Updating master with most recent package features

.git-blame-ignore-revs

@@ -13,3 +13,4 @@ e39995d9be6fc831c7a4a59f09b7a7c0a41ae315  # 12588, percent formatting
 1c5b39ff1d99bbcb2fc0e0071a989b3f3845ff30  # 12603, ruff UP028
 b8b168088cb474f27833f5f9db9d60abe00dca83  # 12779, PR JSONs
 ee64eba6f345e895e3d5e7d2804fa6aa2dac2e6d  # 12781, Header unification
+362f9330925fb79a6adc19a42243672676dec63e  # 12799, UP038

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,13 +15,20 @@ Again, thanks for contributing!
 
 -->
 
-#### Reference issue
-Example: Fixes #1234.
+#### Reference issue (if any)
+
+<!-- Example:
+
+Fixes #1234.
+
+-->
 
 
 #### What does this implement/fix?
-Explain your changes.
+
+<!-- Explain your changes. -->
 
 
 #### Additional information
-Any additional information you think is important.
+
+<!-- Any additional information you think is important. -->

.github/workflows/tests.yml

@@ -99,7 +99,7 @@ jobs:
           sed -i '/dipy/d' environment.yml
           sed -i 's/- mne$/- mne-base/' environment.yml
         if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
@@ -131,4 +131,4 @@ jobs:
       - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-        if: success()
+        if: always()

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    rev: v0.7.0
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -51,12 +51,33 @@ repos:
 
   # sorting
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: file-contents-sorter
         files: ^doc/changes/names.inc|^.mailmap
         args: ["--ignore-case"]
 
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+        files: pyproject.toml
+
+  # dependencies
+  - repo: local
+    hooks:
+      - id: dependency-sync
+        name: Sync dependency list between pyproject.toml and README.rst
+        language: python
+        entry: ./tools/hooks/sync_dependencies.py
+        files: pyproject.toml
+        additional_dependencies: ["mne"]
+
+
+# these should *not* be run on CIs:
+ci:
+  skip: [dependency-sync]  # needs MNE to work, which exceeds the free tier space alloc.
+
 # The following are too slow to run on local commits, so let's only run on CIs:
 #
 #   - repo: https://github.com/pre-commit/mirrors-mypy

README.rst

@@ -43,9 +43,6 @@ only, use pip_ in a terminal:
 
     $ pip install --upgrade mne
 
-The current MNE-Python release requires Python 3.9 or higher. MNE-Python 0.17
-was the last release to support Python 2.7.
-
 For more complete instructions, including our standalone installers and more
 advanced installation methods, please refer to the `installation guide`_.
 
@@ -73,42 +70,20 @@ Dependencies
 
 The minimum required dependencies to run MNE-Python are:
 
+.. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
+
 - `Python <https://www.python.org>`__ ≥ 3.9
-- `NumPy <https://numpy.org>`__ ≥ 1.24
-- `SciPy <https://scipy.org>`__ ≥ 1.10
+- `NumPy <https://numpy.org>`__ ≥ 1.23
+- `SciPy <https://scipy.org>`__ ≥ 1.9
 - `Matplotlib <https://matplotlib.org>`__ ≥ 3.6
 - `Pooch <https://www.fatiando.org/pooch/latest/>`__ ≥ 1.5
 - `tqdm <https://tqdm.github.io>`__
 - `Jinja2 <https://palletsprojects.com/p/jinja/>`__
 - `decorator <https://github.com/micheles/decorator>`__
-- `lazy_loader <https://pypi.org/project/lazy_loader/>`__
-
-For full functionality, some functions require:
-
-- `scikit-learn <https://scikit-learn.org/stable/>`__ ≥ 1.2
-- `Joblib <https://joblib.readthedocs.io/en/latest/index.html>`__ ≥ 1.2 (for parallelization)
-- `mne-qt-browser <https://github.com/mne-tools/mne-qt-browser>`__ ≥ 0.5 (for fast raw data visualization)
-- `Qt <https://www.qt.io>`__ ≥ 5.15 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
-
-  - `PySide6 <https://doc.qt.io/qtforpython-6/>`__ ≥ 6.0
-  - `PyQt6 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 6.0
-  - `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 5.15
-
-- `Numba <https://numba.pydata.org>`__ ≥ 0.56.4
-- `NiBabel <https://nipy.org/nibabel/>`__ ≥ 3.2.1
-- `OpenMEEG <https://openmeeg.github.io>`__ ≥ 2.5.6
-- `pandas <https://pandas.pydata.org>`__ ≥ 1.5.2
-- `Picard <https://pierreablin.github.io/picard/>`__ ≥ 0.3
-- `CuPy <https://cupy.dev>`__ ≥ 9.0.0 (for NVIDIA CUDA acceleration)
-- `DIPY <https://dipy.org>`__ ≥ 1.4.0
-- `imageio <https://imageio.readthedocs.io/en/stable/>`__ ≥ 2.8.0
-- `PyVista <https://pyvista.org>`__ ≥ 0.37 (for 3D visualization)
-- `PyVistaQt <https://qtdocs.pyvista.org>`__ ≥ 0.9 (for 3D visualization)
-- `mffpy <https://github.com/BEL-Public/mffpy>`__ ≥ 0.5.7
-- `h5py <https://www.h5py.org>`__
-- `h5io <https://github.com/h5io/h5io>`__
-- `pymatreader <https://pymatreader.readthedocs.io/en/latest/>`__
+- `lazy-loader <https://pypi.org/project/lazy_loader>`__ ≥ 0.3
+- `packaging <https://packaging.pypa.io/en/stable/>`__
 
