Merge branch 'main' into spectrogram-class

drammock · Mar 13, 2024 · 496958f · 496958f
2 parents e09d3c0 + 2a97333
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -444,8 +444,8 @@ jobs:
 
 
   deploy:
-    machine:
-      image: ubuntu-2004:202111-01
+    docker:
+      - image: cimg/base:current-22.04
     steps:
       - attach_workspace:
           at: /tmp/build

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -30,7 +30,7 @@ jobs:
     needs: style
     runs-on: ubuntu-latest
     steps:
-      - uses: davidslusser/actions_python_bandit@v1.0.0
+      - uses: davidslusser/actions_python_bandit@v1.0.1
         with:
           src: "mne"
           options: "-c pyproject.toml -ll -r"

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: v0.3.0
+    rev: v0.3.2
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -48,7 +48,7 @@ repos:
 
   # mypy
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: mypy
         # Avoid the conflict between mne/__init__.py and mne/__init__.pyi by ignoring the former

diff --git a/README.rst b/README.rst
@@ -88,12 +88,12 @@ For full functionality, some functions require:
 - `scikit-learn <https://scikit-learn.org/stable/>`__ ≥ 1.0
 - `Joblib <https://joblib.readthedocs.io/en/latest/index.html>`__ ≥ 0.15 (for parallelization)
 - `mne-qt-browser <https://github.com/mne-tools/mne-qt-browser>`__ ≥ 0.1 (for fast raw data visualization)
-- `Qt <https://www.qt.io>`__ ≥ 5.12 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
+- `Qt <https://www.qt.io>`__ ≥ 5.15 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
 
   - `PyQt6 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 6.0
   - `PySide6 <https://doc.qt.io/qtforpython-6/>`__ ≥ 6.0
-  - `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 5.12
-  - `PySide2 <https://doc.qt.io/qtforpython-6/gettingstarted/porting_from2.html>`__ ≥ 5.12
+  - `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 5.15
+  - `PySide2 <https://doc.qt.io/qtforpython-6/gettingstarted/porting_from2.html>`__ ≥ 5.15
 
 - `Numba <https://numba.pydata.org>`__ ≥ 0.54.0
 - `NiBabel <https://nipy.org/nibabel/>`__ ≥ 3.2.1

diff --git a/doc/_includes/channel_interpolation.rst b/doc/_includes/channel_interpolation.rst
@@ -59,12 +59,12 @@ where :math:`G_{ds} \in R^{M \times N}` computes :math:`g_{m}(\boldsymbol{r_i},
 
 To interpolate bad channels, one can simply do:
 
-	>>> evoked.interpolate_bads(reset_bads=False)  # doctest: +SKIP
+    >>> evoked.interpolate_bads(reset_bads=False)  # doctest: +SKIP
 
 and the bad channel will be fixed.
 
 .. target for :end-before: channel-interpolation-end-content
 
 .. topic:: Examples:
 
-	* :ref:`ex-interpolate-bad-channels`
+    * :ref:`ex-interpolate-bad-channels`
diff --git a/doc/_includes/forward.rst b/doc/_includes/forward.rst
@@ -130,26 +130,26 @@ transformation symbols (:math:`T_x`) indicate the transformations actually
 present in the FreeSurfer files. Generally,
 
 .. math::    \begin{bmatrix}
-		x_2 \\
-		y_2 \\
-		z_2 \\
-		1
-	        \end{bmatrix} = T_{12} \begin{bmatrix}
-		x_1 \\
-		y_1 \\
-		z_1 \\
-		1
-	        \end{bmatrix} = \begin{bmatrix}
-		R_{11} & R_{12} & R_{13} & x_0 \\
-		R_{21} & R_{22} & R_{23} & y_0 \\
-		R_{31} & R_{32} & R_{33} & z_0 \\
-		0 & 0 & 0 & 1
-	        \end{bmatrix} \begin{bmatrix}
-		x_1 \\
-		y_1 \\
-		z_1 \\
-		1
-	        \end{bmatrix}\ ,
+        x_2 \\
+        y_2 \\
+        z_2 \\
+        1
+            \end{bmatrix} = T_{12} \begin{bmatrix}
+        x_1 \\
+        y_1 \\
+        z_1 \\
+        1
+            \end{bmatrix} = \begin{bmatrix}
+        R_{11} & R_{12} & R_{13} & x_0 \\
+        R_{21} & R_{22} & R_{23} & y_0 \\
+        R_{31} & R_{32} & R_{33} & z_0 \\
+        0 & 0 & 0 & 1
+            \end{bmatrix} \begin{bmatrix}
+        x_1 \\
+        y_1 \\
+        z_1 \\
+        1
+            \end{bmatrix}\ ,
 
 where :math:`x_k`, :math:`y_k`,and :math:`z_k` are the location coordinates in
 two coordinate systems, :math:`T_{12}` is the coordinate transformation from
@@ -161,20 +161,20 @@ files produced by FreeSurfer and MNE.
 The fixed transformations :math:`T_-` and :math:`T_+` are:
 
