Merge remote-tracking branch 'upstream/main' into kernel

* upstream/main: (37 commits)
  Use constrained layout in matplotlib visualization (mne-tools#12050)
  Add raw stc (mne-tools#12001)
  [MRG] update codeowners (mne-tools#12089)
  DOC: Morlet wavelet length in tfr_morlet (mne-tools#12073)
  BUG: Fix bug with mne browser backend (mne-tools#12078)
  Cache avatars (mne-tools#12077)
  BUG: Fix bug with ch_name resolution (mne-tools#12086)
  add unicode roundtrip for FIF (mne-tools#12080)
  add Ivan to names.inc (mne-tools#12081)
  MAINT: Work around PySide 6.5.3 event loop error (mne-tools#12076)
  mne-tools#11608, buggfix and docstring update (mne-tools#12066)
  MAINT: Fix broken examples (mne-tools#12074)
  Add UI Event linking to DraggableColorbar (mne-tools#12057)
  handle lazy loading through .pyi type stubs (mne-tools#12072)
  BUG: Fix bug with sensor_colors (mne-tools#12068)
  clean  up some deprecations (mne-tools#12067)
  Allow not dropping bads when creating or plotting Spectrum objs (mne-tools#12006)
  Collapsible html repr for raw/info (mne-tools#12064)
  BUG: Fix bug with pickling MNEBadsList (mne-tools#12063)
  add details for Denis (mne-tools#12065)
  ...

Author: larsoner

.github/CODEOWNERS

@@ -24,7 +24,7 @@
 #################################################
 
 # Artifact regression
-/mne/preprocessing/_regress.py @wmvanvliet @cbrnr
+/mne/preprocessing/_regress.py @wmvanvliet
 /mne/preprocessing/tests/test_regress.py @wmvanvliet
 
 # Beamforming
@@ -33,25 +33,26 @@
 *lcmv*.py @britta-wstnr
 
 # Channels
-/mne/channels @cbrnr @agramfort @mscheltienne
+/mne/channels @agramfort @mscheltienne @dengemann @jasmainak
 
 # Core sensor-space classes
-/mne/epochs.py @drammock @agramfort @mscheltienne
-/mne/evoked.py @drammock @agramfort @mscheltienne
-/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne
+/mne/epochs.py @drammock @agramfort @mscheltienne @dengemann
+/mne/evoked.py @drammock @agramfort @mscheltienne @dengemann
+/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne @dengemann
 
 # Current-source density
-/mne/preprocessing/_csd.py  @alexrockhill
+/mne/preprocessing/_csd.py  @alexrockhill @dengemann
 
 # Decoding
-/mne/decoding/csp.py @cbrnr @agramfort
+/mne/decoding/csp.py @cbrnr @agramfort @dengemann
+/mne/decoding/*.py @jasmainak
 
 # fNIRS
 /mne/preprocessing/nirs @rob-luke
 *fnirs*.py @rob-luke
 
 # forward
-/mne/forward/ @agramfort
+/mne/forward/ @agramfort @jasmainak
 *forward*.py @agramfort
 
 # Intracranial
@@ -69,19 +70,21 @@
 /mne/io/nirx @rob-luke
 /mne/io/snirf @rob-luke
 /mne/export @sappelhoff @cbrnr
+/mne/io/eeglab.py @jasmainak
+/mne/io/eeglab/tests/test_eeglab.py @jasmainak
 
 # Minimum Norm
 /mne/minimum_norm @agramfort
 
 # Preprocessing
-/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne
-/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne
+/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne @dengemann
+/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne @dengemann
 /mne/preprocessing/*annotate*.py @mscheltienne
 /mne/preprocessing/bads.py @mscheltienne
 /mne/preprocessing/e*g.py @mscheltienne
 
 # Report
-/mne/report @hoechenberger
+/mne/report @hoechenberger @dengemann @jasmainak
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -93,25 +96,28 @@
 /mne/_freesurfer.py @alexrockhill @larsoner
 
