Merge branch 'main' into correct_annot_export

Author: qian-chu

Diff for: .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:

Diff for: .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: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.0.0
+    rev: v1.1.1
     hooks:
       - id: zizmor
 

Diff for: 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:

Diff for: 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

Diff for: 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`:
 

Diff for: 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

Diff for: 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`_.

Diff for: 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`.

Diff for: 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`_.

Diff for: 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`_.

Diff for: 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`_.

Diff for: doc/changes/devel/13062.bugfix.rst

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

Diff for: 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`_.

Diff for: 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`_.

Diff for: 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`_.

Diff for: 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
@@ -284,6 +285,7 @@
 .. _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

Diff for: 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 += """

Diff for: 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},

Diff for: 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)

Diff for: doc/sphinxext/related_software.py

@@ -163,9 +163,9 @@ 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)

Diff for: 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)

Diff for: 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,