Merge branch 'main' into fix-issue-11267

myd7349 · web-flow · commit 440215e7c062 · 2025-06-06T08:54:11.000+08:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.11
+    rev: v0.11.12
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -40,7 +40,7 @@ repos:
 
   # rstcheck
   - repo: https://github.com/rstcheck/rstcheck.git
-    rev: v6.2.4
+    rev: v6.2.5
     hooks:
       - id: rstcheck
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: zizmor
 
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -113,7 +113,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1" pandas neo pymatreader antio defusedxml
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -203,7 +203,7 @@ stages:
             displayName: 'PyQt6'
           - bash: |
               set -eo pipefail
-              python -m pip install "PySide6!=6.8.0,!=6.8.0.1"
+              python -m pip install "PySide6!=6.8.0,!=6.8.0.1,!=6.9.1"
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
               PYTEST_QT_API=PySide6 pytest ${TEST_OPTIONS}
diff --git a/doc/changes/devel/13276.bugfix.rst b/doc/changes/devel/13276.bugfix.rst
@@ -0,0 +1 @@
+Fix bug with :func:`mne.simulation.simulate_raw` and :class:`mne.simulation.SourceSimulator` where using different head positions with ``head_pos`` and a BEM would raise an error, by `Eric Larson`_.
diff --git a/doc/changes/devel/13277.bugfix.rst b/doc/changes/devel/13277.bugfix.rst
@@ -0,0 +1 @@
+Update :func:`mne.viz.plot_alignment` and related functions to support PyVista deprecation of positional arguments by :newcontrib:`user27182`.
diff --git a/doc/changes/names.inc b/doc/changes/names.inc
@@ -22,7 +22,7 @@
 .. _Andrew Quinn: https://github.com/ajquinn
 .. _Aniket Pradhan: https://github.com/Aniket-Pradhan
 .. _Anna Padee: https://github.com/apadee/
-.. _Annalisa Pascarella: https://www.iac.cnr.it/personale/annalisa-pascarella
+.. _Annalisa Pascarella: https://github.com/annapasca
 .. _Anne-Sophie Dubarry: https://github.com/annesodub
 .. _Antoine Collas: https://www.antoinecollas.fr
 .. _Antoine Gauthier: https://github.com/Okamille
@@ -54,7 +54,7 @@
 .. _Cora Kim: https://github.com/kimcoco
 .. _Cristóbal Moënne-Loccoz: https://github.com/cmmoenne
 .. _Dan Wakeman: https://github.com/dgwakeman
-.. _Daniel Carlström Schad: https://github.com/Dod12
+.. _Daniel Carlström Schad: https://github.com/DanielCSchad
 .. _Daniel Hasegan: https://daniel.hasegan.com
 .. _Daniel McCloy: https://dan.mccloy.info
 .. _Daniel Strohmeier: https://github.com/joewalter
@@ -318,6 +318,7 @@
 .. _Toomas Erik Anijärv: https://www.toomaserikanijarv.com/
 .. _Tristan Stenner: https://github.com/tstenner/
 .. _Tziona NessAiver: https://github.com/TzionaN
+.. _user27182: https://github.com/user27182
 .. _Valerii Chirkov: https://github.com/vagechirkov
 .. _Velu Prabhakar Kumaravel: https://github.com/vpKumaravel
 .. _Victor Ferat: https://github.com/vferat
diff --git a/doc/conf.py b/doc/conf.py
@@ -664,6 +664,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://doi.org/10.1167/",  # jov.arvojournals.org
     "https://doi.org/10.1177/",  # journals.sagepub.com
     "https://doi.org/10.3109/",  # www.tandfonline.com
+    "https://hms.harvard.edu/",  # doc/funding.rst
+    "https://stackoverflow.com/questions/21752259/python-why-pickle",  # doc/help/faq
     "https://www.biorxiv.org/content/10.1101/",  # biorxiv.org
     "https://www.researchgate.net/profile/",
     "https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html",
@@ -675,6 +677,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://sourceforge.net/projects/ezwinports/files/",
     "https://www.mathworks.com/products/compiler/matlab-runtime.html",
     "https://medicine.umich.edu/dept/khri/ross-maddox-phd",
+    # TODO https://github.com/mne-tools/curry-python-reader/issues/5
+    "https://github.com/mne-tools/curry-python-reader/README.md",
     # 500 server error
     "https://openwetware.org/wiki/Beauchamp:FreeSurfer",
     # 503 Server error
diff --git a/doc/martinos.rst b/doc/martinos.rst
diff --git a/mne/chpi.py b/mne/chpi.py
@@ -99,8 +99,9 @@ def read_head_pos(fname):
 
     Returns
     -------
-    pos : array, shape (N, 10)
+    quats : array, shape (n_pos, 10)
         The position and quaternion parameters from cHPI fitting.
+        See :func:`mne.chpi.compute_head_pos` for details on the columns.
 