 # TFR
-/mne/time_frequency @drammock @cbrnr @adam2392 @mscheltienne
+/mne/time_frequency @drammock @adam2392 @mscheltienne
 
 # Viz
-/mne/viz @drammock @cbrnr
+/mne/viz @drammock @dengemann
 /mne/viz/_brain @larsoner @wmvanvliet
 /mne/viz/ui_events.py @wmvanvliet
-/tutorials/visualization @larsoner @wmvanvliet
-/examples/visualization @larsoner
+/tutorials/visualization @larsoner @wmvanvliet @dengemann
+/examples/visualization @larsoner @dengemann
+
+# Datasets
+/mne/datasets/brainstorm @jasmainak
 
 #########################
 # Project-level / other #
 #########################
 
 # Examples and tutorials
-/examples @drammock @agramfort
-/tutorials @drammock @agramfort
+/examples @drammock @agramfort @dengemann
+/tutorials @drammock @agramfort @dengemann
 
 # Non-tutorial documentation text and infrastructure
-/doc @larsoner @drammock @agramfort
+/doc @larsoner @drammock @agramfort @dengemann
 /logo @drammock
 
 # Installation documentation
@@ -120,5 +126,5 @@
 # Project infrastructure and CIs
 /*.* @larsoner @drammock  # files in the root directory
 /.circleci @larsoner
-/.github @larsoner @cbrnr
+/.github @larsoner
 /tools @larsoner @drammock

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'

.pre-commit-config.yaml

@@ -7,15 +7,15 @@ repos:
 
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.0.292
     hooks:
       - id: ruff
         name: ruff mne
         files: ^mne/
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.0.292
     hooks:
       - id: ruff
         name: ruff tutorials and examples
@@ -26,7 +26,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         additional_dependencies:

MANIFEST.in

@@ -15,6 +15,7 @@ recursive-include tutorials *.py
 recursive-include tutorials *.txt
 
 recursive-include mne *.py
+recursive-include mne *.pyi
 recursive-include mne/data *
 recursive-include mne/icons *
 recursive-include mne/data/helmets *

Makefile

@@ -33,8 +33,6 @@ sample_data:
 testing_data:
 	@python -c "import mne; mne.datasets.testing.data_path(verbose=True);"
 
-pytest: test
-
 test-no-network: in
 	sudo unshare -n -- sh -c 'MNE_SKIP_NETWORK_TESTS=1 py.test mne'
 

README.rst

@@ -96,7 +96,7 @@ The minimum required dependencies to run MNE-Python are:
 - Python >= 3.8
 - NumPy >= 1.21.2
 - SciPy >= 1.7.1
-- Matplotlib >= 3.4.3
+- Matplotlib >= 3.5.0
 - pooch >= 1.5
 - tqdm
 - Jinja2

doc/overview/images/flow_diagram.svg renamed to doc/_static/flow_diagram.svg

@@ -47,7 +47,7 @@ async function putAvatarsInPage() {
     }
     // finish
     outer.append(title, inner);
-    document.getElementById("institution-logos").after(outer);
+    document.body.append(outer);
 }
 
 putAvatarsInPage();

doc/_static/js/contrib-avatars.js

@@ -0,0 +1,32 @@
+/* inspired by https://tobiasahlin.com/blog/move-from-jquery-to-vanilla-javascript/ */
+
+function documentReady(callback) {
+    if (document.readyState != "loading") callback();
+    else document.addEventListener("DOMContentLoaded", callback);
+}
+
+function setTabs() {
+    var platform = "linux";
+    if (navigator.userAgent.indexOf("Win") !== -1) {
+        platform = "windows";
+    }
+    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";
+    }
+    let all_tab_nodes = document.querySelectorAll(
+        '.platform-selector-tabset')[0].children;
+    let input_nodes = [...all_tab_nodes].filter(
+        child => child.nodeName === "INPUT");
+    let tab_label_nodes = [...document.querySelectorAll('.sd-tab-label')];
+    let correct_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;
+}
+
+documentReady(setTabs);

