Merge branch 'main' into dev-headsurface

.mailmap

@@ -86,6 +86,7 @@ Eduard Ort <[email protected]> examplename <[email protected]>
 Ellen Lau <[email protected]> ellenlau <[email protected]>
 Emily Stephen <[email protected]> Emily P. Stephen <[email protected]>
 Emily Stephen <[email protected]> emilyps14 <[email protected]>
+Emma Bailey <[email protected]> emma-bailey <[email protected]>
 Enrico Varano <[email protected]> enricovara <[email protected]>
 Enzo Altamiranda <[email protected]> enzo <[email protected]>
 Eric Larson <[email protected]> Eric Larson <[email protected]>
@@ -315,6 +316,7 @@ Sara Sommariva <[email protected]> sarasommariva <[email protected]>
 Sebastien Treguer <[email protected]> DataFox <[email protected]>
 Sena Er <[email protected]> Sena <[email protected]>
 Senwen Deng <[email protected]> Senwen DENG <[email protected]>
+Shristi Baral <[email protected]> Shristi Baral <[email protected]>
 Silvia Cotroneo <[email protected]> sfc-neuro <[email protected]>
 Simon Kern <[email protected]> Simon Kern <[email protected]>
 Simon Kern <[email protected]> skjerns <[email protected]>

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.9.6
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -23,7 +23,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.2.2
+    rev: v1.3.1
     hooks:
       - id: zizmor
 

azure-pipelines.yml

@@ -89,6 +89,7 @@ stages:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
           MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
+          MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
           - bash: |
               set -e

doc/changes/devel/13044.newfeature.rst

@@ -0,0 +1 @@
+Add :meth:`mne.Evoked.interpolate_to` to allow interpolating EEG data to other montages, by :newcontrib:`Antoine Collas`.

doc/changes/devel/13083.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with reading digitization points from digitization strings with newer MEGIN systems, by `Eric Larson`_.

doc/changes/devel/13097.bugfix.rst

@@ -0,0 +1 @@
+Fix bug when loading certain EEGLAB files that do not contain a ``nodatchans`` field, by `Clemens Brunner`_.

doc/changes/devel/13100.bugfix.rst

@@ -0,0 +1 @@
+Do not convert the first "New Segment" marker in a BrainVision file to an annotation, as it only contains the recording date (which is already available in ``info["meas_date"]``), by `Clemens Brunner`_.

doc/changes/devel/13101.bugfix.rst

@@ -0,0 +1 @@
+Take units (m or mm) into account when drawing :func:`~mne.viz.plot_evoked_field` on top of :class:`~mne.viz.Brain`, by `Marijn van Vliet`_.

doc/changes/devel/13107.newfeature.rst

@@ -0,0 +1 @@
+The :meth:`mne.Info.save` method now has an ``overwrite`` and a ``verbose`` parameter, by `Stefan Appelhoff`_.

doc/changes/devel/13113.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :func:`mne.io.read_raw_gdf`, by :newcontrib:`Rongfei Jin`.

doc/changes/names.inc

@@ -24,6 +24,7 @@
 .. _Anna Padee: https://github.com/apadee/
 .. _Annalisa Pascarella: https://www.iac.cnr.it/personale/annalisa-pascarella
 .. _Anne-Sophie Dubarry: https://github.com/annesodub
+.. _Antoine Collas: https://www.antoinecollas.fr
 .. _Antoine Gauthier: https://github.com/Okamille
 .. _Antti Rantala: https://github.com/Odingod
 .. _Apoorva Karekal: https://github.com/apoorva6262
@@ -256,7 +257,8 @@
 .. _Romain Derollepot: https://github.com/rderollepot
 .. _Romain Trachel: https://fr.linkedin.com/in/trachelr
 .. _Roman Goj: https://romanmne.blogspot.co.uk
-.. _Ross Maddox: https://www.urmc.rochester.edu/labs/maddox-lab.aspx
+.. _Rongfei Jin: https://github.com/greasycat
+.. _Ross Maddox: https://medicine.umich.edu/dept/khri/ross-maddox-phd
 .. _Rotem Falach: https://github.com/Falach
 .. _Roy Eric Wieske: https://github.com/Randomidous
 .. _Sammi Chekroud: https://github.com/schekroud

