Merge branch 'main' into hed-annotations

.circleci/config.yml

@@ -218,6 +218,9 @@ jobs:
       - restore_cache:
           keys:
             - data-cache-phantom-kit
+      - restore_cache:
+          keys:
+            - data-cache-ds004388
       - run:
           name: Get data
           # This limit could be increased, but this is helpful for finding slow ones
@@ -252,7 +255,7 @@ jobs:
           name: Check sphinx log for warnings (which are treated as errors)
           when: always
           command: |
-            ! grep "^.* (WARNING|ERROR): .*$" sphinx_log.txt
+            ! grep "^.*\(WARNING\|ERROR\): " sphinx_log.txt
       - run:
           name: Show profiling output
           when: always
@@ -393,6 +396,10 @@ jobs:
           key: data-cache-phantom-kit
           paths:
             - ~/mne_data/MNE-phantom-KIT-data  # (1 G)
+      - save_cache:
+          key: data-cache-ds004388
+          paths:
+            - ~/mne_data/ds004388  # (1.8 G)
 
 
   linkcheck:

.github/workflows/autofix.yml

@@ -21,4 +21,4 @@ jobs:
       - run: pip install --upgrade towncrier pygithub gitpython numpy
       - run: python ./.github/actions/rename_towncrier/rename_towncrier.py
       - run: python ./tools/dev/ensure_headers.py
-      - uses: autofix-ci/action@ff86a557419858bb967097bfc916833f5647fa8c
+      - uses: autofix-ci/action@551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef

.github/workflows/check_changelog.yml

@@ -5,6 +5,9 @@ on:  # yamllint disable-line rule:truthy
     types: [opened, synchronize, labeled, unlabeled]
     branches: ["main"]
 
+permissions:
+  contents: read
+
 jobs:
   changelog_checker:
     name: Check towncrier entry in doc/changes/devel/

.github/workflows/circle_artifacts.yml

@@ -1,4 +1,7 @@
 on: [status]  # yamllint disable-line rule:truthy
+permissions:
+  contents: read
+  statuses: write
 jobs:
   circleci_artifacts_redirector_job:
     if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs') }}"

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.3
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -23,7 +23,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: codespell
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.0.0
+    rev: v1.2.2
     hooks:
       - id: zizmor
 

azure-pipelines.yml

@@ -112,7 +112,7 @@ stages:
           - bash: |
               set -e
               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@main" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1" pandas neo pymatreader antio defusedxml
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1" pandas neo pymatreader antio defusedxml
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -243,7 +243,7 @@ stages:
           PYTHONIOENCODING: 'utf-8'
           AZURE_CI_WINDOWS: 'true'
           PYTHON_ARCH: 'x64'
-        timeoutInMinutes: 75
+        timeoutInMinutes: 80
         strategy:
           maxParallel: 4
           matrix:

doc/api/datasets.rst

@@ -18,6 +18,7 @@ Datasets
    brainstorm.bst_auditory.data_path
    brainstorm.bst_resting.data_path
    brainstorm.bst_raw.data_path
+   default_path
    eegbci.load_data
    eegbci.standardize
    fetch_aparc_sub_parcellation

doc/api/preprocessing.rst

@@ -116,6 +116,7 @@ Projections:
    read_ica_eeglab
    read_fine_calibration
    write_fine_calibration
+   apply_pca_obs
 
 :py:mod:`mne.preprocessing.nirs`:
 

doc/api/time_frequency.rst

@@ -31,6 +31,8 @@ Functions that operate on mne-python objects:
 .. autosummary::
    :toctree: ../generated/
 
+   combine_spectrum
+   combine_tfr
    csd_tfr
    csd_fourier
    csd_multitaper

doc/changes/devel/12071.newfeature.rst

@@ -0,0 +1 @@
+Add new ``select`` parameter to :func:`mne.viz.plot_evoked_topo` and :meth:`mne.Evoked.plot_topo` to toggle lasso selection of sensors, by `Marijn van Vliet`_.