doc/_static/js/set_installer_tab.js

@@ -0,0 +1,61 @@
+/* inspired by https://tobiasahlin.com/blog/move-from-jquery-to-vanilla-javascript/ */
+
+function documentReady(callback) {
+    if (document.readyState != "loading") callback();
+    else document.addEventListener("DOMContentLoaded", callback);
+}
+
+async function getRelease() {
+    result = await fetch("https://api.github.com/repos/mne-tools/mne-installers/releases/latest");
+    data = await result.json();
+    return data;
+}
+async function warnVersion() {
+    data = await getRelease();
+    // Take v1.5.1 for example and change to 1.5
+    ids = ["linux-installers", "macos-intel-installers", "macos-apple-installers", "windows-installers"];
+    warn = false;
+    ids.forEach((id) => {
+        label_id = document.getElementById(id);
+        // tab is immediately after label
+        children = [].slice.call(label_id.parentNode.children);
+        div = children[children.indexOf(label_id) + 1];
+        a = div.children[0].children[0];  // div->p->a
+        ending = a.href.split("-").slice(-1)[0];  // Should be one of: ["macOS_Intel.pkg", "macOS_M1.pkg", "Linux.sh", "Windows.exe"]
+        data["assets"].every((asset) => {
+            // find the matching asset
+            if (!asset["browser_download_url"].endsWith(ending)) {
+                return true;  // continue
+            }
+            old_stem = a.href.split("/").slice(-1)[0];
+            new_stem = asset["browser_download_url"].split("/").slice(-1)[0];
+            a.href = asset["browser_download_url"];
+            // also replace the command on Linux
+            if (ending === "Linux.sh") {
+                code = document.getElementById("codecell0");
+            }
+            if (!warn) {
+                // MNE-Python-1.5.1_0-Linux.sh to 1.5 for example
+                old_ver = old_stem.split("-").slice(2)[0].split("_")[0].split(".").slice(0, 2).join(".");
+                new_ver = new_stem.split("-").slice(2)[0].split("_")[0].split(".").slice(0, 2).join(".");
+                if (old_ver !== new_ver) {
+                    warn = `The installers below are for version ${new_ver} as ${old_ver} is no longer supported`;
+                }
+            }
+            return false;  // do not continue
+        });
+    });
+    if (warn) {
+        let outer = document.createElement("div");
+        let title = document.createElement("p");
+        let inner = document.createElement("p");
+        outer.setAttribute("class", "admonition warning");
+        title.setAttribute("class", "admonition-title");
+        title.innerText = "Warning";
+        inner.innerText = warn;
+        outer.append(title, inner);
+        document.querySelectorAll('.platform-selector-tabset')[0].before(outer);
+    }
+}
+
+documentReady(warnVersion);

doc/_static/js/update_installer_version.js

@@ -41,4 +41,6 @@
       </div>
     {% endfor %}
   </div>
+<!-- contributors -->
+{% include 'avatars.html' %}
 </div>

doc/_templates/homepage.html

@@ -17,7 +17,4 @@
 {%- block scripts_end %}
     {{ super() }}
     <script src="https://mne.tools/versionwarning.js"></script>
-    {% if pagename == 'index' %}
-      <script src="{{ pathto('_static/js/contrib-avatars.js', 1) }}"></script>
-    {% endif %}
 {%- endblock %}

doc/_templates/layout.html

@@ -23,23 +23,30 @@ Version 1.6.dev0 (development)
 
