Merge branch 'neuroread' of https://github.com/withmywoessner/mne-python

 into neuroread

.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

.github/CONTRIBUTING.md

@@ -10,4 +10,4 @@ This project and everyone participating in it is governed by the [MNE-Python's C
 
 ## How to contribute
 
-Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/install/contributing.html).
+Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/development/contributing.html).

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,5 @@
 Thanks for contributing a pull request! Please make sure you have read the
-[contribution guidelines](https://mne.tools/dev/install/contributing.html)
+[contribution guidelines](https://mne.tools/dev/development/contributing.html)
 before submitting.
 
 Please be aware that we are a loose team of volunteers so patience is

.github/workflows/tests.yml

@@ -23,14 +23,14 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-      - uses: pre-commit/[email protected].0
+      - uses: pre-commit/[email protected].1
 
   bandit:
     name: Bandit
     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"
@@ -129,5 +129,7 @@ jobs:
           path: ~/mne_data
       - run: ./tools/github_actions_download.sh
       - run: ./tools/github_actions_test.sh
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: success()

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.3.0
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -11,18 +11,14 @@ repos:
         name: ruff lint mne preview
         args: ["--fix", "--preview", "--select=NPY201"]
         files: ^mne/
-      - id: ruff-format
-        name: ruff format mne
-        files: ^mne/
       - id: ruff
-        name: ruff lint tutorials and examples
+        name: ruff lint doc, tutorials, and examples
         # D103: missing docstring in public function
         # D400: docstring first line must end with period
         args: ["--ignore=D103,D400", "--fix"]
-        files: ^tutorials/|^examples/
+        files: ^doc/|^tutorials/|^examples/
       - id: ruff-format
-        name: ruff format tutorials and examples
-        files: ^tutorials/|^examples/
+        files: ^mne/|^doc/|^tutorials/|^examples/
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
@@ -36,7 +32,7 @@ repos:
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]

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

azure-pipelines.yml

@@ -104,7 +104,7 @@ 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@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1,!=6.6.1" "PyQt6-Qt6!=6.6.1" qtpy nibabel sphinx-gallery
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1,!=6.6.1,!=6.6.2" "PyQt6-Qt6!=6.6.1,!=6.6.2" qtpy nibabel sphinx-gallery
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -183,7 +183,7 @@ stages:
             displayName: 'Get test data'
           - bash: |
               set -e
-              python -m pip install "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1"
+              python -m pip install "PyQt6!=6.6.1,!=6.6.2" "PyQt6-Qt6!=6.6.1,!=6.6.2"
               LD_DEBUG=libs python -c "from PyQt6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
           - bash: |
               mne sys_info -pd

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`

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
 ---------------------------------

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

doc/api/events.rst

@@ -55,4 +55,4 @@ Events
    average_movements
    combine_event_ids
    equalize_epoch_counts
-   make_metadata
+   make_metadata

doc/api/file_io.rst

@@ -63,4 +63,4 @@ Base class:
    :toctree: ../generated/
    :template: autosummary/class_no_members.rst
 
-   BaseEpochs
+   BaseEpochs

doc/api/preprocessing.rst

@@ -93,6 +93,7 @@ Projections:
    cortical_signal_suppression
    create_ecg_epochs
    create_eog_epochs
+   find_bad_channels_lof
    find_bad_channels_maxwell
    find_ecg_events
    find_eog_events
@@ -162,6 +163,8 @@ Projections:
    Calibration
    read_eyelink_calibration
    set_channel_types_eyetrack
+   convert_units
+   get_screen_visual_angle
    interpolate_blinks
 
 EEG referencing:

doc/changes/devel/11234.newfeature.rst

@@ -0,0 +1 @@
+Detecting Bad EEG/MEG channels using the local outlier factor (LOF) algorithm in :func:`mne.preprocessing.find_bad_channels_lof`, by :newcontrib:`Velu Prabhakar Kumaravel`.

doc/changes/devel/12206.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :meth:`mne.Epochs.apply_function` where data was handed down incorrectly in parallel processing, by `Dominik Welke`_.

doc/changes/devel/12206.newfeature.rst

@@ -0,0 +1,3 @@
+Custom functions applied via :meth:`mne.io.Raw.apply_function`, :meth:`mne.Epochs.apply_function` or :meth:`mne.Evoked.apply_function` can now use ``ch_idx`` or ``ch_name`` to get access to the currently processed channel during channel wise processing.
+
+:meth:`mne.Evoked.apply_function` can now also work on full data array instead of just channel wise, analogous to :meth:`mne.io.Raw.apply_function` and :meth:`mne.Epochs.apply_function`, by `Dominik Welke`_.

doc/changes/devel/12207.newfeature.rst

@@ -0,0 +1 @@
+Allow :class:`mne.time_frequency.EpochsTFR` as input to :func:`mne.epochs.equalize_epoch_counts`, by `Carina Forster`_.

doc/changes/devel/12237.newfeature.rst

@@ -0,0 +1,2 @@
+Added a helper function :func:`mne.preprocessing.eyetracking.convert_units` to convert eyegaze data from pixel-on-screen values to radians of visual angle. Also added a helper function :func:`mne.preprocessing.eyetracking.get_screen_visual_angle` to get the visual angle that the participant screen subtends, by `Scott Huberty`_.
+

doc/changes/devel/12323.newfeature.rst

@@ -0,0 +1 @@
+Add :meth:`~mne.SourceEstimate.savgol_filter`, :meth:`~mne.SourceEstimate.filter`, :meth:`~mne.SourceEstimate.apply_hilbert`, and :meth:`~mne.SourceEstimate.apply_function` methods to :class:`mne.SourceEstimate` and related classes, by `Hamza Abdelhedi`_.

