Merge branch 'main' into jupyterlite-gh-actions

natinew77-creator · web-flow · commit d37a294b97eb · 2026-06-24T18:34:09.000-04:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -21,14 +21,17 @@ _check_skip: &check_skip
       circleci-agent step halt;
     fi
 
+_machine_image: &machine_image
+  image: ubuntu-2604:2026.05.1
+
 jobs:
   build_docs:
     parameters:
       scheduled:
         type: string
         default: "false"
     machine:
-      image: ubuntu-2404:current
+      <<: *machine_image
     # large 4 vCPUs 15GB mem
     # https://discuss.circleci.com/t/changes-to-remote-docker-reporting-pricing/47759
     resource_class: large
@@ -110,7 +113,7 @@ jobs:
       # Load pip cache
       - restore_cache:
           keys:
-            - pip-cache-0
+            - pip-cache-1
       - restore_cache:
           keys:
             - user-install-bin-cache-310
@@ -122,7 +125,7 @@ jobs:
             ./tools/circleci_dependencies.sh
 
       - save_cache:
-          key: pip-cache-0
+          key: pip-cache-1
           paths:
             - ~/.cache/pip
       - save_cache:
@@ -419,7 +422,7 @@ jobs:
         type: string
         default: "false"
     machine:
-      image: ubuntu-2404:current
+      <<: *machine_image
     resource_class: large
     steps:
       - restore_cache:
@@ -439,7 +442,7 @@ jobs:
           command: ./tools/circleci_bash_env.sh
       - restore_cache:
           keys:
-            - pip-cache-0
+            - pip-cache-1
       - run:
           name: Get Python running
           command: |
@@ -460,7 +463,7 @@ jobs:
 
   deploy:
     machine:
-      image: ubuntu-2404:current
+      <<: *machine_image
     steps:
       - attach_workspace:
           at: /tmp/build
diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml
@@ -16,8 +16,6 @@ jobs:
         with:
           persist-credentials: false
       - uses: actions/setup-python@v6
-        with:
-          python-version: '3.12'
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
diff --git a/.github/workflows/credit.yml b/.github/workflows/credit.yml
@@ -21,8 +21,6 @@ jobs:
         with:
           persist-credentials: true
       - uses: actions/setup-python@v6
-        with:
-          python-version: '3.12'
       - run: pip install pygithub -e .
       - run: python tools/dev/update_credit_json.py
       - run: git add -f doc/sphinxext/prs/*.json
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -19,13 +19,11 @@ jobs:
       - uses: actions/checkout@v6.0.3
         with:
           persist-credentials: false
+          fetch-depth: 0
       - uses: actions/setup-python@v6
-        with:
-          python-version: '3.10'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build twine
+          python -m pip install --upgrade pip packaging build twine
       - run: python -m build --sdist --wheel
       - run: twine check --strict dist/*
       - uses: actions/upload-artifact@v7
diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml
@@ -45,7 +45,7 @@ jobs:
         with:
           version: ">=0.9"
           activate-environment: true
-          python-version: 3.12
+          python-version: "3.12"
       - name: Install dependencies
         run: uv pip install -e . packaging requests tomlkit
       - name: Update tracked dependencies
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -182,15 +182,6 @@ stages:
               PYTEST_QT_API=PyQt6 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
               python -m pip uninstall -yq PyQt6 PyQt6-sip PyQt6-Qt6
             displayName: PyQt6
-          # PyQt5 leaves cruft behind, so run it last
-          - bash: |
-              set -eo pipefail
-              python -m pip install PyQt5
-              mne sys_info -pd
-              mne sys_info -pd | grep "qtpy .* (PyQt5=.*)$"
-              PYTEST_QT_API=PyQt5 pytest -m "not ultraslowtest" ${TEST_OPTIONS}
-              python -m pip uninstall -yq PyQt5 PyQt5-sip PyQt5-Qt5
-            displayName: PyQt5
           - bash: bash <(curl -s https://codecov.io/bash)
             displayName: Codecov
             condition: succeededOrFailed()
diff --git a/doc/_static/style.css b/doc/_static/style.css
@@ -401,27 +401,27 @@ p.centered a img.instlogo {
 }
 