+.. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↑↑↑
 
 Contributing
 ^^^^^^^^^^^^

azure-pipelines.yml

@@ -111,7 +111,7 @@ 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 qtpy nibabel sphinx-gallery PySide6
+              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 qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1"
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -201,7 +201,7 @@ stages:
             displayName: 'PyQt6'
           - bash: |
               set -eo pipefail
-              python -m pip install PySide6
+              python -m pip install "PySide6!=6.8.0,!=6.8.0.1"
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
               PYTEST_QT_API=PySide6 pytest ${TEST_OPTIONS}

doc/Makefile

@@ -76,3 +76,6 @@ view:
 	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(PWD)/_build/html/sg_execution_times.html')"
 
 show: view
+
+serve:
+	python -m http.server -d _build/html

doc/_static/js/set_installer_tab.js

@@ -12,21 +12,34 @@ function setTabs() {
     }
     if (navigator.userAgent.indexOf("Mac") !== -1) {
         // there's no good way to distinguish intel vs M1 in javascript so we
-        // just default to showing the first of the 2 macOS tabs
-        platform = "macos-intel";
+        // just default to showing the most modern macOS installer
+        platform = "macos-apple";
     }
-    let all_tab_nodes = document.querySelectorAll(
-        '.platform-selector-tabset')[0].children;
-    let input_nodes = [...all_tab_nodes].filter(
-        child => child.nodeName === "INPUT");
+    var platform_short = platform.split("-")[0];
+
     let tab_label_nodes = [...document.querySelectorAll('.sd-tab-label')];
-    let correct_label = tab_label_nodes.filter(
+
+    let install_tab_nodes = document.querySelectorAll(
+        '.install-selector-tabset')[0].children;
+    let install_input_nodes = [...install_tab_nodes].filter(
+        child => child.nodeName === "INPUT");
+    let install_label = tab_label_nodes.filter(
         // label.id is drawn from :name: property in the rST, which must
         // be unique across the whole site (*sigh*)
-        label => label.id.startsWith(platform))[0];
-    let input_id = correct_label.getAttribute('for');
-    let correct_input = input_nodes.filter(node => node.id === input_id)[0];
-    correct_input.checked = true;
+        label => label.id.startsWith(`install-${platform}`))[0];
+    let install_id = install_label.getAttribute('for');
+    let install_input = install_input_nodes.filter(node => node.id === install_id)[0];
+    install_input.checked = true;
+
+    let uninstall_tab_nodes = document.querySelectorAll(
+        '.uninstall-selector-tabset')[0].children;
+    let uninstall_input_nodes = [...uninstall_tab_nodes].filter(
+        child => child.nodeName === "INPUT");
+    let uninstall_label = tab_label_nodes.filter(
+        label => label.id.startsWith(`uninstall-${platform_short}`))[0];
+    let uninstall_id = uninstall_label.getAttribute('for');
+    let uninstall_input = uninstall_input_nodes.filter(node => node.id === uninstall_id)[0];
+    uninstall_input.checked = true;
 }
 
 documentReady(setTabs);

doc/_static/js/update_installer_version.js

@@ -54,7 +54,7 @@ async function warnVersion() {
         title.innerText = "Warning";
         inner.innerText = warn;
         outer.append(title, inner);
-        document.querySelectorAll('.platform-selector-tabset')[0].before(outer);
+        document.querySelectorAll('.install-selector-tabset')[0].before(outer);
     }
 }
 