doc/conf.py

@@ -644,6 +644,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
 linkcheck_ignore = [  # will be compiled to regex
     # 403 Client Error: Forbidden
     "https://doi.org/10.1002/",  # onlinelibrary.wiley.com/doi/10.1002/hbm
+    "https://doi.org/10.1016/",  # neuroimage
     "https://doi.org/10.1021/",  # pubs.acs.org/doi/abs
     "https://doi.org/10.1073/",  # pnas.org
     "https://doi.org/10.1093/",  # academic.oup.com/sleep/
@@ -667,10 +668,11 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     r"https://scholar.google.com/scholar\?cites=12188330066413208874&as_ylo=2014",
     r"https://scholar.google.com/scholar\?cites=1521584321377182930&as_ylo=2013",
     "https://www.research.chop.edu/imaging",
-    "http://prdownloads.sourceforge.net/optipng/optipng-0.7.8-win64.zip?download",
+    "http://prdownloads.sourceforge.net/optipng",
     "https://sourceforge.net/projects/aespa/files/",
     "https://sourceforge.net/projects/ezwinports/files/",
     "https://www.mathworks.com/products/compiler/matlab-runtime.html",
+    "https://medicine.umich.edu/dept/khri/ross-maddox-phd",
     # 500 server error
     "https://openwetware.org/wiki/Beauchamp:FreeSurfer",
     # 503 Server error
@@ -694,6 +696,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "http://ilabs.washington.edu",
     "https://psychophysiology.cpmc.columbia.edu",
     "https://erc.easme-web.eu",
+    # Not rendered by linkcheck builder
+    r"ides\.html",
 ]
 linkcheck_anchors = False  # saves a bit of time
 linkcheck_timeout = 15  # some can be quite slow

doc/development/governance.rst

@@ -46,7 +46,9 @@ Governance Model
 Leadership Roles
 ^^^^^^^^^^^^^^^^
 
-The MNE-Python leadership structure shall consist of:
+The MNE-Python leadership structure shall consist of the following groups.
+A list of the current members of the respective groups is maintained at the
+page :ref:`governance-people`.
 
 Maintainer Team
 ---------------

doc/references.bib

@@ -2514,3 +2514,11 @@ @article{OyamaEtAl2015
 	year = {2015},
 	pages = {24--36},
 }
+
+@inproceedings{MellotEtAl2024,
+	title = {Physics-informed and Unsupervised Riemannian Domain Adaptation for Machine Learning on Heterogeneous EEG Datasets},
+	author = {Mellot, Apolline and Collas, Antoine and Chevallier, Sylvain and Engemann, Denis and Gramfort, Alexandre},
+	booktitle = {Proceedings of the 32nd European Signal Processing Conference (EUSIPCO)},
+	year = {2024},
+	address = {Lyon, France}
+}

doc/sphinxext/credit_tools.py

@@ -39,6 +39,16 @@
 
 # Allowed singletons
 single_names = "btkcodedev buildqa sviter Akshay".split()
+# Surnames where we have more than one distinct contributor:
+name_counts = dict(
+    Bailey=2,
+    Das=2,
+    Drew=2,
+    Li=2,
+    Peterson=2,
+    Wong=2,
+    Zhang=2,
+)
 # Exceptions, e.g., abbrevitaions in first/last name or all-caps
 exceptions = [
     "T. Wang",
@@ -217,16 +227,6 @@ def generate_credit_rst(app=None, *, verbose=False):
         )
 