 /* ************************************************************ funders page */
-ul.current li {
+ul.currentsponsor li {
     margin-left: calc(var(--mne-sponsor-logo-lg) + 0.5rem);
     text-indent: calc(-1 * var(--mne-sponsor-logo-lg) - 0.5rem);
     padding-bottom: 0.75rem;
 }
-ul.former li {
+ul.formersponsor li {
     margin-left: calc(var(--mne-sponsor-logo-sm) + 1rem);
     text-indent: calc(-1 * var(--mne-sponsor-logo-sm) - 1rem);
     padding-bottom: 0.5rem;
 }
-ul.current li img,
-ul.former li img {
+ul.currentsponsor li img,
+ul.formersponsor li img {
     background-color: unset !important;
     box-sizing: content-box;
     object-fit: contain;
 }
-ul.current li img {
+ul.currentsponsor li img {
     max-height: calc(0.4 * var(--mne-sponsor-logo-lg));
     width: var(--mne-sponsor-logo-lg);
 }
-ul.former li img {
+ul.formersponsor li img {
     max-height: calc(0.5 * var(--mne-sponsor-logo-sm));
     width: var(--mne-sponsor-logo-sm);
 }
diff --git a/doc/_templates/homepage.html b/doc/_templates/homepage.html
@@ -23,15 +23,15 @@
     <!-- current funders -->
     {% for item in current_sponsors -%}
       <div class="card my-1 mx-2 {{ item.klass }}">
-        <a href="{{ pathto('credit/funding.html', 1) }}">
+        <a href="{{ pathto('credits/sponsors.html', 1) }}">
             <img class="card-img" src="{{ pathto('_static/funding/' + item.img, 1) }}" title="{{ item.title }}" alt="{{ item.title }}">
         </a>
       </div>
     {% endfor %}
     <!-- current partner institutions -->
     {% for inst in current_institutions -%}
       <div class="card my-1 mx-2 {{ inst.klass }}">
-        <a href="{{ pathto('credit/funding.html#supporting-institutions', 1) }}">
+        <a href="{{ pathto('credits/sponsors.html#supporting-institutions', 1) }}">
           <img class="card-img" src="{{ pathto('_static/institution_logos/' + inst.img, 1) }}" title="{{ inst.name }}" alt="{{ inst.name }}"/>
         </a>
       </div>
diff --git a/doc/changes/dev/13981.dependency.rst b/doc/changes/dev/13981.dependency.rst
@@ -0,0 +1 @@
+PyQt5 is no longer an officially supported Qt binding, by `Eric Larson`_.
diff --git a/doc/changes/names.inc b/doc/changes/names.inc
@@ -50,7 +50,7 @@
 .. _btkcodedev: https://github.com/btkcodedev
 .. _buildqa: https://github.com/buildqa
 .. _Carina Forster: https://github.com/CarinaFo
-.. _Carlos de la Torre-Ortiz: https://ctorre.me
+.. _Carlos de la Torre-Ortiz: https://github.com/c-torre
 .. _Cathy Nangini: https://github.com/KatiRG
 .. _Chetan Gohil: https://github.com/cgohil8
 .. _Chris Bailey: https://github.com/cjayb
@@ -239,7 +239,7 @@
 .. _Mohammad Daneshzand: https://github.com/mdaneshzand
 .. _Mojackhak: https://github.com/Mojackhak
 .. _Moritz Gerster: https://github.com/moritz-gerster
-.. _Motofumi Fushimi: https://github.com/motofumi-fushimi/motofumi-fushimi.github.io
+.. _Motofumi Fushimi: https://github.com/motofumi-fushimi
 .. _Nabil Alibou: https://github.com/nabilalibou
 .. _Natalie Klein: https://github.com/natalieklein
 .. _Nathalie Gayraud: https://github.com/ngayraud
diff --git a/doc/conf.py b/doc/conf.py
@@ -822,6 +822,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://doi.org/10.1126/",  # www.science.org
     "https://doi.org/10.1137/",  # epubs.siam.org
     "https://doi.org/10.1145/",  # dl.acm.org
+    "https://doi.org/10.5281/",  # zenodo.org
     "https://doi.org/10.1155/",  # www.hindawi.com/journals/cin
     "https://doi.org/10.1161/",  # www.ahajournals.org
     "https://doi.org/10.1162/",  # direct.mit.edu/neco/article/
@@ -832,6 +833,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://doi.org/10.3390/",  # mdpi.com
     "https://hms.harvard.edu/",  # doc/funding.rst
     "https://stackoverflow.com/questions/21752259/python-why-pickle",  # doc/help/faq
+    "https://mitpress.mit.edu/9780262525855",  # works but linkcheck fails to resolve
+    "https://zenodo.org",  # doc/help/faq
     "https://blender.org",
     "https://home.alexk101.dev",
     "https://www.mq.edu.au/",
@@ -876,8 +879,12 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://psychophysiology.cpmc.columbia.edu",
     "https://erc.easme-web.eu",
     "https://www.crnl.fr",
+    # Spurious failure
+    "https://megcore.nih.gov/index.php/Staff",
     # Not rendered by linkcheck builder
     r"ides\.html",
+    # Sponsors not rendered properly by linkcheck builder
+    "{{inst.url}}",
 ]
 linkcheck_anchors = False  # saves a bit of time
 linkcheck_timeout = 15  # some can be quite slow
diff --git a/doc/credits/sponsors.rst b/doc/credits/sponsors.rst
@@ -7,7 +7,7 @@ Sponsors
 