doc/changes/devel/12656.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :func:`mne.export.export_raw` does not correct for recording start time (:attr:`raw.first_time <mne.io.Raw.first_time>`) when exporting Raw instances to EDF or EEGLAB formats, by `Qian Chu`_.

doc/changes/devel/12910.newfeature.rst

@@ -0,0 +1 @@
+Added the option to return taper weights from :func:`mne.time_frequency.tfr_array_multitaper`, and taper weights are now stored in the :class:`mne.time_frequency.BaseTFR` objects, by `Thomas Binns`_.

doc/changes/devel/13037.newfeature.rst

@@ -0,0 +1 @@
+Add PCA-OBS preprocessing for the removal of heart-artefacts from EEG or ESG datasets via :func:`mne.preprocessing.apply_pca_obs`, by :newcontrib:`Emma Bailey` and :newcontrib:`Steinn Hauser Magnusson`.

doc/changes/devel/13054.newfeature.rst

@@ -0,0 +1 @@
+Added :func:`mne.time_frequency.combine_tfr` to allow combining TFRs across tapers, by `Thomas Binns`_.

doc/changes/devel/13056.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with saving of anonymized data when helium info is present in measurement info, by `Eric Larson`_.

doc/changes/devel/13058.newfeature.rst

@@ -0,0 +1 @@
+Add the function :func:`mne.time_frequency.combine_spectrum` for combining data across :class:`mne.time_frequency.Spectrum` objects, and allow :func:`mne.grand_average` to operate on :class:`mne.time_frequency.Spectrum` objects, by `Thomas Binns`_.

doc/changes/devel/13062.bugfix.rst

@@ -0,0 +1 @@
+Fix computation of time intervals in :func:`mne.preprocessing.compute_fine_calibration` by `Eric Larson`_.

doc/changes/devel/13063.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in the colorbars created by :func:`mne.viz.plot_evoked_topomap` by `Santeri Ruuskanen`_.

doc/changes/devel/13065.bugfix.rst

@@ -0,0 +1,7 @@
+Improved sklearn class compatibility and compliance, which resulted in some parameters of classes having an underscore appended to their name during ``fit``, such as:
+
+- :class:`mne.decoding.FilterEstimator` parameter ``picks`` passed to the initializer is set as ``est.picks_``
+- :class:`mne.decoding.UnsupervisedSpatialFilter` parameter ``estimator`` passed to the initializer is set as ``est.estimator_``
+
+Unused ``verbose`` class parameters (that had no effect) were removed from :class:`~mne.decoding.PSDEstimator`, :class:`~mne.decoding.TemporalFilter`, and :class:`~mne.decoding.FilterEstimator` as well.
+Changes by `Eric Larson`_.

doc/changes/devel/13067.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where taper weights were not correctly applied when computing multitaper power with :meth:`mne.Epochs.compute_tfr` and :func:`mne.time_frequency.tfr_array_multitaper`, by `Thomas Binns`_.

doc/changes/devel/13069.bugfix.rst

@@ -0,0 +1 @@
+Fix bug cause by unnecessary assertion when loading mixed frequency EDFs without preloading :func:`mne.io.read_raw_edf` by `Simon Kern`_.

doc/changes/devel/13070.bugfix.rst

@@ -0,0 +1 @@
+Return events when requested even when current matches the desired sfreq in :meth:`mne.io.Raw.resample` by :newcontrib:`Roy Eric Wieske`.

doc/changes/devel/13082.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with automated Mesa 3D detection for proper 3D option setting on systems with software rendering, by `Eric Larson`_.

