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

.github/CODEOWNERS

@@ -33,18 +33,18 @@
 *lcmv*.py @britta-wstnr
 
 # Channels
-/mne/channels @agramfort @mscheltienne
+/mne/channels @agramfort @mscheltienne @dengemann
 
 # 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
 
 # fNIRS
 /mne/preprocessing/nirs @rob-luke
@@ -74,14 +74,14 @@
 /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
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -96,22 +96,22 @@
 /mne/time_frequency @drammock @adam2392 @mscheltienne
 
 # Viz
-/mne/viz @drammock
+/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
 
 #########################
 # 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

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 *

doc/_static/js/contrib-avatars.js

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

doc/_templates/homepage.html

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

doc/_templates/layout.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/changes/devel.rst

@@ -23,25 +23,28 @@ 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`_)
 - 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`_)
 - 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`_)
@@ -56,12 +59,15 @@ Bugs
 - 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 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/changes/names.inc

@@ -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

doc/conf.py

@@ -103,6 +103,7 @@
     "sphinxcontrib.bibtex",
     "sphinxcontrib.youtube",
     # homegrown
+    "contrib_avatars",
     "gen_commands",
     "gen_names",
     "gh_substitutions",
@@ -200,7 +201,7 @@
     "path-like": ":term:`path-like`",
     "array-like": ":term:`array_like <numpy:array_like>`",
     "Path": ":class:`python:pathlib.Path`",
-    "bool": ":class:`python:bool`",
+    "bool": ":ref:`bool <python:typebool>`",
     # Matplotlib
     "colormap": ":ref:`colormap <matplotlib:colormaps>`",
     "color": ":doc:`color <matplotlib:api/colors_api>`",
@@ -1621,6 +1622,7 @@ def reset_warnings(gallery_conf, fname):
 co = "connectivity"
 mne_conn = "https://mne.tools/mne-connectivity/stable"
 tu = "auto_tutorials"
+pr = "preprocessing"
 di = "discussions"
 sm = "source-modeling"
 fw = "forward"
@@ -1666,7 +1668,7 @@ def reset_warnings(gallery_conf, fname):
     f"{tu}/{sd}/plot_phantom_4DBTi.html": f"{tu}/{nv}/90_phantom_4DBTi.html",
     f"{tu}/{sd}/plot_brainstorm_auditory.html": f"{tu}/io/60_ctf_bst_auditory.html",
     f"{tu}/{sd}/plot_sleep.html": f"{tu}/clinical/60_sleep.html",
-    f"{tu}/{di}/plot_background_filtering.html": f"{tu}/preprocessing/25_background_filtering.html",  # noqa E501
+    f"{tu}/{di}/plot_background_filtering.html": f"{tu}/{pr}/25_background_filtering.html",  # noqa E501
     f"{tu}/{di}/plot_background_statistics.html": f"{tu}/{sn}/10_background_stats.html",
     f"{tu}/{sn}/plot_stats_cluster_erp.html": f"{tu}/{sn}/20_erp_stats.html",
     f"{tu}/{sn}/plot_stats_cluster_1samp_test_time_frequency.html": f"{tu}/{sn}/40_cluster_1samp_time_freq.html",  # noqa E501
@@ -1681,7 +1683,7 @@ def reset_warnings(gallery_conf, fname):
     f"{tu}/{si}/plot_creating_data_structures.html": f"{tu}/{si}/10_array_objs.html",
     f"{tu}/{si}/plot_point_spread.html": f"{tu}/{si}/70_point_spread.html",
     f"{tu}/{si}/plot_dics.html": f"{tu}/{si}/80_dics.html",
-    f"{tu}/{tf}/plot_eyetracking.html": f"{tu}/preprocessing/90_eyetracking_data.html",
+    f"{tu}/{tf}/plot_eyetracking.html": f"{tu}/{pr}/90_eyetracking_data.html",
     f"{ex}/{co}/mne_inverse_label_connectivity.html": f"{mne_conn}/{ex}/mne_inverse_label_connectivity.html",  # noqa E501
     f"{ex}/{co}/cwt_sensor_connectivity.html": f"{mne_conn}/{ex}/cwt_sensor_connectivity.html",  # noqa E501
     f"{ex}/{co}/mixed_source_space_connectivity.html": f"{mne_conn}/{ex}/mixed_source_space_connectivity.html",  # noqa E501
@@ -1692,6 +1694,7 @@ def reset_warnings(gallery_conf, fname):
     f"{ex}/{co}/mne_inverse_psi_visual.html": f"{mne_conn}/{ex}/mne_inverse_psi_visual.html",  # noqa E501
     f"{ex}/{co}/sensor_connectivity.html": f"{mne_conn}/{ex}/sensor_connectivity.html",
     f"{ex}/{vi}/publication_figure.html": f"{tu}/{vi}/10_publication_figure.html",
+    f"{ex}/{vi}/sensor_noise_level.html": f"{tu}/{pr}/50_artifact_correction_ssp.html",
 }
 
 

doc/sphinxext/_avatar_template.html

@@ -0,0 +1,7 @@
+<html>
+    <head>
+        <script src="../_static/js/contrib-avatars.js"></script>
+    </head>
+    <body>
+    </body>
+</html>

doc/sphinxext/contrib_avatars.py

@@ -0,0 +1,34 @@
+from pathlib import Path
+
+from selenium import webdriver
+from selenium.webdriver.common.by import By
+from selenium.webdriver.support.ui import WebDriverWait
+from selenium.common.exceptions import WebDriverException
+
+
+def generate_contrib_avatars(app, config):
+    """Render a template webpage with avatars generated by JS and a GitHub API call."""
+    root = Path(app.srcdir)
+    infile = root / "sphinxext" / "_avatar_template.html"
+    outfile = root / "_templates" / "avatars.html"
+    try:
+        options = webdriver.ChromeOptions()
+        options.add_argument("--headless=new")
+        driver = webdriver.Chrome(options=options)
+    except WebDriverException:
+        options = webdriver.FirefoxOptions()
+        options.add_argument("--headless=new")
+        driver = webdriver.Firefox(options=options)
+    driver.get(f"file://{infile}")
+    wait = WebDriverWait(driver, 20)
+    wait.until(lambda d: d.find_element(by=By.ID, value="contributor-avatars"))
+    body = driver.find_element(by=By.TAG_NAME, value="body").get_attribute("innerHTML")
+    with open(outfile, "w") as fid:
+        fid.write(body)
+    driver.quit()
+
+
+def setup(app):
+    """Set up the Sphinx app."""
+    app.connect("config-inited", generate_contrib_avatars)
+    return