 Maintenance and development of MNE-Python is currently supported by the following funding agencies and partners:
 
-.. rst-class:: list-unstyled current
+.. rst-class:: list-unstyled currentsponsor
 
 - |nih| **National Institutes of Health:**
   `R01-NS104585 <https://reporter.nih.gov/project-details/10175064>`_
@@ -18,7 +18,7 @@ Maintenance and development of MNE-Python is currently supported by the followin
 Past sponsors
 -------------
 
-.. rst-class:: list-unstyled former
+.. rst-class:: list-unstyled formersponsor
 
 - |nih| National Institutes of Health:
   `R01-EB009048 <https://reporter.nih.gov/project-details/9053482>`_,
@@ -56,7 +56,7 @@ Supporting institutions
 
 Some institutions support their employees’ contributions to MNE-Python as part of normal work duties. Current supporting institutions include:
 
-.. rst-class:: list-unstyled current
+.. rst-class:: list-unstyled currentsponsor
 
 {% for inst in current_institutions %}
 {% if not inst.name.endswith("_dk") %}
diff --git a/doc/development/roadmap.rst b/doc/development/roadmap.rst
@@ -273,7 +273,7 @@ Time-frequency visualization
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 We implemented a viewer for interactive visualization of volumetric
 source-time-frequency (5-D) maps on MRI slices (orthogonal 2D viewer).
-`NutmegTrip <https://github.com/fieldtrip/fieldtrip/tree/master/contrib/nutmegtrip>`__
+`NutmegTrip <https://github.com/fieldtrip/fieldtrip/tree/20260408/contrib/nutmegtrip>`__
 (written by Sarang Dalal) provides similar functionality in MATLAB in
 conjunction with FieldTrip. Example of NutmegTrip's source-time-frequency mode
 in action (click for link to YouTube):
diff --git a/doc/install/advanced.rst b/doc/install/advanced.rst
@@ -104,14 +104,14 @@ instructions for installing from a ``git clone`` in the :ref:`contributing`.
 Choosing the Qt framework
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The ``conda-forge`` version of MNE-Python ships with PyQt5. If you would like to
+The ``conda-forge`` version of MNE-Python ships with PySide6. If you would like to
 use a different binding, you can instead install MNE-Python via ``pip``:
 
