Merge remote-tracking branch 'upstream/main' into cola5

* upstream/main: (24 commits)
  Allow int-like as ID of make_fixed_length_events (mne-tools#11748)
  Easycap-M43 montage (mne-tools#11744)
  ENH: Create a Calibrations class for eyetracking data (mne-tools#11719)
  Fix alphabetical order in overview/people.rst, fix sphinx formatting in docstrings and set verbose to keyword-only (mne-tools#11745)
  Add Mathieu Scheltienne to MNE-Python Steering Council (mne-tools#11741)
  removed requirement for curv.*h files to create Brain object (mne-tools#11704)
  [BUG] Fix mne.viz.Brain.add_volume_labels matrix ordering bug (mne-tools#11730)
  Fix installer links (mne-tools#11729)
  MAINT: Update for PyVista deprecation (mne-tools#11727)
  MAINT: Update roadmap (mne-tools#11724)
  MAINT: Update download link [skip azp] [skip cirrus] [skip actions]
  fix case for chpi_info[1] == None (mne-tools#11714)
  Add cmap argument for mne.viz.utils.plot_sensors (mne-tools#11720)
  BUG: Fix one more PySide6 bug (mne-tools#11723)
  MAINT: Fix PySide6 and PyVista compat (mne-tools#11721)
  MRG: If _check_fname() cannot find a file, display the path in quotation marks to help spot accidental trailing spaces (mne-tools#11718)
  Add "array-like" to `_validate_type()` (mne-tools#11713)
  MAINT: Avoid problematic PySide6 (mne-tools#11715)
  Fix installer links (mne-tools#11709)
  Updating change log after PR mne-tools#11575 (mne-tools#11707)
  ...

azure-pipelines.yml

@@ -80,7 +80,7 @@ stages:
   jobs:
   - job: Ultraslow_PG
     pool:
-      vmImage: 'ubuntu-20.04'
+      vmImage: 'ubuntu-22.04'
     variables:
       DISPLAY: ':99'
       OPENBLAS_NUM_THREADS: '1'
@@ -107,7 +107,7 @@ stages:
     - bash: |
         set -e
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
-        python -m pip install --progress-bar off mne-qt-browser[opengl] pyvista scikit-learn pytest-error-for-skips python-picard "PySide6!=6.3.0,!=6.4.0,!=6.4.0.1,!=6.5.0" qtpy
+        python -m pip install --progress-bar off mne-qt-browser[opengl] pyvista scikit-learn pytest-error-for-skips python-picard "PySide6!=6.5.1" qtpy
         python -m pip uninstall -yq mne
         python -m pip install --progress-bar off --upgrade -e .[test]
       displayName: 'Install dependencies with pip'
@@ -149,7 +149,7 @@ stages:
 
   - job: Qt
     pool:
-      vmImage: 'ubuntu-20.04'
+      vmImage: 'ubuntu-22.04'
     variables:
       DISPLAY: ':99'
       OPENBLAS_NUM_THREADS: '1'
@@ -196,6 +196,8 @@ stages:
     - bash: |
         set -e
         python -m pip install PyQt6
+        # Uncomment if "xcb not found" Qt errors/segfaults come up again
+        # 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()"
         mne sys_info -pd
         mne sys_info -pd | grep "qtpy .* (PyQt6=.*)$"
         pytest -m "not slowtest" ${TEST_OPTIONS}

doc/_includes/institutional-partners.rst

@@ -19,6 +19,7 @@ Current partners
 - `Children’s Hospital of Philadelphia Research Institute <https://www.research.chop.edu/imaging/>`_
 - `Donders Institute for Brain, Cognition and Behaviour at Radboud University <https://www.ru.nl/donders/>`_
 - `Harvard Medical School <https://hms.harvard.edu/>`_
+- `Human Neuroscience Platform at Fondation Campus Biotech Geneva <https://hnp.fcbg.ch/>`_
 - `Institut national de recherche en informatique et en automatique <https://www.inria.fr/>`_
 - `Karl-Franzens-Universität Graz <https://www.uni-graz.at/>`_
 - `Massachusetts General Hospital <https://www.massgeneral.org/>`_

doc/changes/latest.inc

@@ -23,13 +23,24 @@ Current (1.5.dev0)
 
