[pull] main from mne-tools:main

.pre-commit-config.yaml

@@ -54,7 +54,7 @@ repos:
     rev: v6.0.0
     hooks:
       - id: file-contents-sorter
-        files: ^doc/changes/names.inc|^.mailmap
+        files: ^doc/changes/names.inc|^.mailmap|^doc/sphinxext/related_software.txt
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort

azure-pipelines.yml

@@ -52,7 +52,7 @@ stages:
           - bash: |
               set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip build
-              python -m pip install --progress-bar off -ve .[hdf5,test]
+              python -m pip install --progress-bar off -ve .[hdf5] --group=test
               python -m pip uninstall -yq pytest-qt  # don't want to set up display, etc. for this
               pre-commit install --install-hooks
             displayName: Install dependencies
@@ -116,7 +116,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml
               python -m pip uninstall -yq mne
-              python -m pip install --progress-bar off --upgrade -e .[test]
+              python -m pip install --progress-bar off --upgrade -e . --group=test
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e
@@ -173,7 +173,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
-              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
+              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

doc/changes/dev/13452.other.rst

@@ -0,0 +1,3 @@
+Removed development dependencies from user-visible "extras"; they're now dependency
+groups only visible to developers (and can be installed for example via
+``pip install --group dev`` with pip version 25.1 or later), by `Richard Höchenberger`_

doc/changes/dev/13456.newfeature.rst

@@ -0,0 +1 @@
+The ``rename_channels`` method now has an ``on_missing`` parameter to control behavior on channel mismatch, by `Stefan Appelhoff`_.

doc/changes/names.inc

@@ -34,6 +34,7 @@
 .. _Asish Panda: https://github.com/kaichogami
 .. _Austin Hurst: https://github.com/a-hurst
 .. _Ben Beasley: https://github.com/musicinmybrain
+.. _Bradley Voytek: https://github.com/voytek
 .. _Britta Westner: https://britta-wstnr.github.io
 .. _Bruno Aristimunha: https://bruaristimunha.github.io
 .. _Bruno Nicenboim: https://bnicenboim.github.io
@@ -132,6 +133,7 @@
 .. _Jan Sedivy: https://github.com/honzaseda
 .. _Jan Sosulski: https://jan-sosulski.de
 .. _Jan Zerfowski: https://github.com/jzerfowski
+.. _Jan-Mathijs Schoeffelen: https://github.com/schoffelen
 .. _Jasper van den Bosch: https://github.com/ilogue
 .. _Jean-Baptiste Schiratti: https://github.com/jbschiratti
 .. _Jean-Rémi King: https://github.com/kingjr
@@ -202,6 +204,7 @@
 .. _Matteo Anelli: https://github.com/matteoanelli
 .. _Matthias Dold: https://matthiasdold.de
 .. _Matthias Eberlein: https://github.com/MatthiasEb
+.. _Matti Hämäläinen: https://research.aalto.fi/en/persons/matti-h%C3%A4m%C3%A4l%C3%A4inen/
 .. _Matti Toivonen: https://github.com/mattitoi
 .. _Mauricio Cespedes Tenorio: https://github.com/mcespedes99
 .. _Michal Žák: https://github.com/michalrzak
@@ -229,6 +232,7 @@
 .. _Noah Markowitz: https://github.com/nmarkowitz
 .. _Okba Bekhelifi: https://github.com/okbalefthanded
 .. _Olaf Hauk: https://neuroscience.cam.ac.uk/member/olafhauk
+.. _Ole Jensen: https://www.psy.ox.ac.uk/people/ole-jensen
 .. _Oleh Kozynets: https://github.com/OlehKSS
 .. _Pablo Mainar: https://github.com/pablomainar
 .. _Pablo-Arias: https://github.com/Pablo-Arias

doc/development/contributing.rst

@@ -304,11 +304,11 @@ be reflected the next time you open a Python interpreter and ``import mne``
 Finally, we'll add a few dependencies that are not needed for running
 MNE-Python, but are needed for locally running our test suite::
 
-    $ pip install -e ".[test]"
+    $ pip install --group=test
 
 And for building our documentation::
 
-    $ pip install -e ".[doc]"
+    $ pip install --group=doc
     $ conda install graphviz
 
 .. note::

doc/overview/people.rst

@@ -34,7 +34,12 @@ Steering Council
 Advisory Board
 --------------
 
-The advisory board is currently unfilled.
+* `Alex Gramfort`_
+* `Bradley Voytek`_
+* `Jan-Mathijs Schoeffelen`_
+* `Liberty Hamilton`_
+* `Matti Hämäläinen`_
+* `Ole Jensen`_
 
 
 .. _governance-cpgrl:

doc/sphinxext/related_software.txt

@@ -0,0 +1,37 @@
+# cross-domain-saliency-maps requirements are onerous (torch and tensorflow)
+# so we don't add it here, and install it separately in circleci_dependencies.sh
+alphaCSC
+autoreject
+bycycle
+conpy
+curryreader
+eeg_positions
+emd
+fooof
+meegkit
+meggie
+mne-ari
+mne-bids-pipeline
+mne-faster
+mne-features
+mne-icalabel
+mne-lsl
+mne-microstates
+mne-nirs
+mne-rsa
+mnelab
+neurodsp
+neurokit2
+niseq
+nitime
+pactools
+plotly
+pycrostates
+pyprep
+pyriemann
+python-picard
+sesameeg
+sleepecg
+tensorpac
+wfdb
+yasa

mne/_fiff/meas_info.py

@@ -626,12 +626,17 @@ def set_channel_types(self, mapping, *, on_unit_change="warn", verbose=None):
         return self
 
     @verbose
-    def rename_channels(self, mapping, allow_duplicates=False, *, verbose=None):
+    def rename_channels(
+        self, mapping, allow_duplicates=False, *, on_missing="raise", verbose=None
+    ):
         """Rename channels.
 