 .. code-block:: console
 
-    $ pip install "mne[full]"          # uses PyQt6
-    $ pip install "mne[full-pyqt6]"    # same as above
-    $ pip install "mne[full-pyside6]"  # use PySide6
+    $ pip install "mne[full]"          # uses PySide6
+    $ pip install "mne[full-pyside6]"  # same as above
+    $ pip install "mne[full-pyqt6]"    # uses PyQt6
     $ pip install "mne[full-no-qt]"    # don't install any Qt binding
 
 .. _CUDA:
diff --git a/doc/links.inc b/doc/links.inc
@@ -20,7 +20,7 @@
 .. _`MNE-HCP`: http://mne.tools/mne-hcp
 .. _`MNE-Realtime`: https://mne.tools/mne-realtime
 .. _`MNE-LSL`: https://mne.tools/mne-lsl
-.. _`MNE-RT`: https://payamsash.github.io/mne-rt/
+.. _`MNE-RT`: https://mne-rt-org.github.io/mne-rt/
 .. _`MNE-gui-addons`: https://mne.tools/mne-gui-addons
 .. _`MNE-MATLAB`: https://github.com/mne-tools/mne-matlab
 .. _`MNE-Docker`: https://github.com/mne-tools/mne-docker
diff --git a/doc/references.bib b/doc/references.bib
@@ -2375,7 +2375,7 @@ @book{Luck2014
   edition = {2nd},
   publisher = {The MIT Press},
   address = {Cambridge, MA},
-  url = {https://mitpress.mit.edu/books/introduction-event-related-potential-technique-second-edition},
+  url = {https://mitpress.mit.edu/9780262525855/an-introduction-to-the-event-related-potential-technique},
   isbn = {978-0-262-52585-5}
 }
 
diff --git a/doc/sphinxext/mne_doc_utils.py b/doc/sphinxext/mne_doc_utils.py
@@ -4,6 +4,7 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
+import functools
 import gc
 import os
 import time
@@ -17,9 +18,7 @@
 
 import mne
 from mne.utils import (
-    _assert_no_instances as _assert_no_instances_mne,
-)
-from mne.utils import (
+    _assert_no_instances,
     _get_extra_data_path,
     sizeof_fmt,
 )
@@ -123,14 +122,20 @@ def reset_warnings(gallery_conf, fname):
 t0 = time.time()
 
 
-def _assert_no_instances(cls, when):
+def _reraise_extension_error(func):
     """Wrap our internal one but make the traceback nicer when it fails."""
-    try:
-        _assert_no_instances_mne(cls, when)
-    except Exception as exc:
-        raise ExtensionError(str(exc)) from None
+
+    @functools.wraps(func)
+    def _wrapper(gallery_conf, fname, when):
+        try:
+            return func(gallery_conf, fname, when)
+        except Exception:
+            raise ExtensionError(f"{func.__name__} failed: {when=}, {fname=}")
+
+    return _wrapper
 
 
+@_reraise_extension_error
 def reset_modules(gallery_conf, fname, when):
     """Do the reset."""
     import matplotlib.pyplot as plt
diff --git a/examples/visualization/eyetracking_plot_heatmap.py b/examples/visualization/eyetracking_plot_heatmap.py
@@ -82,8 +82,10 @@
 # start at a value greater than the darkest value in our previous heatmap, which will
 # make the darkest colors of the heatmap transparent.
 