 Enhancements
 ~~~~~~~~~~~~
-- None yet
+- Add ``cmap`` argument for the :func:`mne.viz.plot_sensors` (:gh:`11720` by :newcontrib:`Gennadiy Belonosov`)
+- When failing to locate a file, we now print the full path in quotation marks to help spot accidentally added trailing spaces (:gh:`11718` by `Richard Höchenberger`_)
+- Add standard montage lookup table for ``easycap-M43`` (:gh:`11744` by :newcontrib:`Diptyajit Das`)
+- Added :class:`mne.preprocessing.eyetracking.Calibration` to store eye-tracking calibration info, and :func:`mne.preprocessing.eyetracking.read_eyelink_calibration` to read calibration data from EyeLink systems (:gh:`11719` by `Scott Huberty`_)
 
 Bugs
 ~~~~
+- Fix bug that required curv.*h files to create Brain object (:gh:`11704` by :newcontrib:`Aaron Earle-Richardson`)
+- Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`)
+- Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_)
 - Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_)
-- Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks`(:gh:`11696` by `Mathieu Scheltienne`_)
+- Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
+- Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks (:gh:`11696` by `Mathieu Scheltienne`_)
+- Fix bug with overlapping text for :meth:`mne.Evoked.plot` (:gh:`11698` by `Alex Rockhill`_)
+- For :func:`mne.io.read_raw_eyelink`, the default value of the ``gap_description`` parameter is now ``'BAD_ACQ_SKIP'``, following MNE convention (:gh:`11719` by `Scott Huberty`_)
+- Allow int-like for the argument ``id`` of `~mne.make_fixed_length_events` (:gh:`11748` by `Mathieu Scheltienne`_)
 
 API changes
 ~~~~~~~~~~~
-- None yet
+- The ``baseline`` argument can now be array-like (e.g. ``list``, ``tuple``, ``np.ndarray``, ...) instead of only a ``tuple`` (:gh:`11713` by `Clemens Brunner`_)
+- Deprecated ``gap_description`` keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_)

doc/changes/names.inc

@@ -1,3 +1,5 @@
+.. _Aaron Earle-Richardson: https://github.com/Aaronearlerichardson
+
 .. _Abram Hindle: https://softwareprocess.es
 
 .. _Adam Li: https://github.com/adam2392
@@ -118,6 +120,8 @@
 
 .. _Dinara Issagaliyeva: https://github.com/dissagaliyeva
 
+.. _Diptyajit Das: https://github.com/dasdiptyajit
+
 .. _Dirk Gütlin: https://github.com/DiGyt
 
 .. _Dmitrii Altukhov: https://github.com/dmalt
@@ -170,6 +174,8 @@
 
 .. _Fu-Te Wong: https://github.com/zuxfoucault
 
+.. _Gennadiy Belonosov: https://github.com/Genuster
+
 .. _Geoff Brookshire: https://github.com/gbrookshire
 
 .. _George O'Neill: https://georgeoneill.github.io
@@ -256,6 +262,8 @@
 
 .. _Joshua Bear: https://github.com/joshbear
 
+.. _Joshua Calder-Travis: https://github.com/jCalderTravis
+
 .. _Joshua Teves: https://github.com/jbteves
 
 .. _Judy D Zhu: https://github.com/JD-Zhu

doc/conf.py

@@ -398,6 +398,7 @@
     r"\.fromkeys",
     r"\.items",
     r"\.keys",
+    r"\.move_to_end",
     r"\.pop",
     r"\.popitem",
     r"\.setdefault",
@@ -735,6 +736,7 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
     ("py:class", "(k, v), remove and return some (key, value) pair as a"),
     ("py:class", "_FuncT"),  # type hint used in @verbose decorator
     ("py:class", "mne.utils._logging._FuncT"),
+    ("py:class", "None.  Remove all items from od."),
 ]
 nitpick_ignore_regex = [
     ("py:.*", r"mne\.io\.BaseRaw.*"),
@@ -1125,6 +1127,12 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
             url="https://www.ru.nl/donders/",
             size=xl,
         ),
+        dict(
+            name="Human Neuroscience Platforn at Fondation Campus Biotech Geneva",  # noqa E501
+            img="FCBG.svg",
+            url="https://hnp.fcbg.ch/",
+            size=sm,
+        ),
     ],
     # \u00AD is an optional hyphen (not rendered unless needed)
     # If these are changed, the Makefile should be updated, too

doc/file_io.rst

@@ -61,4 +61,4 @@ Base class:
    :toctree: generated
    :template: autosummary/class_no_members.rst
 
-   BaseEpochs
+   BaseEpochs