doc/changes/names.inc

@@ -73,6 +73,7 @@
 .. _Eberhard Eich: https://github.com/ebeich
 .. _Eduard Ort: https://github.com/eort
 .. _Emily Stephen: https://github.com/emilyps14
+.. _Emma Bailey: https://www.cbs.mpg.de/employees/bailey
 .. _Enrico Varano: https://github.com/enricovara/
 .. _Enzo Altamiranda: https://www.linkedin.com/in/enzoalt
 .. _Eric Larson: https://larsoner.com
@@ -257,6 +258,7 @@
 .. _Roman Goj: https://romanmne.blogspot.co.uk
 .. _Ross Maddox: https://www.urmc.rochester.edu/labs/maddox-lab.aspx
 .. _Rotem Falach: https://github.com/Falach
+.. _Roy Eric Wieske: https://github.com/Randomidous
 .. _Sammi Chekroud: https://github.com/schekroud
 .. _Samu Taulu: https://phys.washington.edu/people/samu-taulu
 .. _Samuel Deslauriers-Gauthier: https://github.com/sdeslauriers
@@ -284,6 +286,7 @@
 .. _Stanislas Chambon: https://github.com/Slasnista
 .. _Stefan Appelhoff: https://stefanappelhoff.com
 .. _Stefan Repplinger: https://github.com/stfnrpplngr
+.. _Steinn Hauser Magnusson: https://github.com/steinnhauser
 .. _Steven Bethard: https://github.com/bethard
 .. _Steven Bierer: https://github.com/neurolaunch
 .. _Steven Gutstein: https://github.com/smgutstein

doc/conf.py

@@ -355,6 +355,7 @@
     "n_frequencies",
     "n_tests",
     "n_samples",
+    "n_peaks",
     "n_permutations",
     "nchan",
     "n_points",
@@ -1289,7 +1290,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     rst_prolog += f"""
 .. |{icon}| raw:: html
 
-    <i class="{' '.join(classes + (f'fa-{icon}',))}"></i>
+    <i class="{" ".join(classes + (f"fa-{icon}",))}"></i>
 """
 
 rst_prolog += """

doc/references.bib

@@ -1335,6 +1335,16 @@ @inproceedings{NdiayeEtAl2016
   year = {2016}
 }
 
+@article{NiazyEtAl2005,
+  author = {Niazy, R. K. and Beckmann, C.F. and Iannetti, G.D. and Brady, J. M. and Smith, S. M.},
+  title = {Removal of FMRI environment artifacts from EEG data using optimal basis sets},
+  journal = {NeuroImage},
+  year = {2005},
+  volume = {28},
+  pages = {720-737},
+  doi = {10.1016/j.neuroimage.2005.06.067.}
+}
+
 @article{NicholsHolmes2002,
   author = {Nichols, Thomas E. and Holmes, Andrew P.},
   doi = {10.1002/hbm.1058},

doc/sphinxext/credit_tools.py

@@ -169,7 +169,7 @@ def generate_credit_rst(app=None, *, verbose=False):
                 if author["e"] is not None:
                     if author["e"] not in name_map:
                         unknown_emails.add(
-                            f'{author["e"].ljust(29)} '
+                            f"{author['e'].ljust(29)} "
                             "https://github.com/mne-tools/mne-python/pull/"
                             f"{commit}/files"
                         )
@@ -178,9 +178,9 @@ def generate_credit_rst(app=None, *, verbose=False):
                 else:
                     name = author["n"]
                     if name in manual_renames:
-                        assert _good_name(
-                            manual_renames[name]
-                        ), f"Bad manual rename: {name}"
+                        assert _good_name(manual_renames[name]), (
+                            f"Bad manual rename: {name}"
+                        )
                         name = manual_renames[name]
                     if " " in name:
                         first, last = name.rsplit(" ", maxsplit=1)

doc/sphinxext/mne_doc_utils.py

@@ -97,6 +97,8 @@ def reset_warnings(gallery_conf, fname):
         r"numpy\.core is deprecated and has been renamed to numpy\._core",
         # matplotlib
         "__array_wrap__ must accept context and return_scalar.*",
+        # nibabel
+        "__array__ implementation doesn't accept.*",
     ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             "ignore", message=f".*{key}.*", category=DeprecationWarning

