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Merged
larsoner merged 6 commits into from
Apr 3, 2026
Merged

MAINT: Remove tomli, tomlsort, and ruff from test group #13809

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08b9609
MAINT: Remove tomli and tomlsort from test deps
larsoner Apr 3, 2026
a52945c
Restore ruff
larsoner Apr 3, 2026
a27138c
FIX: Groups
larsoner Apr 3, 2026
b6f1d7c
FIX: Fix examples
larsoner Apr 3, 2026
9f337f4
FIX: Joy
larsoner Apr 3, 2026
e7ce877
FIX: Maybe
larsoner Apr 3, 2026
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6 changes: 4 additions & 2 deletions examples/inverse/multi_dipole_model.py
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Expand Up @@ -45,6 +45,7 @@
cov_fname = meg_path / "sample_audvis-shrunk-cov.fif"
bem_dir = data_path / "subjects" / "sample" / "bem"
bem_fname = bem_dir / "sample-5120-5120-5120-bem-sol.fif"
trans_fname = meg_path / "sample_audvis_raw-trans.fif"

###############################################################################
# Read the MEG data from the audvis experiment. Make epochs and evokeds for the
Expand Down Expand Up @@ -102,8 +103,9 @@
cov_fit_right["projs"] = evoked_fit_right.info["projs"]

# Fit the dipoles with the subset of sensors.
dip_left, _ = mne.fit_dipole(evoked_fit_left, cov_fit_left, bem)
dip_right, _ = mne.fit_dipole(evoked_fit_right, cov_fit_right, bem)
kwargs = dict(bem=bem, trans=trans_fname)
dip_left, _ = mne.fit_dipole(evoked_fit_left, cov_fit_left, **kwargs)
dip_right, _ = mne.fit_dipole(evoked_fit_right, cov_fit_right, **kwargs)

###############################################################################
# Now that we have the location and orientations of the dipoles, compute the
Expand Down
6 changes: 3 additions & 3 deletions examples/stats/r_interop.py
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@@ -1,9 +1,9 @@
"""
.. _r-interop:

============================
Integrating with R via rpy2
============================
===============================
Integrating with R via ``rpy2``
===============================

This example shows how to run a mass-univariate 2-sample t-test on
:class:`~mne.Epochs` data in Python using :func:`scipy.stats.ttest_ind`,
Expand Down
4 changes: 1 addition & 3 deletions pyproject.toml
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Expand Up @@ -24,7 +24,6 @@ doc = [
"pyvistaqt >= 0.11", # released 2023-06-30, no newer version available
"pyxdf",
"pyzmq != 24.0.0",
"rpy2",
"scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21
"seaborn >= 0.5, != 0.11.2",
"selenium >= 4.27.1",
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@larsoner larsoner Apr 3, 2026

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Maybe this one should move, too -- this is really only needed for making the contrib viz which only CircleCI does on a regular basis. But we can add stuff like this later if it becomes problematic (haven't heard many complaints about selenium installs so far)

Expand All @@ -36,6 +35,7 @@ doc = [
"sphinxcontrib-towncrier >= 0.5.0a0",
"sphinxcontrib-youtube",
]
doc-full = ["rpy2", {include-group = "doc"}]
# Dependencies in a separate group for uv lockfile generation, currently only used for
# the 'old' environment CI test run
lockfile_extras = [
Expand All @@ -55,8 +55,6 @@ test = [
"pytest-rerunfailures",
"pytest-timeout >= 2.2",
"ruff >= 0.1",
"toml-sort",
"tomli; python_version < '3.11'",
"twine",
"vulture",
"wheel >= 0.21",
Expand Down
4 changes: 3 additions & 1 deletion tools/circleci_dependencies.sh
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Expand Up @@ -4,10 +4,12 @@ ONLY_BINARY="--only-binary \"numpy,dipy,scipy,matplotlib,pandas,statsmodels,netC

set -x
python -m pip install --upgrade "pip>=25.1" build
# rpy2 3.6.7 (or its deps) cause problems with our installed R version, so pin them
python -m pip install --upgrade --progress-bar off $ONLY_BINARY \
-ve .[full] \
--group=test \
--group=doc \
--group=doc-full \
"rpy2==3.6.6" "rpy2-rinterface==3.6.5" "rpy2-robjects==3.6.4" \
-r doc/sphinxext/related_software.txt \
"git+https://github.com/mne-tools/mne-bids.git" \
"git+https://github.com/mne-tools/mne-qt-browser.git" \
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11 changes: 8 additions & 3 deletions tutorials/preprocessing/90_eyetracking_data.py
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Expand Up @@ -8,7 +8,6 @@
In this tutorial we will explore simultaneously recorded eye-tracking and EEG data from
a pupillary light reflex task. We will combine the eye-tracking and EEG data, and plot
the ERP and pupil response to the light flashes (i.e. the pupillary light reflex).

"""

# Authors: Scott Huberty <seh33@uw.edu>
Expand Down Expand Up @@ -230,7 +229,13 @@

# Skip baseline correction for now. We will apply baseline correction later.
epochs = mne.Epochs(
raw_et, events=et_events, event_id=event_dict, tmin=-0.3, tmax=3, baseline=None
raw_et,
events=et_events,
event_id=event_dict,
tmin=-0.3,
tmax=3,
baseline=None,
picks="all", # include eyetracking channels in the epochs
)
del raw_et # free up some memory
epochs[:8].plot(
Expand All @@ -251,4 +256,4 @@
# Finally, let's plot the evoked responses to the light flashes to get a sense of the
# average pupillary light response, and the associated ERP in the EEG data.

epochs.apply_baseline().average().plot(picks=occipital + pupil)
epochs.apply_baseline().average(picks="all").plot(picks=occipital + pupil)
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