Merge branch 'main' into EEGLAB_anno_bug

withmywoessner · Mar 12, 2024 · d5ea24b · d5ea24b
2 parents ec5de79 + 9006789
commit d5ea24b
Show file tree

Hide file tree

Showing 19 changed files with 176 additions and 151 deletions.
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/[email protected].0
+      - uses: davidslusser/[email protected].1
         with:
           src: "mne"
           options: "-c pyproject.toml -ll -r"

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/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/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/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`_
 

diff --git a/doc/changes/v0.17.rst b/doc/changes/v0.17.rst
@@ -234,7 +234,7 @@ API
   In 0.19
     The ``stim_channel`` keyword arguments will be removed from ``read_raw_...`` functions.
 
-- Calling :meth:``mne.io.pick.pick_info`` removing channels that are needed by compensation matrices (``info['comps']``) no longer raises ``RuntimeException`` but instead logs an info level message. By `Luke Bloy`_
+- Calling ``mne.io.pick.pick_info`` removing channels that are needed by compensation matrices (``info['comps']``) no longer raises ``RuntimeException`` but instead logs an info level message. By `Luke Bloy`_
 
 - :meth:`mne.Epochs.save` now has the parameter ``fmt`` to specify the desired format (precision) saving epoched data, by `Stefan Repplinger`_, `Eric Larson`_ and `Alex Gramfort`_
 
@@ -274,44 +274,44 @@ Authors
 
 People who contributed to this release  (in alphabetical order):
 
-* 	Alexandre Gramfort
-* 	Antoine Gauthier
-* 	Britta Westner
-* 	Christian Brodbeck
-* 	Clemens Brunner
-* 	Daniel McCloy
-* 	David Sabbagh
-* 	Denis A. Engemann
-* 	Eric Larson
-* 	Ezequiel Mikulan
-* 	Henrich Kolkhorst
-* 	Hubert Banville
-* 	Jasper J.F. van den Bosch
-* 	Jen Evans
-* 	Joan Massich
-* 	Johan van der Meer
-* 	Jona Sassenhagen
-* 	Kambiz Tavabi
-* 	Lorenz Esch
-* 	Luke Bloy
-* 	Mainak Jas
-* 	Manu Sutela
-* 	Marcin Koculak
-* 	Marijn van Vliet
-* 	Mikolaj Magnuski
-* 	Peter J. Molfese
-* 	Sam Perry
-* 	Sara Sommariva
-* 	Sergey Antopolskiy
-* 	Sheraz Khan
-* 	Stefan Appelhoff
-* 	Stefan Repplinger
-* 	Steven Bethard
-* 	Teekuningas
-* 	Teon Brooks
-* 	Thomas Hartmann
-* 	Thomas Jochmann
-* 	Tom Dupré la Tour
-* 	Tristan Stenner
-* 	buildqa
-* 	jeythekey
+* Alexandre Gramfort
+* Antoine Gauthier
+* Britta Westner
+* Christian Brodbeck
+* Clemens Brunner
+* Daniel McCloy
+* David Sabbagh
+* Denis A. Engemann
+* Eric Larson
+* Ezequiel Mikulan
+* Henrich Kolkhorst
+* Hubert Banville
+* Jasper J.F. van den Bosch
+* Jen Evans
+* Joan Massich
+* Johan van der Meer
+* Jona Sassenhagen
+* Kambiz Tavabi
+* Lorenz Esch
+* Luke Bloy
+* Mainak Jas
+* Manu Sutela
+* Marcin Koculak
+* Marijn van Vliet
+* Mikolaj Magnuski
+* Peter J. Molfese
+* Sam Perry
+* Sara Sommariva
+* Sergey Antopolskiy
+* Sheraz Khan
+* Stefan Appelhoff
+* Stefan Repplinger
+* Steven Bethard
+* Teekuningas
+* Teon Brooks
+* Thomas Hartmann
+* Thomas Jochmann
+* Tom Dupré la Tour
+* Tristan Stenner
+* buildqa
+* jeythekey
diff --git a/doc/changes/v1.2.rst b/doc/changes/v1.2.rst
@@ -63,7 +63,7 @@ Bugs
 
 API changes
 ~~~~~~~~~~~
-- In meth:`mne.Evoked.plot`, the default value of the ``spatial_colors`` parameter has been changed to ``'auto'``, which will use spatial colors if channel locations are available (:gh:`11201` by :newcontrib:`Hüseyin Orkun Elmas` and `Daniel McCloy`_)
+- In :meth:`mne.Evoked.plot`, the default value of the ``spatial_colors`` parameter has been changed to ``'auto'``, which will use spatial colors if channel locations are available (:gh:`11201` by :newcontrib:`Hüseyin Orkun Elmas` and `Daniel McCloy`_)
 - Starting with this release we now follow the Python convention of using ``FutureWarning`` instead of ``DeprecationWarning`` to signal user-facing changes to our API (:gh:`11120` by `Daniel McCloy`_)
 - The ``names`` parameter of :func:`mne.viz.plot_arrowmap` and :func:`mne.viz.plot_regression_weights` has been deprecated; sensor names will be automatically drawn from the ``info_from`` or ``model`` parameter (respectively), and can be hidden, shown, or altered via the ``show_names`` parameter (:gh:`11123` by `Daniel McCloy`_)
 - The ``bands`` parameter of :meth:`mne.Epochs.plot_psd_topomap` now accepts :class:`dict` input; legacy :class:`tuple` input is supported, but discouraged for new code (:gh:`11050` by `Daniel McCloy`_)

diff --git a/doc/documentation/datasets.rst b/doc/documentation/datasets.rst
@@ -516,7 +516,7 @@ Contains both EEG (EGI) and eye-tracking (ASCII format) data recorded from a
 pupillary light reflex experiment, stored in separate files. 1 participant fixated
 on the screen while short light flashes appeared. Event onsets were recorded by a
 photodiode attached to the screen and were sent to both the EEG and eye-tracking
-systems. 
+systems.
 
 .. topic:: Examples
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 cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_.