.print_dir_tree` to the output to four levels of folders, for
+# :func:`mne_bids.print_dir_tree` to the output to four levels of folders, for
 # better readability in this example.
 
 print_dir_tree(bids_root, max_depth=4)

examples/update_bids_datasets.py

@@ -48,7 +48,7 @@
 #
 # We can use MNE-BIDS to print a tree of all
 # included files and folders. We pass the ``max_depth`` parameter to
-# `mne_bids.print_dir_tree` to the output to three levels of folders, for
+# :func:`mne_bids.print_dir_tree` to the output to three levels of folders, for
 # better readability in this example.
 
 print_dir_tree(bids_root, max_depth=3)

mne_bids/conftest.py

@@ -13,6 +13,15 @@ def pytest_configure(config):
     config.addinivalue_line("usefixtures", "monkeypatch_mne")
 
 
+@pytest.fixture(autouse=True)
+def close_all():
+    """Close all figures after each test."""
+    yield
+    import matplotlib.pyplot as plt
+
+    plt.close("all")
+
+
 @pytest.fixture(scope="session")
 def monkeypatch_mne():
     """Monkeypatch MNE to ensure we have download=False everywhere in tests."""

mne_bids/path.py

@@ -901,7 +901,7 @@ def update(self, *, check=None, **kwargs):
             If a boolean, controls whether to enforce BIDS conformity. This
             will set the ``.check`` attribute accordingly. If ``None``, rely on
             the existing ``.check`` attribute instead, which is set upon
-            `mne_bids.BIDSPath` instantiation. Defaults to ``None``.
+            :class:`mne_bids.BIDSPath` instantiation. Defaults to ``None``.
         **kwargs : dict
             It can contain updates for valid BIDSPath entities:
             'subject', 'session', 'task', 'acquisition', 'processing', 'run',
@@ -1018,7 +1018,7 @@ def match(self, ignore_json=True, check=False):
         check : bool
             If ``True``, only returns paths that conform to BIDS. If ``False``
             (default), the ``.check`` attribute of the returned
-            `mne_bids.BIDSPath` object will be set to ``True`` for paths that
+            :class:`mne_bids.BIDSPath` object will be set to ``True`` for paths that
             do conform to BIDS, and to ``False`` for those that don't.
 
         Returns
@@ -2382,7 +2382,7 @@ def find_matching_paths(
     check : bool
         If ``True``, only returns paths that conform to BIDS. If ``False``
         (default), the ``.check`` attribute of the returned
-        `mne_bids.BIDSPath` object will be set to ``True`` for paths that
+        :class:`mne_bids.BIDSPath` object will be set to ``True`` for paths that
         do conform to BIDS, and to ``False`` for those that don't.
 
     Returns
@@ -2459,7 +2459,7 @@ def _fnames_to_bidspaths(fnames, root, check=False):
     check : bool
         If ``True``, only returns paths that conform to BIDS. If ``False``
         (default), the ``.check`` attribute of the returned
-        `mne_bids.BIDSPath` object will be set to ``True`` for paths that
+        :class:`mne_bids.BIDSPath` object will be set to ``True`` for paths that
         do conform to BIDS, and to ``False`` for those that don't.
 
     Returns

mne_bids/tests/data/tiny_bids/code/make_tiny_bids_dataset.py

@@ -5,6 +5,7 @@
 
 # %%
 import json
+from datetime import date
 from pathlib import Path
 
 import mne
@@ -45,7 +46,7 @@
     "last_name": "Musterperson",
     "first_name": "Maxi",
     "middle_name": "Luka",
-    "birthday": (1970, 10, 20),
+    "birthday": date(1970, 10, 20),
     "sex": 2,
     "hand": 3,
 }

mne_bids/tests/test_read.py

@@ -827,12 +827,9 @@ def test_handle_chpi_reading(tmp_path):
 
     with (
         pytest.warns(RuntimeWarning, match="Defaulting to .* mne.Raw object"),
-        pytest.warns(
-            RuntimeWarning, match="This file contains raw Internal Active Shielding"
-        ),
         pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
-        raw_read = read_raw_bids(bids_path)
+        raw_read = read_raw_bids(bids_path, extra_params=dict(allow_maxshield="yes"))
 