         Parameters
         ----------
         %(mapping_rename_channels_duplicates)s
+        %(on_missing_ch_names)s
+
+            .. versionadded:: 1.11.0
         %(verbose)s
 
         Returns
@@ -652,7 +657,7 @@ def rename_channels(self, mapping, allow_duplicates=False, *, verbose=None):
         info = self if isinstance(self, Info) else self.info
 
         ch_names_orig = list(info["ch_names"])
-        rename_channels(info, mapping, allow_duplicates)
+        rename_channels(info, mapping, allow_duplicates, on_missing=on_missing)
 
         # Update self._orig_units for Raw
         if isinstance(self, BaseRaw):

mne/channels/channels.py

@@ -1126,13 +1126,18 @@ def _check_pos_sphere(pos):
 
 
 @verbose
-def rename_channels(info, mapping, allow_duplicates=False, *, verbose=None):
+def rename_channels(
+    info, mapping, allow_duplicates=False, *, on_missing="raise", verbose=None
+):
     """Rename channels.
 
     Parameters
     ----------
     %(info_not_none)s Note: modified in place.
     %(mapping_rename_channels_duplicates)s
+    %(on_missing_ch_names)s
+
+        .. versionadded:: 1.11.0
     %(verbose)s
 
     See Also
@@ -1148,14 +1153,30 @@ def rename_channels(info, mapping, allow_duplicates=False, *, verbose=None):
 
     # first check and assemble clean mappings of index and name
     if isinstance(mapping, dict):
+        if on_missing in ["warn", "ignore"]:
+            new_mapping = {
+                ch_old: ch_new
+                for ch_old, ch_new in mapping.items()
+                if ch_old in ch_names
+            }
+        else:
+            new_mapping = mapping
+
+        if new_mapping != mapping and on_missing == "warn":
+            warn(
+                "Channel rename map contains keys that are not present in the object "
+                "to be renamed. These will be ignored."
+            )
+
         _check_dict_keys(
-            mapping,
+            new_mapping,
             ch_names,
             key_description="channel name(s)",
             valid_key_source="info",
         )
         new_names = [
-            (ch_names.index(ch_name), new_name) for ch_name, new_name in mapping.items()
+            (ch_names.index(ch_name), new_name)
+            for ch_name, new_name in new_mapping.items()
         ]
     elif callable(mapping):
         new_names = [(ci, mapping(ch_name)) for ci, ch_name in enumerate(ch_names)]

mne/channels/montage.py

@@ -379,13 +379,19 @@ def plot(
             axes=axes,
         )
 
-    @fill_doc
-    def rename_channels(self, mapping, allow_duplicates=False):
+    @verbose
+    def rename_channels(
+        self, mapping, allow_duplicates=False, *, on_missing="raise", verbose=None
+    ):
         """Rename the channels.
 
         Parameters
         ----------
         %(mapping_rename_channels_duplicates)s
+        %(on_missing_ch_names)s
+
+            .. versionadded:: 1.11.0
+        %(verbose)s
 
         Returns
         -------
@@ -395,7 +401,7 @@ def rename_channels(self, mapping, allow_duplicates=False):
         from .channels import rename_channels
 
         temp_info = create_info(list(self._get_ch_pos()), 1000.0, "eeg")
-        rename_channels(temp_info, mapping, allow_duplicates)
+        rename_channels(temp_info, mapping, allow_duplicates, on_missing=on_missing)
         self.ch_names = temp_info["ch_names"]
         return self
 

mne/channels/tests/test_channels.py

@@ -100,7 +100,12 @@ def test_rename_channels():
     # Error Tests
     # Test channel name exists in ch_names
     mapping = {"EEG 160": "EEG060"}
+    ch_names_orig = info.ch_names[::]
     pytest.raises(ValueError, rename_channels, info, mapping)
+    rename_channels(info, mapping, on_missing="ignore")
+    assert info.ch_names == ch_names_orig
+    with pytest.warns(RuntimeWarning, match="Channel rename map contains keys that *"):
+        rename_channels(info, mapping, on_missing="warn")
     # Test improper mapping configuration
     mapping = {"MEG 2641": 1.0}
     pytest.raises(TypeError, rename_channels, info, mapping)

mne/utils/tests/test_config.py

@@ -132,7 +132,11 @@ def test_sys_info_complete():
     sys_info(fid=out, check_version=False, dependencies="developer")
     out = out.getvalue()
     pyproject = tomllib.loads(pyproject.read_text("utf-8"))
-    deps = pyproject["project"]["optional-dependencies"]["test_extra"]
+    deps = [
+        dep
+        for dep in pyproject["dependency-groups"]["test_extra"]
+        if not isinstance(dep, dict)
+    ]
     for dep in deps:
         dep = dep.split("[")[0].split(">")[0].strip()
         assert f" {dep}" in out, f"Missing in dev config: {dep}"