Merge branch 'main' into correct_annot_export

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
+    rev: v0.8.4
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -78,11 +78,11 @@ repos:
         language: python
         entry: ./tools/hooks/sync_dependencies.py
         files: pyproject.toml
-        additional_dependencies: ["mne"]
+        additional_dependencies: ["mne==1.9.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v0.9.2
+    rev: v0.10.0
     hooks:
       - id: zizmor
 

Makefile

@@ -44,7 +44,7 @@ test-doc: sample_data testing_data
 	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --ignore=./doc/conf.py --ignore=doc/sphinxext --fulltrace
 
 pre-commit:
-	@pre-commit run -a
+	@pre-commit run -a --show-diff-on-failure
 
 # Aliases for stuff we used to support or users might think of
 ruff: pre-commit

README.rst

@@ -72,7 +72,7 @@ The minimum required dependencies to run MNE-Python are:
 
 .. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
 
-- `Python <https://www.python.org>`__ ≥ 3.9
+- `Python <https://www.python.org>`__ ≥ 3.10
 - `NumPy <https://numpy.org>`__ ≥ 1.23
 - `SciPy <https://scipy.org>`__ ≥ 1.9
 - `Matplotlib <https://matplotlib.org>`__ ≥ 3.6

doc/changes/devel/13028.bugfix.rst

@@ -0,0 +1 @@
+Fix epoch indexing in :class:`mne.time_frequency.EpochsTFRArray` when initialising the class with the default ``drop_log`` parameter, by `Thomas Binns`_.

doc/changes/devel/13042.bugfix.rst

@@ -0,0 +1 @@
+Fix loading and saving of :class:`~mne.time_frequency.EpochsSpectrum` objects that contain slash-separators in their condition names, by `Daniel McCloy`_.

environment.yml

@@ -23,16 +23,16 @@ dependencies:
   - joblib
   - jupyter
   - lazy_loader >=0.3
-  - matplotlib >=3.6
+  - matplotlib >=3.7
   - mffpy >=0.5.7
   - mne-qt-browser
   - nibabel
   - nilearn
   - numba
-  - numpy >=1.23,<3
+  - numpy >=1.25,<3
   - openmeeg >=2.5.5
   - packaging
-  - pandas
+  - pandas >=2.0
   - pillow
   - pip
   - pooch >=1.5
@@ -47,7 +47,7 @@ dependencies:
   - qdarkstyle !=3.2.2
   - qtpy
   - scikit-learn
-  - scipy >=1.9
+  - scipy >=1.11
   - sip
   - snirf
   - statsmodels

mne/channels/montage.py

@@ -361,8 +361,7 @@ def __repr__(self):
     def plot(
         self,
         *,
-        scale=None,
-        scale_factor=None,
+        scale=1.0,
         show_names=True,
         kind="topomap",
         show=True,
@@ -373,7 +372,6 @@ def plot(
         return plot_montage(
             self,
             scale=scale,
-            scale_factor=scale_factor,
             show_names=show_names,
             kind=kind,
             show=show,

mne/commands/mne_flash_bem.py

@@ -95,17 +95,6 @@ def run():
             "been registered with the T1.mgz file."
         ),
     )
-    parser.add_option(
-        "-n",
-        "--noconvert",
-        dest="noconvert",
-        action="store_true",
-        default=False,
-        help=(
-            "[DEPRECATED] Assume that the Flash MRI images "
-            "have already been converted to mgz files"
-        ),
-    )
     parser.add_option(
         "-u",
         "--unwarp",
@@ -139,15 +128,6 @@ def run():
         help="Use copies instead of symlinks for surfaces",
         action="store_true",
     )
-    parser.add_option(
-        "-p",
-        "--flash-path",
-        dest="flash_path",
-        default=None,
-        help="[DEPRECATED] The directory containing flash5.mgz "
-        "files (defaults to "
-        "$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps",
-    )
 
     options, _ = parser.parse_args()
 

mne/commands/tests/test_commands.py

@@ -334,7 +334,7 @@ def test_flash_bem(tmp_path):
 
     # First test without flash30
     with ArgvSetter(
-        ("-d", tempdir, "-s", "sample", "-n", "-r", "-3"),
+        ("-d", tempdir, "-s", "sample", "-r", "-3"),
         disable_stdout=False,
         disable_stderr=False,
     ):
@@ -361,7 +361,6 @@ def test_flash_bem(tmp_path):
             tempdir,
             "-s",
             "sample",
-            "-n",
             "-3",
             str(mridata_path / "flash" / "mef30.mgz"),
             "-5",

mne/conftest.py

@@ -34,6 +34,7 @@
     _pl,
     _record_warnings,
     _TempDir,
+    check_version,
     numerics,
 )
 