-cmap.set_under("k", alpha=0)  # make the lowest values transparent
-ax = plt.subplot()
+cmap = cmap.with_extremes(
+    under=(0.0, 0.0, 0.0, 0.0)
+)  # make the lowest values transparent
+_, ax = plt.subplots(figsize=(6, 3.5), layout="constrained")
 ax.imshow(plt.imread(stim_fpath))
 plot_gaze(
     epochs["natural"],
diff --git a/mne/conftest.py b/mne/conftest.py
@@ -669,10 +669,6 @@ def _check_pyqtgraph(request):
             pytest.skip(f'Test "{f_name}" was skipped for mne-qt-browser < 0.2.0')
     except Exception:
         pytest.skip("Requires mne_qt_browser")
-    else:
-        ver = mne_qt_browser.__version__
-        if api != "PyQt5" and _compare_version(ver, "<=", "0.2.6"):
-            pytest.skip(f"mne_qt_browser {ver} requires PyQt5, API is {api}")
 
 
 @pytest.fixture
diff --git a/mne/viz/backends/_pyvista.py b/mne/viz/backends/_pyvista.py
@@ -968,8 +968,11 @@ def _volume(
         resolution,
         blending,
         center,
-        interpolation,
+        interpolation="linear",
     ):
+        # Note: this method is used by mne-gui-addons, so we should be mindful of
+        # backwards compatibility when changing it.
+
         # Now we can actually construct the visualization
         grid = pyvista.ImageData(
             dimensions=dimensions,
diff --git a/mne/viz/ui_events.py b/mne/viz/ui_events.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/tools/circleci_bash_env.sh b/tools/circleci_bash_env.sh
diff --git a/tools/github_actions_env_vars.sh b/tools/github_actions_env_vars.sh
diff --git a/tools/install_pre_requirements.sh b/tools/install_pre_requirements.sh
diff --git a/tools/setup_xvfb.sh b/tools/setup_xvfb.sh
diff --git a/tutorials/epochs/20_visualize_epochs.py b/tutorials/epochs/20_visualize_epochs.py
diff --git a/tutorials/epochs/60_make_fixed_length_epochs.py b/tutorials/epochs/60_make_fixed_length_epochs.py
diff --git a/tutorials/evoked/10_evoked_overview.py b/tutorials/evoked/10_evoked_overview.py
diff --git a/tutorials/evoked/20_visualize_evoked.py b/tutorials/evoked/20_visualize_evoked.py

Original file line number	Diff line number	Diff line change
`@@ -401,27 +401,27 @@ p.centered a img.instlogo {`
`401`	`401`	`}`
`402`	`402`
`403`	`403`	`/* ************************************************************ funders page */`
`404`		`-ul.current li {`
	`404`	`+ul.currentsponsor li {`
`405`	`405`	`margin-left: calc(var(--mne-sponsor-logo-lg) + 0.5rem);`
`406`	`406`	`text-indent: calc(-1 * var(--mne-sponsor-logo-lg) - 0.5rem);`
`407`	`407`	`padding-bottom: 0.75rem;`
`408`	`408`	`}`
`409`		`-ul.former li {`
	`409`	`+ul.formersponsor li {`
`410`	`410`	`margin-left: calc(var(--mne-sponsor-logo-sm) + 1rem);`
`411`	`411`	`text-indent: calc(-1 * var(--mne-sponsor-logo-sm) - 1rem);`
`412`	`412`	`padding-bottom: 0.5rem;`
`413`	`413`	`}`
`414`		`-ul.current li img,`
`415`		`-ul.former li img {`
	`414`	`+ul.currentsponsor li img,`
	`415`	`+ul.formersponsor li img {`
`416`	`416`	`background-color: unset !important;`
`417`	`417`	`box-sizing: content-box;`
`418`	`418`	`object-fit: contain;`
`419`	`419`	`}`
`420`		`-ul.current li img {`
	`420`	`+ul.currentsponsor li img {`
`421`	`421`	`max-height: calc(0.4 * var(--mne-sponsor-logo-lg));`
`422`	`422`	`width: var(--mne-sponsor-logo-lg);`
`423`	`423`	`}`
`424`		`-ul.former li img {`
	`424`	`+ul.formersponsor li img {`
`425`	`425`	`max-height: calc(0.5 * var(--mne-sponsor-logo-sm));`
`426`	`426`	`width: var(--mne-sponsor-logo-sm);`
`427`	`427`	`}`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+PyQt5 is no longer an officially supported Qt binding, by `Eric Larson`_.