     See Also
     --------
@@ -126,8 +127,9 @@ def write_head_pos(fname, pos):
     ----------
     fname : path-like
         The filename to write.
-    pos : array, shape (N, 10)
+    pos : array, shape (n_pos, 10)
         The position and quaternion parameters from cHPI fitting.
+        See :func:`mne.chpi.compute_head_pos` for details on the columns.
 
     See Also
     --------
@@ -141,7 +143,9 @@ def write_head_pos(fname, pos):
     _check_fname(fname, overwrite=True)
     pos = np.array(pos, np.float64)
     if pos.ndim != 2 or pos.shape[1] != 10:
-        raise ValueError("pos must be a 2D array of shape (N, 10)")
+        raise ValueError(
+            f"pos must be a 2D array of shape (N, 10), got shape {pos.shape}"
+        )
     with open(fname, "wb") as fid:
         fid.write(
             " Time       q1       q2       q3       q4       q5       "
@@ -157,16 +161,17 @@ def head_pos_to_trans_rot_t(quats):
 
     Parameters
     ----------
-    quats : ndarray, shape (N, 10)
+    quats : ndarray, shape (n_pos, 10)
         MaxFilter-formatted position and quaternion parameters.
+        See :func:`mne.chpi.read_head_pos` for details on the columns.
 
     Returns
     -------
-    translation : ndarray, shape (N, 3)
+    translation : ndarray, shape (n_pos, 3)
         Translations at each time point.
-    rotation : ndarray, shape (N, 3, 3)
+    rotation : ndarray, shape (n_pos, 3, 3)
         Rotations at each time point.
-    t : ndarray, shape (N,)
+    t : ndarray, shape (n_pos,)
         The time points.
 
     See Also
@@ -929,7 +934,8 @@ def compute_head_pos(
     Returns
     -------
     quats : ndarray, shape (n_pos, 10)
-        The ``[t, q1, q2, q3, x, y, z, gof, err, v]`` for each fit.
+        MaxFilter-formatted head position parameters. The columns correspond to
+        ``[t, q1, q2, q3, x, y, z, gof, err, v]`` for each time point.
 
     See Also
     --------
diff --git a/mne/commands/tests/test_commands.py b/mne/commands/tests/test_commands.py
@@ -4,6 +4,7 @@
 
 import glob
 import os
+import platform
 import shutil
 from os import path as op
 from pathlib import Path
@@ -102,8 +103,12 @@ def test_compare_fiff():
     check_usage(mne_compare_fiff)
 