 Enhancements
 ~~~~~~~~~~~~
-- Improve tests for saving splits with `Epochs` (:gh:`11884` by `Dmitrii Altukhov`_)
+- Improve tests for saving splits with :class:`mne.Epochs` (:gh:`11884` by `Dmitrii Altukhov`_)
 - Added functionality for linking interactive figures together, such that changing one figure will affect another, see :ref:`tut-ui-events` and :mod:`mne.viz.ui_events`. Current figures implementing UI events are :func:`mne.viz.plot_topomap` and :func:`mne.viz.plot_source_estimates` (:gh:`11685` :gh:`11891` by `Marijn van Vliet`_)
 - HTML anchors for :class:`mne.Report` now reflect the ``section-title`` of the report items rather than using a global incrementor ``global-N`` (:gh:`11890` by `Eric Larson`_)
 - Added public :func:`mne.io.write_info` to complement :func:`mne.io.read_info` (:gh:`11918` by `Eric Larson`_)
 - Added option ``remove_dc`` to to :meth:`Raw.compute_psd() <mne.io.Raw.compute_psd>`, :meth:`Epochs.compute_psd() <mne.Epochs.compute_psd>`, and :meth:`Evoked.compute_psd() <mne.Evoked.compute_psd>`, to allow skipping DC removal when computing Welch or multitaper spectra (:gh:`11769` by `Nikolai Chapochnikov`_)
 - Add the possibility to provide a float between 0 and 1 as ``n_grad``, ``n_mag`` and ``n_eeg`` in `~mne.compute_proj_raw`, `~mne.compute_proj_epochs` and `~mne.compute_proj_evoked` to select the number of vectors based on the cumulative explained variance (:gh:`11919` by `Mathieu Scheltienne`_)
+- Add extracting all time courses in a label using :func:`mne.extract_label_time_course` without applying an aggregation function (like ``mean``) (:gh:`12001` by `Hamza Abdelhedi`_)
 - Added support for Artinis fNIRS data files to :func:`mne.io.read_raw_snirf` (:gh:`11926` by `Robert Luke`_)
 - Add helpful error messages when using methods on empty :class:`mne.Epochs`-objects (:gh:`11306` by `Martin Schulz`_)
+- Add support for passing a :class:`python:dict` as ``sensor_color`` to specify per-channel-type colors in :func:`mne.viz.plot_alignment` (:gh:`12067` by `Eric Larson`_)
 - Add inferring EEGLAB files' montage unit automatically based on estimated head radius using :func:`read_raw_eeglab(..., montage_units="auto") <mne.io.read_raw_eeglab>` (:gh:`11925` by `Jack Zhang`_, :gh:`11951` by `Eric Larson`_)
 - Add :class:`~mne.time_frequency.EpochsSpectrumArray` and :class:`~mne.time_frequency.SpectrumArray` to support creating power spectra from :class:`NumPy array <numpy.ndarray>` data (:gh:`11803` by `Alex Rockhill`_)
+- Add support for writing forward solutions to HDF5 and convenience function :meth:`mne.Forward.save` (:gh:`12036` by `Eric Larson`_)
 - Refactored internals of :func:`mne.read_annotations` (:gh:`11964` by `Paul Roujansky`_)
+- By default MNE-Python creates matplotlib figures with ``layout='constrained'`` rather than the default ``layout='tight'`` (:gh:`12050` by `Mathieu Scheltienne`_ and `Eric Larson`_)
 - Enhance :func:`~mne.viz.plot_evoked_field` with a GUI that has controls for time, colormap, and contour lines (:gh:`11942` by `Marijn van Vliet`_)
+- Add :class:`mne.viz.ui_events.UIEvent` linking for interactive colorbars, allowing users to link figures and change the colormap and limits interactively. This supports :func:`~mne.viz.plot_evoked_topomap`, :func:`~mne.viz.plot_ica_components`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_projs_topomap`, :meth:`~mne.Evoked.plot_image`, and :meth:`~mne.Epochs.plot_image` (:gh:`12057` by `Santeri Ruuskanen`_)
 
 Bugs
 ~~~~
 - Fix bugs with :func:`mne.preprocessing.realign_raw` where the start of ``other`` was incorrectly cropped; and onsets and durations in ``other.annotations`` were left unsynced with the resampled data (:gh:`11950` by :newcontrib:`Qian Chu`)