doc/sphinxext/related_software.py

@@ -163,16 +163,17 @@ def _get_packages() -> dict[str, str]:
     assert not dups, f"Duplicates in MANUAL_PACKAGES and PYPI_PACKAGES: {sorted(dups)}"
     # And the installer and PyPI-only should be disjoint:
     dups = set(PYPI_PACKAGES) & set(packages)
-    assert (
-        not dups
-    ), f"Duplicates in PYPI_PACKAGES and installer packages: {sorted(dups)}"
+    assert not dups, (
+        f"Duplicates in PYPI_PACKAGES and installer packages: {sorted(dups)}"
+    )
     for name in PYPI_PACKAGES | set(MANUAL_PACKAGES):
         if name not in packages:
             packages.append(name)
     # Simple alphabetical order
     packages = sorted(packages, key=lambda x: x.lower())
     packages = [RENAMES.get(package, package) for package in packages]
     out = dict()
+    reasons = []
     for package in status_iterator(
         packages, f"Adding {len(packages)} related software packages: "
     ):
@@ -183,12 +184,17 @@ def _get_packages() -> dict[str, str]:
             else:
                 md = importlib.metadata.metadata(package)
         except importlib.metadata.PackageNotFoundError:
-            pass  # raise a complete error later
+            reasons.append(f"{package}: not found, needs to be installed")
+            continue  # raise a complete error later
         else:
             # Every project should really have this
+            do_continue = False
             for key in ("Summary",):
                 if key not in md:
-                    raise ExtensionError(f"Missing {repr(key)} for {package}")
+                    reasons.extend(f"{package}: missing {repr(key)}")
+                    do_continue = True
+            if do_continue:
+                continue
             # It is annoying to find the home page
             url = None
             if "Home-page" in md:
@@ -204,15 +210,17 @@ def _get_packages() -> dict[str, str]:
                     if url is not None:
                         break
                 else:
-                    raise RuntimeError(
-                        f"Could not find Home-page for {package} in:\n"
-                        f"{sorted(set(md))}\nwith Summary:\n{md['Summary']}"
+                    reasons.append(
+                        f"{package}: could not find Home-page in {sorted(md)}"
                     )
+                    continue
             out[package]["url"] = url
             out[package]["description"] = md["Summary"].replace("\n", "")
-    bad = [package for package in packages if not out[package]]
-    if bad and REQUIRE_METADATA:
-        raise ExtensionError(f"Could not find metadata for:\n{' '.join(bad)}")
+    reason_str = "\n".join(reasons)
+    if reason_str and REQUIRE_METADATA:
+        raise ExtensionError(
+            f"Could not find suitable metadata for related software:\n{reason_str}"
+        )
 
     return out
 

doc/sphinxext/unit_role.py

@@ -10,8 +10,7 @@ def unit_role(name, rawtext, text, lineno, inliner, options={}, content=[]):  #
 
     def pass_error_to_sphinx(rawtext, text, lineno, inliner):
         msg = inliner.reporter.error(
-            "The :unit: role requires a space-separated number and unit; "
-            f"got {text}",
+            f"The :unit: role requires a space-separated number and unit; got {text}",
             line=lineno,
         )
         prb = inliner.problematic(rawtext, rawtext, msg)

examples/decoding/linear_model_patterns.py

@@ -79,7 +79,7 @@
 
 # Extract and plot spatial filters and spatial patterns
 for name, coef in (("patterns", model.patterns_), ("filters", model.filters_)):
-    # We fitted the linear model onto Z-scored data. To make the filters
+    # We fit the linear model on Z-scored data. To make the filters
     # interpretable, we must reverse this normalization step
     coef = scaler.inverse_transform([coef])[0]
 

examples/inverse/vector_mne_solution.py

@@ -79,7 +79,7 @@
 # inverse was computed with loose=0.2
 print(
     "Absolute cosine similarity between source normals and directions: "
-    f'{np.abs(np.sum(directions * inv["source_nn"][2::3], axis=-1)).mean()}'
+    f"{np.abs(np.sum(directions * inv['source_nn'][2::3], axis=-1)).mean()}"
 )
 brain_max = stc_max.plot(
     initial_time=peak_time,