@@ -636,21 +637,13 @@ def _use_backend(backend_name, interactive):
 
 def _check_skip_backend(name):
     from mne.viz.backends._utils import _notebook_vtk_works
-    from mne.viz.backends.tests._utils import (
-        has_imageio_ffmpeg,
-        has_pyvista,
-        has_pyvistaqt,
-    )
 
-    if not has_pyvista():
-        pytest.skip("Test skipped, requires pyvista.")
-    if not has_imageio_ffmpeg():
-        pytest.skip("Test skipped, requires imageio-ffmpeg")
+    pytest.importorskip("pyvista")
+    pytest.importorskip("imageio_ffmpeg")
     if name == "pyvistaqt":
+        pytest.importorskip("pyvistaqt")
         if not _check_qt_version():
             pytest.skip("Test skipped, requires Qt.")
-        if not has_pyvistaqt():
-            pytest.skip("Test skipped, requires pyvistaqt")
     else:
         assert name == "notebook", name
         if not _notebook_vtk_works():
@@ -660,10 +653,8 @@ def _check_skip_backend(name):
 @pytest.fixture(scope="session")
 def pixel_ratio():
     """Get the pixel ratio."""
-    from mne.viz.backends.tests._utils import has_pyvista
-
     # _check_qt_version will init an app for us, so no need for us to do it
-    if not has_pyvista() or not _check_qt_version():
+    if not check_version("pyvista", "0.32") or not _check_qt_version():
         return 1.0
     from qtpy.QtCore import Qt
     from qtpy.QtWidgets import QMainWindow

mne/datasets/eegbci/eegbci.py

@@ -9,7 +9,7 @@
 from os import path as op
 from pathlib import Path
 
-from ...utils import _url_to_local_path, logger, verbose, warn
+from ...utils import _url_to_local_path, logger, verbose
 from ..utils import _do_path_update, _downloader_params, _get_path, _log_time_size
 
 EEGMI_URL = "https://physionet.org/files/eegmmidb/1.0.0/"
@@ -94,10 +94,9 @@ def data_path(url, path=None, force_update=False, update_path=None, *, verbose=N
 
 @verbose
 def load_data(
-    subjects=None,
-    runs=None,
+    subjects,
+    runs,
     *,
-    subject=None,
     path=None,
     force_update=False,
     update_path=None,
@@ -117,9 +116,6 @@ def load_data(
         The subjects to use. Can be in the range of 1-109 (inclusive).
     runs : int | list of int
         The runs to use (see Notes for details).
-    subject : int
-        This parameter is deprecated and will be removed in mne version 1.9.
-        Please use ``subjects`` instead.
     path : None | path-like
         Location of where to look for the EEGBCI data. If ``None``, the environment
         variable or config parameter ``MNE_DATASETS_EEGBCI_PATH`` is used. If neither
@@ -170,22 +166,6 @@ def load_data(
     """
     import pooch
 
-    # XXX: Remove this with mne 1.9 ↓↓↓
-    # Also remove the subject parameter at that point.
-    # Also remove the `None` default for subjects and runs params at that point.
-    if subject is not None:
-        subjects = subject
-        warn(
-            "The ``subject`` parameter is deprecated and will be removed in version "
-            "1.9. Use the ``subjects`` parameter (note the `s`) to suppress this "
-            "warning.",
-            FutureWarning,
-        )
-        del subject
-    if subjects is None or runs is None:
-        raise ValueError("You must pass the parameters ``subjects`` and ``runs``.")
-    # ↑↑↑
-
     t0 = time.time()
 
     if not hasattr(subjects, "__iter__"):

mne/datasets/eegbci/tests/test_eegbci.py

@@ -2,7 +2,6 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
-import pytest
 
 from mne.datasets import eegbci
 
@@ -14,14 +13,3 @@ def test_eegbci_download(tmp_path, fake_retrieve):
         fnames = eegbci.load_data(subj, runs=[3], path=tmp_path, update_path=False)
         assert len(fnames) == 1, subj
     assert fake_retrieve.call_count == 4
-
-    # XXX: remove in version 1.9
-    with pytest.warns(FutureWarning, match="The ``subject``"):
-        fnames = eegbci.load_data(
-            subject=subjects, runs=[3], path=tmp_path, update_path=False
-        )
-        assert len(fnames) == 4
-
-    # XXX: remove in version 1.9
-    with pytest.raises(ValueError, match="You must pass the parameters"):
-        fnames = eegbci.load_data(path=tmp_path, update_path=False)

mne/decoding/csp.py

@@ -18,7 +18,6 @@
     _verbose_safe_false,
     fill_doc,
     pinv,
-    warn,
 )
 