 .. math::    T_{-} = \begin{bmatrix}
-		0.99 & 0 & 0 & 0 \\
-		0 & 0.9688 & 0.042 & 0 \\
-		0 & -0.0485 & 0.839 & 0 \\
-		0 & 0 & 0 & 1
-	        \end{bmatrix}
+        0.99 & 0 & 0 & 0 \\
+        0 & 0.9688 & 0.042 & 0 \\
+        0 & -0.0485 & 0.839 & 0 \\
+        0 & 0 & 0 & 1
+            \end{bmatrix}
 
 and
 
 .. math::    T_{+} = \begin{bmatrix}
-		0.99 & 0 & 0 & 0 \\
-		0 & 0.9688 & 0.046 & 0 \\
-		0 & -0.0485 & 0.9189 & 0 \\
-		0 & 0 & 0 & 1
-	        \end{bmatrix}
+        0.99 & 0 & 0 & 0 \\
+        0 & 0.9688 & 0.046 & 0 \\
+        0 & -0.0485 & 0.9189 & 0 \\
+        0 & 0 & 0 & 1
+            \end{bmatrix}
 
 .. note::
    This section does not discuss the transformation between the MRI voxel
@@ -352,11 +352,11 @@ coordinates (:math:`r_D`) by
 where
 
 .. math::    T = \begin{bmatrix}
-		e_x & 0 \\
-		e_y & 0 \\
-		e_z & 0 \\
-		r_{0D} & 1
-	        \end{bmatrix}\ .
+        e_x & 0 \\
+        e_y & 0 \\
+        e_z & 0 \\
+        r_{0D} & 1
+            \end{bmatrix}\ .
 
 Calculation of the magnetic field
 ---------------------------------

diff --git a/doc/_includes/ssp.rst b/doc/_includes/ssp.rst
@@ -101,12 +101,12 @@ The EEG average reference is the mean signal over all the sensors. It is
 typical in EEG analysis to subtract the average reference from all the sensor
 signals :math:`b^{1}(t), ..., b^{n}(t)`. That is:
 
-.. math::	{b}^{j}_{s}(t) = b^{j}(t) - \frac{1}{n}\sum_{k}{b^k(t)}
+.. math:: {b}^{j}_{s}(t) = b^{j}(t) - \frac{1}{n}\sum_{k}{b^k(t)}
    :name: eeg_proj
 
 where the noise term :math:`b_{n}^{j}(t)` is given by
 
-.. math:: 	b_{n}^{j}(t) = \frac{1}{n}\sum_{k}{b^k(t)}
+.. math:: b_{n}^{j}(t) = \frac{1}{n}\sum_{k}{b^k(t)}
    :name: noise_term
 
 Thus, the projector vector :math:`P_{\perp}` will be given by

diff --git a/doc/api/events.rst b/doc/api/events.rst
@@ -55,4 +55,4 @@ Events
    average_movements
    combine_event_ids
    equalize_epoch_counts
-   make_metadata
+   make_metadata
diff --git a/doc/api/file_io.rst b/doc/api/file_io.rst
@@ -63,4 +63,4 @@ Base class:
    :toctree: ../generated/
    :template: autosummary/class_no_members.rst
 
-   BaseEpochs
+   BaseEpochs
diff --git a/doc/changes/devel/12474.bugfix.rst b/doc/changes/devel/12474.bugfix.rst
@@ -0,0 +1 @@
+- Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_
diff --git a/doc/changes/devel/12481.bugfix.rst b/doc/changes/devel/12481.bugfix.rst
@@ -0,0 +1 @@
+- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_.
diff --git a/doc/changes/devel/12483.bugfix.rst b/doc/changes/devel/12483.bugfix.rst
@@ -0,0 +1 @@
+Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_.
diff --git a/doc/changes/devel/12484.bugfix.rst b/doc/changes/devel/12484.bugfix.rst
@@ -0,0 +1 @@
+- Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_
diff --git a/doc/changes/devel/12489.bugfix.rst b/doc/changes/devel/12489.bugfix.rst
@@ -0,0 +1 @@
+Fix cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_.
diff --git a/doc/changes/devel/12491.dependency.rst b/doc/changes/devel/12491.dependency.rst
@@ -0,0 +1 @@
+The minimum supported version of Qt bindings is 5.15, by `Eric Larson`_.
diff --git a/doc/changes/v0.10.rst b/doc/changes/v0.10.rst
@@ -91,7 +91,7 @@ BUG
 
 - Fix dropping of events after downsampling stim channels by `Marijn van Vliet`_
 
-- Fix scaling in :func:``mne.viz.utils._setup_vmin_vmax`` by `Jaakko Leppakangas`_
+- Fix scaling in ``mne.viz.utils._setup_vmin_vmax`` by `Jaakko Leppakangas`_
 
 - Fix order of component selection in :class:`mne.decoding.CSP` by `Clemens Brunner`_
 

diff --git a/doc/changes/v0.12.rst b/doc/changes/v0.12.rst
@@ -129,7 +129,7 @@ BUG
 
 - Fix bug in :func:`mne.io.Raw.save` where, in rare cases, automatically split files could end up writing an extra empty file that wouldn't be read properly by `Eric Larson`_
 
-- Fix :class:``mne.realtime.StimServer`` by removing superfluous argument ``ip`` used while initializing the object by `Mainak Jas`_.
+- Fix ``mne.realtime.StimServer`` by removing superfluous argument ``ip`` used while initializing the object by `Mainak Jas`_.
 