 
+# should match ".*valid tag.*" but conda-linux intermittently fails for some reason
+@pytest.mark.filterwarnings("ignore:Invalid tag.*:RuntimeWarning")
 def test_show_fiff(tmp_path):
     """Test mne compare_fiff."""
+    if os.getenv("MNE_CI_KIND", "") == "conda" and platform.system() == "Linux":
+        pytest.skip("Skipping test on conda-linux due to intermittent failures")
     check_usage(mne_show_fiff)
     with ArgvSetter((raw_fname,)):
         mne_show_fiff.run()
@@ -112,9 +117,7 @@ def test_show_fiff(tmp_path):
     bad_fname = tmp_path / "test_bad_raw.fif"
     with open(bad_fname, "wb") as fout, open(raw_fname, "rb") as fin:
         fout.write(fin.read(100000))
-    # should match ".*valid tag.*" but conda-linux intermittently fails for some reason
-    with _record_warnings():
-        lines = show_fiff(bad_fname, output=list)
+    lines = show_fiff(bad_fname, output=list)
     last_line = lines[-1]
     assert last_line.endswith(">>>>BAD @9015")
     assert "302  = FIFF_EPOCH (734412b >f4)" in last_line
diff --git a/mne/forward/_compute_forward.py b/mne/forward/_compute_forward.py
@@ -35,6 +35,7 @@ def _dup_coil_set(coils, coord_frame, t):
     if t is not None:
         coord_frame = t["to"]
         for coil in coils:
+            assert isinstance(coil, dict), f"Coil must be a dict, got {type(coil)}"
             for key in ("ex", "ey", "ez"):
                 if key in coil:
                     coil[key] = apply_trans(t["trans"], coil[key], False)
@@ -794,6 +795,7 @@ def _compute_forwards_meeg(rr, *, sensors, fwd_data, n_jobs, silent=False):
     mri_Q, bem_rr, fun = fwd_data["mri_Q"], fwd_data["bem_rr"], fwd_data["fun"]
     solutions = fwd_data["solutions"]
     del fwd_data
+    rr = np.ascontiguousarray(rr)  # usually true but not guaranteed, e.g. in dipole.py
     for coil_type, sens in sensors.items():
         coils = sens["defs"]
         compensator = sens.get("compensator", None)
@@ -835,6 +837,9 @@ def _compute_forwards(rr, *, bem, sensors, n_jobs, verbose=None):
     solver = bem.get("solver", "mne")
     _check_option("solver", solver, ("mne", "openmeeg"))
     if bem["is_sphere"] or solver == "mne":
+        # This modifies "sensors" in place, so let's copy it in case the calling
+        # function needs to reuse it (e.g., in simulate_raw.py)
+        sensors = deepcopy(sensors)
         fwd_data = _prep_field_computation(rr, sensors=sensors, bem=bem, n_jobs=n_jobs)
         Bs = _compute_forwards_meeg(
             rr, sensors=sensors, fwd_data=fwd_data, n_jobs=n_jobs
diff --git a/mne/simulation/tests/test_raw.py b/mne/simulation/tests/test_raw.py
@@ -38,6 +38,7 @@
     compute_head_pos,
     get_chpi_info,
     read_head_pos,
+    write_head_pos,
 )
 from mne.datasets import testing
 from mne.io import RawArray, read_raw_fif
@@ -54,6 +55,7 @@
 from mne.source_space._source_space import _compare_source_spaces
 from mne.surface import _get_ico_surface
 from mne.tests.test_chpi import _assert_quats
+from mne.transforms import _affine_to_quat
 from mne.utils import catch_logging
 
 raw_fname_short = Path(__file__).parents[2] / "io" / "tests" / "data" / "test_raw.fif"
@@ -251,6 +253,11 @@ def test_simulate_raw_sphere(raw_data, tmp_path):
 
     # head pos
     head_pos_sim = _get_head_pos_sim(raw)
+    head_pos_sim_2 = np.zeros((len(head_pos_sim), 10))
+    for ii, (t, mat) in enumerate(head_pos_sim.items()):
+        head_pos_sim_2[ii, :7] = [t] + list(_affine_to_quat(mat))
+    head_pos_sim_3 = tmp_path / "head_pos.txt"
+    write_head_pos(head_pos_sim_3, head_pos_sim_2)
 
     #
     # Test raw simulation with basic parameters
@@ -259,11 +266,9 @@ def test_simulate_raw_sphere(raw_data, tmp_path):
     cov = read_cov(cov_fname)
     cov["projs"] = raw.info["projs"]
     raw.info["bads"] = raw.ch_names[:1]
-    sphere_norad = make_sphere_model("auto", None, raw.info)
     raw_meg = raw.copy().pick("meg")
-    raw_sim = simulate_raw(
-        raw_meg.info, stc, trans, src, sphere_norad, head_pos=head_pos_sim
-    )
+    raw_sim = simulate_raw(raw_meg.info, stc, trans, src, sphere, head_pos=head_pos_sim)
+    raw_data = raw_sim[:][0]
     # Test IO on processed data
     test_outname = tmp_path / "sim_test_raw.fif"
     raw_sim.save(test_outname)
@@ -307,12 +312,14 @@ def test_simulate_raw_sphere(raw_data, tmp_path):
     )
     del raw_sim, raw_sim_2
 