 
@@ -304,7 +303,6 @@ def plot_patterns(
         info,
         components=None,
         *,
-        average=None,
         ch_type=None,
         scalings=None,
         sensors=True,
@@ -342,7 +340,6 @@ def plot_patterns(
             :func:`mne.create_info`.
         components : float | array of float | None
            The patterns to plot. If ``None``, all components will be shown.
-        %(average_plot_evoked_topomap)s
         %(ch_type_topomap)s
         scalings : dict | float | None
             The scalings of the channel types to be applied for plotting.
@@ -391,9 +388,6 @@ def plot_patterns(
         if components is None:
             components = np.arange(self.n_components)
 
-        if average is not None:
-            warn("`average` is deprecated and will be removed in 1.10.", FutureWarning)
-
         # set sampling frequency to have 1 component per time point
         info = cp.deepcopy(info)
         with info._unlock():
@@ -403,7 +397,6 @@ def plot_patterns(
         # the call plot_topomap
         fig = patterns.plot_topomap(
             times=components,
-            average=average,
             ch_type=ch_type,
             scalings=scalings,
             sensors=sensors,
@@ -438,7 +431,6 @@ def plot_filters(
         info,
         components=None,
         *,
-        average=None,
         ch_type=None,
         scalings=None,
         sensors=True,
@@ -476,7 +468,6 @@ def plot_filters(
             :func:`mne.create_info`.
         components : float | array of float | None
            The patterns to plot. If ``None``, all components will be shown.
-        %(average_plot_evoked_topomap)s
         %(ch_type_topomap)s
         scalings : dict | float | None
             The scalings of the channel types to be applied for plotting.
@@ -525,9 +516,6 @@ def plot_filters(
         if components is None:
             components = np.arange(self.n_components)
 
-        if average is not None:
-            warn("`average` is deprecated and will be removed in 1.10.", FutureWarning)
-
         # set sampling frequency to have 1 component per time point
         info = cp.deepcopy(info)
         with info._unlock():
@@ -537,7 +525,6 @@ def plot_filters(
         # the call plot_topomap
         fig = filters.plot_topomap(
             times=components,
-            average=average,
             ch_type=ch_type,
             scalings=scalings,
             sensors=sensors,

mne/decoding/ems.py

@@ -188,7 +188,7 @@ def compute_ems(
             data[:, this_picks] /= np.std(data[:, this_picks])
 
     # Setup cross-validation. Need to use _set_cv to deal with sklearn
-    # deprecation of cv objects.
+    # changes in cv object handling.
     y = epochs.events[:, 2]
     _, cv_splits = _set_cv(cv, "classifier", X=y, y=y)
 

mne/decoding/tests/test_base.py

@@ -320,7 +320,7 @@ def test_get_coef_multiclass(n_features, n_targets):
     ],
 )
 # TODO: Need to fix this properly in LinearModel
-@pytest.mark.filterwarnings("ignore:'multi_class' was deprecated in.*:FutureWarning")
+@pytest.mark.filterwarnings("ignore:'multi_class' was depr.*:FutureWarning")
 @pytest.mark.filterwarnings("ignore:lbfgs failed to converge.*:")
 def test_get_coef_multiclass_full(n_classes, n_channels, n_times):
     """Test a full example with pattern extraction."""

mne/fixes.py

@@ -22,12 +22,10 @@
 from math import log
 
 import numpy as np
+from packaging.version import parse
 
 ###############################################################################
-# distutils
-
-# distutils has been deprecated since Python 3.10 and was removed
-# from the standard library with the release of Python 3.12.
+# distutils LooseVersion removed in Python 3.12
 
 
 def _compare_version(version_a, operator, version_b):
@@ -48,8 +46,6 @@ def _compare_version(version_a, operator, version_b):
     bool
         The result of the version comparison.
     """
-    from packaging.version import parse
-
     mapping = {"<": "lt", "<=": "le", "==": "eq", "!=": "ne", ">=": "ge", ">": "gt"}
     with warnings.catch_warnings(record=True):
         warnings.simplefilter("ignore")

mne/html_templates/repr/_acquisition.html.jinja

@@ -81,7 +81,7 @@
     <td>{{ "%0.2f" | format(info["sfreq"]) }} Hz</td>
 </tr>
 {% endif %}
-{% if inst is defined and inst.times is defined %}
+{% if inst is defined and inst | has_attr("times") and inst.times is defined %}
 <tr class="repr-element {{ section_class_name }} {{ collapsed_row_class }}">
     <td class="mne-repr-section-toggle"></td>
     <td>Time points</td>