     # Check for duplicate names based on last name, and also singleton names.
-    # Below are surnames where we have more than one distinct contributor:
-    name_counts = dict(
-        Das=2,
-        Drew=2,
-        Li=2,
-        Peterson=2,
-        Wong=2,
-        Zhang=2,
-    )
-    # Below are allowed singleton names
     last_map = defaultdict(lambda: set())
     bad_names = set()
     for these_stats in stats.values():
@@ -245,10 +245,11 @@ def generate_credit_rst(app=None, *, verbose=False):
         if len(names) > name_counts.get(last, 1):
             bad_names.append(f"Duplicates:    {sorted(names)}")
     if bad_names:
-        raise RuntimeError(
-            "Unexpected possible duplicates or bad names found:\n"
-            + "\n".join(bad_names)
+        what = (
+            "Unexpected possible duplicates or bad names found, "
+            f"consider modifying {'/'.join(Path(__file__).parts[-3:])}:\n"
         )
+        raise RuntimeError(what + "\n".join(bad_names))
 
     unknown_emails = set(
         email
@@ -258,9 +259,8 @@ def generate_credit_rst(app=None, *, verbose=False):
         and "dependabot[bot]" not in email
         and "github-actions[bot]" not in email
     )
-    assert len(unknown_emails) == 0, "Unknown emails\n" + "\n".join(
-        sorted(unknown_emails)
-    )
+    what = "Unknown emails, consider adding to .mailmap:\n"
+    assert len(unknown_emails) == 0, what + "\n".join(sorted(unknown_emails))
 
     logger.info("Biggest included commits/PRs:")
     commits = dict(

doc/sphinxext/prs/12071.json

@@ -0,0 +1,67 @@
+{
+  "merge_commit_sha": "aca49655b10fc17679142e07c5d46659be1099da",
+  "authors": [
+    {
+      "n": "Marijn van Vliet",
+      "e": "[email protected]"
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Daniel McCloy",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "doc/changes/devel/12071.newfeature.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/epochs.py": {
+      "a": 2,
+      "d": 0
+    },
+    "mne/evoked.py": {
+      "a": 2,
+      "d": 0
+    },
+    "mne/viz/_figure.py": {
+      "a": 3,
+      "d": 3
+    },
+    "mne/viz/_mpl_figure.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/viz/evoked.py": {
+      "a": 12,
+      "d": 1
+    },
+    "mne/viz/tests/test_raw.py": {
+      "a": 14,
+      "d": 25
+    },
+    "mne/viz/tests/test_topo.py": {
+      "a": 35,
+      "d": 1
+    },
+    "mne/viz/tests/test_utils.py": {
+      "a": 69,
+      "d": 0
+    },
+    "mne/viz/topo.py": {
+      "a": 81,
+      "d": 15
+    },
+    "mne/viz/ui_events.py": {
+      "a": 20,
+      "d": 0
+    },
+    "mne/viz/utils.py": {
+      "a": 108,
+      "d": 63
+    }
+  }
+}

doc/sphinxext/prs/12656.json

@@ -0,0 +1,35 @@
+{
+  "merge_commit_sha": "3c6a054093d305a98757a97398e5e34988a3aced",
+  "authors": [
+    {
+      "n": "Qian Chu",
+      "e": null
+    }
+  ],
+  "changes": {
+    "doc/changes/devel/12656.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/export/_brainvision.py": {
+      "a": 7,
+      "d": 0
+    },
+    "mne/export/_edf.py": {
+      "a": 4,
+      "d": 1
+    },
+    "mne/export/_eeglab.py": {
+      "a": 11,
+      "d": 5
+    },
+    "mne/export/_export.py": {
+      "a": 7,
+      "d": 1
+    },
+    "mne/export/tests/test_export.py": {
+      "a": 82,
+      "d": 7
+    }
+  }
+}

doc/sphinxext/prs/12828.json

@@ -0,0 +1,43 @@
+{
+  "merge_commit_sha": "176f64ff061136cf5628d76535a8d7e2e164d399",
+  "authors": [
+    {
+      "n": "Shristi Baral",
+      "e": null
+    },
+    {
+      "n": "shristi",
+      "e": "[email protected]"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    },
+    {
+      "n": "Daniel McCloy",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "doc/changes/devel/12828.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "doc/changes/names.inc": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/source_estimate.py": {
+      "a": 7,
+      "d": 0
+    },
+    "mne/utils/docs.py": {
+      "a": 6,
+      "d": 0
+    },
+    "mne/viz/_3d.py": {
+      "a": 13,
+      "d": 3
+    }
+  }
+}