doc/_static/style.css

@@ -13,6 +13,20 @@
 
 
 html[data-theme="light"] {
+    /* pydata-sphinx-theme overrides */
+    /* ↓↓↓ use default "info" colors for "primary" */
+    --pst-color-primary: #276be9;
+    --pst-color-primary-bg: #dce7fc;
+    /* ↓↓↓ use default "primary" colors for "info" */
+    --pst-color-info: var(--pst-teal-500);
+    --pst-color-info-bg: var(--pst-teal-200);
+    /* ↓↓↓ use "warning" colors for "secondary" */
+    --pst-color-secondary: var(--pst-color-warning);
+    --pst-color-secondary-bg: var(--pst-color-warning-bg);
+    /* ↓↓↓ make sure new primary (link) color propogates to links on code */
+    --pst-color-inline-code-links: var(--pst-color-link);
+    /* ↓↓↓ make sure new secondary (hover) color propogates to hovering on table rows */
+    --pst-color-table-row-hover-bg: var(--pst-color-secondary-bg);
     /* topbar logo links */
     --mne-color-github: #000;
     --mne-color-discourse: #d0232b;
@@ -21,8 +35,6 @@ html[data-theme="light"] {
     --copybtn-opacity: 0.75;
     /* card header bg color */
     --mne-color-card-header: rgba(0, 0, 0, 0.05);
-    /* section headings */
-    --mne-color-heading: #003e80;
     /* sphinx-gallery overrides */
     --sg-download-a-background-color: var(--pst-color-primary);
     --sg-download-a-background-image: unset;
@@ -33,6 +45,20 @@ html[data-theme="light"] {
     --sg-download-a-hover-box-shadow-2: none;
 }
 html[data-theme="dark"] {
+    /* pydata-sphinx-theme overrides */
+    /* ↓↓↓ use default "info" colors for "primary" */
+    --pst-color-primary: #79a3f2;
+    --pst-color-primary-bg: #06245d;
+    /* ↓↓↓ use default "primary" colors for "info" */
+    --pst-color-info: var(--pst-teal-400);
+    --pst-color-info-bg: var(--pst-teal-800);
+    /* ↓↓↓ use "warning" colors for "secondary" */
+    --pst-color-secondary: var(--pst-color-warning);
+    --pst-color-secondary-bg: var(--pst-color-warning-bg);
+    /* ↓↓↓ make sure new primary (link) color propogates to links on code */
+    --pst-color-inline-code-links: var(--pst-color-link);
+    /* ↓↓↓ make sure new secondary (hover) color propogates to hovering on table rows */
+    --pst-color-table-row-hover-bg: var(--pst-color-secondary-bg);
     /* topbar logo links */
     --mne-color-github: rgb(240, 246, 252);  /* from their logo SVG */
     --mne-color-discourse: #FFF9AE;  /* from their logo SVG */
@@ -41,8 +67,6 @@ html[data-theme="dark"] {
     --copybtn-opacity: 0.25;
     /* card header bg color */
     --mne-color-card-header: rgba(255, 255, 255, 0.2);
-    /* section headings */
-    --mne-color-heading: #b8cbe0;
     /* sphinx-gallery overrides */
     --sg-download-a-background-color: var(--pst-color-primary);
     --sg-download-a-background-image: unset;
@@ -52,9 +76,6 @@ html[data-theme="dark"] {
     --sg-download-a-hover-box-shadow-1: none;
     --sg-download-a-hover-box-shadow-2: none;
 }
-h1, h2, h3, h4, h5, h6 {
-    color: var(--mne-color-heading);
-}
 
 /* ************************************************************ Sphinx fixes */
 
@@ -161,20 +182,45 @@ iframe.sg_report {
     top: 0;
 }
 
-/* TODO: Either pydata-sphinx-theme (for using Bootstrap) or sphinx-gallery (for adding table formatting) should fix this */
-.table-striped-columns>:not(caption)>tr>:nth-child(2n),.table-striped>tbody>tr:nth-of-type(odd)>* {
-    --bs-table-accent-bg: var(--bs-table-striped-bg);
+/* ******************************************************** HTML repr tables */
+
+/* make table responsive to pydata-sphinx-theme's light/dark mode */
+.table > :not(caption) > * > * {
     color: var(--pst-color-text-base);
 }
-.table-hover>tbody>tr:hover>* {
-    --bs-table-accent-bg: var(--bs-table-hover-bg);
-    color: var(--pst-color-text-base);
+.mne-repr-table tbody tr:hover {
+    background-color: var(--pst-color-table-row-hover-bg);
 }
-.rendered_html table {
-    color: var(--pst-color-text-base);
+.mne-repr-section-toggle > button > svg > path {
+    fill: var(--pst-color-text-base);
 }
-
-
+/* make the expand/collapse button look nicer */
+.mne-repr-section-toggle > button {
+    padding: 20%;
+}
+/* make section header rows more distinct (and harmonize with pydata-sphinx-theme table
+style in the process). Color copied from pydata-sphinx-theme; 2px copied from bootstrap.
+*/
+.mne-repr-table th {
+    border-bottom: 2px solid var(--pst-color-primary);
+}
+/* harmonize the channel names buttons with the rest of the table */
+.mne-ch-names-btn {
+    font-size: inherit;
+    padding: 0.25rem;
+    min-width: 1.5rem;
+    font-weight: bold;
+}
+/*
+.mne-ch-names-btn:hover {
+    background-color: var(--pst-color-);
+    text-decoration: underline;
+}
+.mne-ch-names-btn:focus-visible {
+    outline: 0.1875rem solid var(--pst-color-accent);
+    outline-offset: 0.1875rem;
+}
+*/
 /* ***************************************************** sphinx-design fixes */
 p.btn a {
     color: unset;