     # cHPI "off" according to sidecar, but present in the data
     meg_json_data_chpi_mismatch = meg_json_data.copy()

mne_bids/tests/test_write.py

@@ -14,7 +14,7 @@
 import shutil as sh
 import sys
 import warnings
-from datetime import datetime, timedelta, timezone
+from datetime import date, datetime, timedelta, timezone
 from glob import glob
 from pathlib import Path
 
@@ -102,6 +102,8 @@
 
 def _wrap_read_raw(read_raw):
     def fn(fname, *args, **kwargs):
+        if str(fname).endswith(".mff") and check_version("mne", "1.8"):
+            kwargs["events_as_annotations"] = True
         raw = read_raw(fname, *args, **kwargs)
         raw.info["line_freq"] = 60
         return raw
@@ -222,9 +224,12 @@ def test_write_participants(_bids_validate, tmp_path):
 
     # add fake participants data
     raw.set_meas_date(datetime(year=1994, month=1, day=26, tzinfo=timezone.utc))
+    birthday = (1993, 1, 26)
+    if check_version("mne", "1.8"):
+        birthday = date(*birthday)
     raw.info["subject_info"] = {
         "his_id": subject_id2,
-        "birthday": (1993, 1, 26),
+        "birthday": birthday,
         "sex": 1,
         "hand": 2,
     }
@@ -707,9 +712,12 @@ def test_fif(_bids_validate, tmp_path):
     # data
     # change the gender but don't force overwrite.
     raw = _read_raw_fif(raw_fname)
+    birthday = (1994, 1, 26)
+    if check_version("mne", "1.8"):
+        birthday = date(*birthday)
     raw.info["subject_info"] = {
         "his_id": subject_id2,
-        "birthday": (1994, 1, 26),
+        "birthday": birthday,
         "sex": 2,
         "hand": 1,
     }

mne_bids/write.py

@@ -11,7 +11,7 @@
 import sys
 import warnings
 from collections import OrderedDict, defaultdict
-from datetime import datetime, timedelta, timezone
+from datetime import date, datetime, timedelta, timezone
 from pathlib import Path
 
 import mne
@@ -456,12 +456,14 @@ def _participants_tsv(raw, subject_id, fname, overwrite=False):
 
         # determine the age of the participant
         age = subject_info.get("birthday", None)
+        if isinstance(age, tuple):  # can be removed once MNE >= 1.8 is required
+            age = date(*age)
         meas_date = raw.info.get("meas_date", None)
         if isinstance(meas_date, (tuple, list, np.ndarray)):
             meas_date = meas_date[0]
 
         if meas_date is not None and age is not None:
-            bday = datetime(age[0], age[1], age[2], tzinfo=timezone.utc)
+            bday = datetime(age.year, age.month, age.day, tzinfo=timezone.utc)
             if isinstance(meas_date, datetime):
                 meas_datetime = meas_date
             else:
@@ -1408,7 +1410,7 @@ def write_raw_bids(
         already loaded from disk unless ``allow_preload`` is explicitly set
         to ``True``. See warning for the ``allow_preload`` parameter.
     bids_path : BIDSPath
-        The file to write. The `mne_bids.BIDSPath` instance passed here
+        The file to write. The :class:`mne_bids.BIDSPath` instance passed here
         **must** have the ``subject``, ``task``, and ``root`` attributes set.
         If the ``datatype`` attribute is not set, it will be inferred from the
         recording data type found in ``raw``. In case of multiple data types,

pyproject.toml

@@ -59,12 +59,13 @@ full = [
 ]
 
 # Dependencies for running the test infrastructure
-test = ["mne_bids[full]", "pytest", "pytest-cov", "pytest-sugar", "ruff"]
+test = ["mne_bids[full]", "pytest >= 8", "pytest-cov", "pytest-sugar", "ruff"]
 
 # Dependencies for building the documentation
 doc = [
     "nilearn",
-    "sphinx",
+    # TODO: Remove pin once https://github.com/sphinx-doc/sphinx/issues/12589 is fixed
+    "sphinx!=7.4.6,!=7.4.5,!=7.4.4,!=7.4.3,!=7.4.2,!=7.4.1,!=7.4.0",
     "sphinx_gallery",
     "sphinx-copybutton",
     "pydata-sphinx-theme",
@@ -148,4 +149,6 @@ filterwarnings = [
     # old MNE _fake_click
     "ignore:The .*_event function was deprecated in Matplotlib.*:",
     "ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
+    # matplotlib
+    "ignore:Figure.*is non-interactive.*cannot be shown:UserWarning",
 ]