doc/changes/devel/12324.bugfix.rst

@@ -0,0 +1 @@
+Add ``tol`` parameter to :meth:`mne.events_from_annotations` so that the user can specify the tolerance to ignore rounding errors of event onsets when using ``chunk_duration`` is not None (default is 1e-8), by `Michiru Kaneda`_

doc/changes/devel/12382.apichange.rst

@@ -0,0 +1 @@
+Change :func:`mne.stc_near_sensors` ``surface`` default from the ``'pial'`` surface to the surface in ``src`` if ``src`` is not ``None`` in version 1.8, by `Alex Rockhill`_.

doc/changes/devel/12382.bugfix.rst

@@ -0,0 +1 @@
+Fix bad channels not handled properly in :func:`mne.stc_near_sensors` by `Alex Rockhill`_.

doc/changes/devel/12393.bugfix.rst

@@ -0,0 +1 @@
+Change how samples are read when using ``data_format='auto'`` in :func:`mne.io.read_raw_cnt`, by `Jacob Woessner`_.

doc/changes/devel/12420.other.rst

@@ -0,0 +1 @@
+Clarify in the :ref:`EEG referencing tutorial <tut-set-eeg-ref>` that an average reference projector ready is required for inverse modeling, by :newcontrib:`Nabil Alibou`

doc/changes/devel/12430.bugfix.rst

@@ -0,0 +1 @@
+Reformats channel and detector lookup in :func:`mne.io.read_raw_snirf` from array based to dictionary based. Removes incorrect assertions that every detector and source must have data associated with every registered optode position, by :newcontrib:`Alex Kiefer`.

doc/changes/devel/12436.bugfix.rst

@@ -0,0 +1 @@
+Fix :ref:`tut-working-with-seeg` use of :func:`mne.stc_near_sensors` to use the :class:`mne.VolSourceEstimate` positions and not the pial surface, by `Alex Rockhill`_

doc/changes/devel/12443.newfeature.rst

@@ -0,0 +1 @@
+Add option to pass ``image_kwargs`` to :class:`mne.Report.add_epochs` to allow adjusting e.g. ``vmin`` and ``vmax`` of the epochs image in the report, by `Sophie Herbst`_.

doc/changes/devel/12444.bugfix.rst

@@ -0,0 +1 @@
+Fix validation of ``ch_type`` in :func:`mne.preprocessing.annotate_muscle_zscore`, by `Mathieu Scheltienne`_.

doc/changes/devel/12445.newfeature.rst

@@ -0,0 +1 @@
+Add support for multiple raw instances in :func:`mne.preprocessing.compute_average_dev_head_t` by `Eric Larson`_.

doc/changes/devel/12446.newfeature.rst

@@ -0,0 +1 @@
+Support partial pathlength factors for each wavelength in :func:`mne.preprocessing.nirs.beer_lambert_law`, by :newcontrib:`Richard Scholz`.

doc/changes/devel/12450.other.rst

@@ -0,0 +1 @@
+Move private data preparation functions for BrainVision export from ``pybv`` to ``mne``, by `Clemens Brunner`_.

doc/changes/devel/12451.bugfix.rst

@@ -0,0 +1 @@
+Fix errant redundant use of ``BIDSPath.split`` when writing split raw and epochs data, by `Eric Larson`_.

doc/changes/devel/12451.dependency.rst

@@ -0,0 +1 @@
+``pytest-harvest`` is no longer used as a test dependency, by `Eric Larson`_.

doc/changes/devel/12454.newfeature.rst

@@ -0,0 +1 @@
+Completing PR 12453. Add option to pass ``image_kwargs`` per channel type to :class:`mne.Report.add_epochs`.

doc/changes/devel/12456.bugfix.rst

@@ -0,0 +1 @@
+Disable config parser interpolation when reading BrainVision files, which allows using the percent sign as a regular character in channel units, by `Clemens Brunner`_.

doc/changes/devel/12461.other.rst

@@ -0,0 +1 @@
+Fix dead links in ``README.rst`` documentation by :newcontrib:`Will Turner`.

doc/changes/devel/12462.newfeature.rst

@@ -0,0 +1 @@
+:func:`mne.epochs.make_metadata` now accepts strings as ``tmin`` and ``tmax`` parameter values, simplifying metadata creation based on time-varying events such as responses to a stimulus, by `Richard Höchenberger`_.

doc/changes/devel/12463.newfeature.rst

@@ -0,0 +1 @@
+Include date of acquisition and filter parameters in ``raw.info`` for :func:`mne.io.read_raw_neuralynx` by `Kristijan Armeni`_.

doc/changes/devel/12470.bugfix.rst

@@ -0,0 +1 @@
+- Fix the default color of :meth:`mne.viz.Brain.add_text` to properly contrast with the figure background color, by `Marijn van Vliet`_.

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`_

doc/changes/devel/12481.bugfix.rst

@@ -0,0 +1 @@
+- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_.

doc/changes/devel/12483.bugfix.rst

@@ -0,0 +1 @@
+Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_.

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`_.

doc/changes/devel/12491.dependency.rst

@@ -0,0 +1 @@
+The minimum supported version of Qt bindings is 5.15, by `Eric Larson`_.