doc/changes/devel/12366.newfeature.rst

@@ -0,0 +1 @@
+Add support for `dict` type argument ``ref_channels`` to :func:`mne.set_eeg_reference`, to allow flexible re-referencing (e.g. ``raw.set_eeg_reference(ref_channels={'A1': ['A2', 'A3']})`` will set the new A1 data to be ``A1 - mean(A2, A3)``), by `Alex Lepauvre`_ and `Qian Chu`_ and `Daniel McCloy`_.

doc/changes/devel/12787.other.rst

@@ -0,0 +1 @@
+Use custom code in :func:`mne.sys_info` to get the amount of physical memory and a more informative CPU name instead of using the ``psutil`` package, by `Clemens Brunner`_.

doc/changes/devel/12792.newfeature.rst

@@ -1 +1 @@
-Add reader for ANT Neuro files in the ``*.cnt`` format with :func:`~mne.io.read_raw_ant`, by `Mathieu Scheltienne`_ and `Eric Larson`_.
+Add reader for ANT Neuro files in the ``*.cnt`` format with :func:`~mne.io.read_raw_ant`, by `Mathieu Scheltienne`_, `Eric Larson`_ and `Proloy Das`_.

doc/changes/devel/12827.other.rst

@@ -0,0 +1 @@
+Improve documentation clarity of ``fit_transform`` methods for :class:`mne.decoding.SSD`, :class:`mne.decoding.CSP`, and :class:`mne.decoding.SPoC` classes, by `Thomas Binns`_.

doc/changes/devel/12829.apichange.rst

@@ -0,0 +1 @@
+Deprecate ``average`` parameter in ``plot_filters`` and ``plot_patterns`` methods of the :class:`mne.decoding.CSP` and :class:`mne.decoding.SPoC` classes, by `Thomas Binns`_.

doc/changes/devel/12830.newfeature.rst

@@ -0,0 +1 @@
+:func:`mne.channels.read_custom_montage` may now read a newer version of the ``.elc`` ASA Electrode file format, by `Stefan Appelhoff`_.

doc/changes/devel/12834.dependency.rst

@@ -0,0 +1,2 @@
+Importing from ``mne.decoding`` now explicitly requires ``scikit-learn`` to be installed,
+by `Eric Larson`_.

doc/changes/devel/12842.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :meth:`mne.Epochs.compute_tfr` could not be used with the multitaper method and complex or phase outputs, by `Thomas Binns`_.

doc/changes/devel/12843.bugfix.rst

@@ -0,0 +1,3 @@
+Fixed a bug where split FIF files that were read and then appended to other
+:class:`mne.io.Raw` instances had their ``BAD boundary`` annotations incorrectly offset
+in samples by the number of split files, by `Eric Larson`_.

doc/changes/devel/12843.other.rst

@@ -0,0 +1 @@
+Improve handling of filenames in ``raw.filenames`` by using :class:`~pathlib.Path` instead of :class:`str`, by `Mathieu Scheltienne`_.

doc/changes/devel/12844.other.rst

@@ -0,0 +1 @@
+Improve automatic figure scaling of :func:`mne.viz.plot_events`, and event_id and count overview legend when a high amount of unique events is supplied, by `Stefan Appelhoff`_.

doc/changes/devel/12846.bugfix.rst

@@ -0,0 +1,2 @@
+Enforce SI units for Eyetracking data (eyegaze data should be radians of visual angle, not pixels. Pupil size data should be meters).
+Updated tutorials so demonstrate how to convert data to SI units before analyses, by `Scott Huberty`_.

doc/changes/devel/12853.bugfix.rst

@@ -0,0 +1 @@
+Prevent the ``colorbar`` parameter being ignored in topomap plots such as :meth:`mne.time_frequency.Spectrum.plot_topomap`, by `Thomas Binns`_.

doc/changes/devel/12862.other.rst

@@ -0,0 +1 @@
+:meth:`mne.preprocessing.ICA.find_bads_muscle` can now be run when passing an ``inst`` without sensor positions. However, it will just use the first of three criteria (slope) to find muscle-related ICA components, by `Stefan Appelhoff`_.

doc/changes/devel/12871.newfeature.rst

@@ -0,0 +1,2 @@
+Added the ``title`` argument to :func:`mne.viz.create_3d_figure`, and
+``color`` and ``position`` arguments to :func:`mne.viz.set_3d_title`, by `Eric Larson`_.