-    # check that different interpolations are similar given small movements
+    # check that different interpolations are similar given small movements,
+    # using different input forms of head_pos
     raw_sim = simulate_raw(
         raw.info, stc, trans, src, sphere, head_pos=head_pos_sim, interp="linear"
     )
+    assert_allclose(raw_sim.get_data("meg"), raw_data, rtol=0.02)
     raw_sim_hann = simulate_raw(
-        raw.info, stc, trans, src, sphere, head_pos=head_pos_sim, interp="hann"
+        raw.info, stc, trans, src, sphere, head_pos=head_pos_sim_3, interp="hann"
     )
     assert_allclose(raw_sim[:][0], raw_sim_hann[:][0], rtol=1e-1, atol=1e-14)
     del raw_sim_hann
@@ -391,7 +398,7 @@ def test_simulate_raw_bem(raw_data):
     cov = make_ad_hoc_cov(raw.info)
     # The tolerance for the BEM is surprisingly high but I get the same
     # result when using MNE-C and Xfit, even when using a proper 5120 BEM :(
-    for use_raw, bem, tol in ((raw_sim_sph, sphere, 4), (raw_sim_bem, bem_fname, 31)):
+    for use_raw, bem, tol in ((raw_sim_sph, sphere, 6), (raw_sim_bem, bem_fname, 31)):
         events = find_events(use_raw, "STI 014")
         assert len(locs) == 6
         evoked = Epochs(use_raw, events, 1, 0, tmax, baseline=None).average()
@@ -425,6 +432,18 @@ def test_simulate_raw_bem(raw_data):
     assert_allclose(amp0 / amp1, wf_sim[0] / wf_sim[1], rtol=1e-5)
     assert amp2 == 0
     assert raw_sim.n_times == ss.n_times
+    # smoke test that different head positions can be used as well
+    head_pos_sim = {1.0: raw.info["dev_head_t"]["trans"]}
+    raw_sim_2 = simulate_raw(
+        raw.info,
+        ss,
+        src=src_ss,
+        bem=bem_fname,
+        first_samp=first_samp,
+        head_pos=head_pos_sim,
+    )
+    data_2 = raw_sim_2.get_data()
+    assert_allclose(data, data_2, rtol=1e-7)
 
 
 @pytest.mark.slowtest  # slow on Windows Azure
diff --git a/mne/viz/backends/_pyvista.py b/mne/viz/backends/_pyvista.py
@@ -594,7 +594,7 @@ def tube(
                 color = None
             else:
                 scalars = None
-            tube = line.tube(radius, n_sides=self.tube_n_sides)
+            tube = line.tube(radius=radius, n_sides=self.tube_n_sides)
             actor = _add_mesh(
                 plotter=self.plotter,
                 mesh=tube,
diff --git a/pyproject.toml b/pyproject.toml
@@ -134,7 +134,7 @@ full-no-qt = [
   "xlrd",
 ]
 full-pyqt6 = ["mne[full]"]
-full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1"]
+full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1, != 6.9.1"]
 # Dependencies for MNE-Python functions that use HDF5 I/O
 hdf5 = ["h5io >= 0.2.4", "pymatreader"]
 # Dependencies for running the test infrastructure
diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh
@@ -23,7 +23,7 @@ if [ ! -z "$CONDA_ENV" ]; then
 elif [[ "${MNE_CI_KIND}" == "pip" ]]; then
 	# Only used for 3.13 at the moment, just get test deps plus a few extras
 	# that we know are available
-	INSTALL_ARGS="nibabel scikit-learn numpydoc PySide6 mne-qt-browser pandas h5io mffpy defusedxml numba"
+	INSTALL_ARGS="nibabel scikit-learn numpydoc PySide6!=6.9.1 mne-qt-browser pandas h5io mffpy defusedxml numba"
 	INSTALL_KIND="test"
 else
 	test "${MNE_CI_KIND}" == "pip-pre"
diff --git a/tools/hooks/update_environment_file.py b/tools/hooks/update_environment_file.py
@@ -56,6 +56,8 @@ def split_dep(dep):
     # `environment.yaml` breaks the solver
     if package_name == "PySide6":
         version_spec = version_spec.replace("!=6.7.0,", "")
+        # not on CF yet either
+        version_spec = version_spec.replace(",!=6.9.1", "")
     elif package_name == "vtk":
         # TODO VERSION remove once we support VTK 9.4
         version_spec = "=9.3.1=qt_*"

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Fix bug with :func:`mne.simulation.simulate_raw` and :class:`mne.simulation.SourceSimulator` where using different head positions with ``head_pos`` and a BEM would raise an error, by `Eric Larson`_.
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+Update :func:`mne.viz.plot_alignment` and related functions to support PyVista deprecation of positional arguments by :newcontrib:`user27182`.