 - Fix removal of projectors in :func:`mne.preprocessing.maxwell_filter` in ``st_only=True`` mode by `Eric Larson`_
 
@@ -175,37 +175,37 @@ Authors
 
 The committer list for this release is the following (preceded by number of commits):
 
-* 348	Eric Larson
-* 347	Jaakko Leppakangas
-* 157	Alexandre Gramfort
-* 139	Jona Sassenhagen
-* 67	Jean-Remi King
-* 32	Chris Holdgraf
-* 31	Denis A. Engemann
-* 30	Mainak Jas
-* 16	Christopher J. Bailey
-* 13	Marijn van Vliet
-* 10	Mark Wronkiewicz
-* 9	Teon Brooks
-* 9	kaichogami
-* 8	Clément Moutard
-* 5	Camilo Lamus
-* 5	mmagnuski
-* 4	Christian Brodbeck
-* 4	Daniel McCloy
-* 4	Yousra Bekhti
-* 3	Fede Raimondo
-* 1	Jussi Nurminen
-* 1	MartinBaBer
-* 1	Mikolaj Magnuski
-* 1	Natalie Klein
-* 1	Niklas Wilming
-* 1	Richard Höchenberger
-* 1	Sagun Pai
-* 1	Sourav Singh
-* 1	Tom Dupré la Tour
-* 1	jona-sassenhagen@
-* 1	kambysese
-* 1	pbnsilva
-* 1	sviter
-* 1	zuxfoucault
+* 348 Eric Larson
+* 347 Jaakko Leppakangas
+* 157 Alexandre Gramfort
+* 139 Jona Sassenhagen
+* 67 Jean-Remi King
+* 32 Chris Holdgraf
+* 31 Denis A. Engemann
+* 30 Mainak Jas
+* 16 Christopher J. Bailey
+* 13 Marijn van Vliet
+* 10 Mark Wronkiewicz
+* 9 Teon Brooks
+* 9 kaichogami
+* 8 Clément Moutard
+* 5 Camilo Lamus
+* 5 mmagnuski
+* 4 Christian Brodbeck
+* 4 Daniel McCloy
+* 4 Yousra Bekhti
+* 3 Fede Raimondo
+* 1 Jussi Nurminen
+* 1 MartinBaBer
+* 1 Mikolaj Magnuski
+* 1 Natalie Klein
+* 1 Niklas Wilming
+* 1 Richard Höchenberger
+* 1 Sagun Pai
+* 1 Sourav Singh
+* 1 Tom Dupré la Tour
+* 1 jona-sassenhagen@
+* 1 kambysese
+* 1 pbnsilva
+* 1 sviter
+* 1 zuxfoucault
diff --git a/doc/changes/v0.13.rst b/doc/changes/v0.13.rst
@@ -198,7 +198,7 @@ API
 
 - Deprecated ``mne.time_frequency.cwt_morlet`` and ``mne.time_frequency.single_trial_power`` in favour of :func:`mne.time_frequency.tfr_morlet` with parameter average=False, by `Jean-Remi King`_ and `Alex Gramfort`_
 
-- Add argument ``mask_type`` to func:`mne.read_events` and func:`mne.find_events` to support MNE-C style of trigger masking by `Teon Brooks`_ and `Eric Larson`_
+- Add argument ``mask_type`` to :func:`mne.read_events` and :func:`mne.find_events` to support MNE-C style of trigger masking by `Teon Brooks`_ and `Eric Larson`_
 
 - Extended Infomax is now the new default in :func:`mne.preprocessing.infomax` (``extended=True``), by `Clemens Brunner`_
 

diff --git a/doc/changes/v0.15.rst b/doc/changes/v0.15.rst
@@ -226,7 +226,7 @@ API
 
 - ``mne.viz.decoding.plot_gat_times``, ``mne.viz.decoding.plot_gat_matrix`` are now deprecated. Use matplotlib instead as shown in the examples, by `Jean-Remi King`_ and `Alex Gramfort`_
 
-- Add ``norm_trace`` parameter to control single-epoch covariance normalization in :class:mne.decoding.CSP, by `Jean-Remi King`_
+- Add ``norm_trace`` parameter to control single-epoch covariance normalization in :class:`mne.decoding.CSP`, by `Jean-Remi King`_
 
 - Allow passing a list of channel names as ``show_names`` in function  :func:`mne.viz.plot_sensors` and methods :meth:`mne.Evoked.plot_sensors`, :meth:`mne.Epochs.plot_sensors` and :meth:`mne.io.Raw.plot_sensors` to show only a subset of channel names by `Jaakko Leppakangas`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		- Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		- Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		The minimum supported version of Qt bindings is 5.15, by `Eric Larson`_.