 - Fix bug where ``encoding`` argument was ignored when reading annotations from an EDF file (:gh:`11958` by :newcontrib:`Andrew Gilbert`)
+- Mark tests ``test_adjacency_matches_ft`` and ``test_fetch_uncompressed_file`` as network tests (:gh:`12041` by :newcontrib:`Maksym Balatsko`)
+- Fix bug with :func:`mne.channels.read_ch_adjacency` (:gh:`11608` by :newcontrib:`Ivan Zubarev`)
 - Fix bugs with saving splits for :class:`~mne.Epochs` (:gh:`11876` by `Dmitrii Altukhov`_)
 - Fix bug with multi-plot 3D rendering where only one plot was updated (:gh:`11896` by `Eric Larson`_)
 - Fix bug where subject birthdays were not correctly read by :func:`mne.io.read_raw_snirf` (:gh:`11912` by `Eric Larson`_)
@@ -53,10 +60,16 @@ Bugs
 - Fix bug with :meth:`~mne.viz.Brain.add_annotation` when reading an annotation from a file with both hemispheres shown (:gh:`11946` by `Marijn van Vliet`_)
 - Fix bug with axis clip box boundaries in :func:`mne.viz.plot_evoked_topo` and related functions (:gh:`11999` by `Eric Larson`_)
 - Fix bug with ``subject_info`` when loading data from and exporting to EDF file (:gh:`11952` by `Paul Roujansky`_)
-- Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` :gh:`12017` by `Paul Roujansky`_)
+- Fix bug with delayed checking of :class:`info["bads"] <mne.Info>` (:gh:`12038` by `Eric Larson`_)
+- Fix bug with :func:`mne.viz.plot_alignment` where ``sensor_colors`` were not handled properly on a per-channel-type basis (:gh:`12067` by `Eric Larson`_)
+- Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` :gh:`12017` :gh:`12044` by `Paul Roujansky`_)
 - Add missing ``overwrite`` and ``verbose`` parameters to :meth:`Transform.save() <mne.transforms.Transform.save>` (:gh:`12004` by `Marijn van Vliet`_)
+- Fix parsing of eye-link :class:`~mne.Annotations` when ``apply_offsets=False`` is provided to :func:`~mne.io.read_raw_eyelink` (:gh:`12003` by `Mathieu Scheltienne`_)
 - Correctly prune channel-specific :class:`~mne.Annotations` when creating :class:`~mne.Epochs` without the channel(s) included in the channel specific annotations (:gh:`12010` by `Mathieu Scheltienne`_)
+- Fix :func:`~mne.viz.plot_volume_source_estimates` with :class:`~mne.VolSourceEstimate` which include a list of vertices (:gh:`12025` by `Mathieu Scheltienne`_)
+- Add support for non-ASCII characters in Annotations, Evoked comments, etc when saving to FIFF format (:gh:`12080` by `Daniel McCloy`_)
 - Correctly handle passing ``"eyegaze"`` or ``"pupil"`` to :meth:`mne.io.Raw.pick` (:gh:`12019` by `Scott Huberty`_)
+- Fix bug with :func:`~mne.viz.plot_raw` where changing ``MNE_BROWSER_BACKEND`` via :func:`~mne.set_config` would have no effect within a Python session (:gh:`12078` by `Santeri Ruuskanen`_)
 
 API changes
 ~~~~~~~~~~~

doc/connectivity.rst renamed to doc/api/connectivity.rst

@@ -184,6 +184,8 @@
 
 .. _George O'Neill: https://georgeoneill.github.io
 
+.. _Gonzalo Reina: https://greina.me/
+
 .. _Guillaume Dumas: https://mila.quebec/en/person/guillaume-dumas
 
 .. _Guillaume Favelier: https://github.com/GuillaumeFavelier
@@ -210,6 +212,8 @@
 
 .. _Ilias Machairas: https://github.com/JungleHippo
 
+.. _Ivan Zubarev: https://github.com/zubara
+
 .. _Ivana Kojcic: https://github.com/ikojcic
 
 .. _Jaakko Leppakangas: https://github.com/jaeilepp
@@ -320,6 +324,8 @@
 
 .. _Mainak Jas: https://jasmainak.github.io
 
+.. _Maksym Balatsko: https://github.com/mbalatsko
+
 .. _Marcin Koculak: https://github.com/mkoculak
 
 .. _Marian Dovgialo: https://github.com/mdovgialo