Merge branch 'main' of https://github.com/mne-tools/mne-python into m…

…it_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: .*$" 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/tests.yml

@@ -93,37 +93,36 @@ jobs:
         with:
           qt: true
           pyvista: false
+          wm: false
       # Python (if pip)
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
         if: startswith(matrix.kind, 'pip')
       # Python (if conda)
-      - name: Remove numba and dipy
-        run: |  # TODO: Remove when numba 0.59 and dipy 1.8 land on conda-forge
-          sed -i '/numba/d' environment.yml
-          sed -i '/dipy/d' environment.yml
-          sed -i 's/- mne$/- mne-base/' environment.yml
-        if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
+      - name: Fixes for conda
+        run: |
+          # For some reason on Linux we get crashes
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            sed -i "/numba/d" environment.yml
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            sed -i "" "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+          fi
+        if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
-            mamba
-            nomkl
         if: ${{ !startswith(matrix.kind, 'pip') }}
-      # Make sure we have the right Python
-      - run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"
-        if: matrix.os == 'macos-14'
-      - run: ./tools/github_actions_dependencies.sh
+      - run: bash ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
-      - run: ./tools/get_minimal_commands.sh
+      - run: bash ./tools/get_minimal_commands.sh
         if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'
-      - run: ./tools/github_actions_infos.sh
+      - run: bash ./tools/github_actions_infos.sh
       # Check Qt
-      - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
+      - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND
         if: env.MNE_QT_BACKEND != ''
       - name: Run tests with no testing data
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/
@@ -133,8 +132,8 @@ jobs:
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
-      - run: ./tools/github_actions_download.sh
-      - run: ./tools/github_actions_test.sh
+      - run: bash ./tools/github_actions_download.sh
+      - run: bash ./tools/github_actions_test.sh  # for some reason on macOS we need to run "bash X" in order for a failed test run to show up
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -70,19 +70,19 @@ repos:
         name: Copy dependency changes from pyproject.toml to environment.yml
         language: python
         entry: ./tools/hooks/update_environment_file.py
-        files: pyproject.toml
+        files: '^(pyproject.toml|tools/hooks/update_environment_file.py)$'
   - repo: local
     hooks:
       - id: dependency-sync
         name: Copy core dependencies from pyproject.toml to README.rst
         language: python
         entry: ./tools/hooks/sync_dependencies.py
-        files: pyproject.toml
+        files: '^(pyproject.toml|tools/hooks/sync_dependencies.py)$'
         additional_dependencies: ["mne==1.9.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v0.10.0
+    rev: v1.1.1
     hooks:
       - id: zizmor
 

azure-pipelines.yml

@@ -88,6 +88,7 @@ stages:
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
+          MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
         steps:
           - bash: |
               set -e
@@ -111,7 +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 pytest-error-for-skips python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1"
+              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'
@@ -132,7 +133,7 @@ stages:
             displayName: 'Cache testing data'
           - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
             displayName: 'Get test data'
-          - script: pytest --error-for-skips -m "ultraslowtest or pgtest" --tb=short --cov=mne --cov-report=xml --cov-report=html -vv mne
+          - script: pytest -m "ultraslowtest or pgtest" --tb=short --cov=mne --cov-report=xml -vv mne
             displayName: 'slow and mne-qt-browser tests'
           # Coverage
           - bash: bash <(curl -s https://codecov.io/bash)
@@ -144,19 +145,18 @@ stages:
               testRunTitle: 'Publish test results for $(Agent.JobName)'
               failTaskOnFailedTests: true
             condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@1
+          - task: PublishCodeCoverageResults@2
             inputs:
-              codeCoverageTool: Cobertura
               summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-              reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
 
       - job: Qt
         pool:
           vmImage: 'ubuntu-22.04'
         variables:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
-          TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-report=html --cov-append -vv mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/gui mne/report"
+          TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-append -vv mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/gui mne/report"
+          MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
         steps:
           - bash: ./tools/setup_xvfb.sh
             displayName: 'Install Ubuntu dependencies'
@@ -192,6 +192,7 @@ stages:
               set -eo pipefail
               python -m pip install PyQt6
               LD_DEBUG=libs python -c "from PyQt6.QtWidgets import QApplication, QWidget; app = QApplication([]); import matplotlib; matplotlib.use('QtAgg'); import matplotlib.pyplot as plt; plt.figure()"
+            displayName: 'Check Qt import'
           - bash: |
               set -eo pipefail
               mne sys_info -pd
@@ -226,11 +227,9 @@ stages:
               testRunTitle: 'Publish test results for $(Agent.JobName)'
               failTaskOnFailedTests: true
             condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@1
+          - task: PublishCodeCoverageResults@2
             inputs:
-              codeCoverageTool: Cobertura
               summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-              reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
 
       - job: Windows
         pool:
@@ -244,7 +243,7 @@ stages:
           PYTHONIOENCODING: 'utf-8'
           AZURE_CI_WINDOWS: 'true'
           PYTHON_ARCH: 'x64'
-        timeoutInMinutes: 75
+        timeoutInMinutes: 80
         strategy:
           maxParallel: 4
           matrix:
@@ -285,7 +284,7 @@ stages:
             displayName: 'Cache testing data'
           - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
             displayName: 'Get test data'
-          - script: pytest -m "not (slowtest or pgtest)" --tb=short --cov=mne --cov-report=xml --cov-report=html -vv mne
+          - script: pytest -m "not (slowtest or pgtest)" --tb=short --cov=mne --cov-report=xml -vv mne
             displayName: 'Run tests'
           - bash: bash <(curl -s https://codecov.io/bash)
             displayName: 'Codecov'
@@ -296,8 +295,6 @@ stages:
               testRunTitle: 'Publish test results for $(Agent.JobName) $(TEST_MODE) $(PYTHON_VERSION)'
               failTaskOnFailedTests: true
             condition: succeededOrFailed()
-          - task: PublishCodeCoverageResults@1
+          - task: PublishCodeCoverageResults@2
             inputs:
-              codeCoverageTool: Cobertura
               summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
-              reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'

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/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/12828.bugfix.rst

@@ -0,0 +1 @@
+Fixed behavior of :func:`mne.viz.plot_source_estimates` where the ``title`` was not displayed properly, by :newcontrib:`Shristi Baral`.

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/13048.bugfix.rst

@@ -0,0 +1 @@
+Fix input boxes for the max value not showing when plotting fieldlines with :func:`~mne.viz.plot_evoked_field` when ``show_density=False``, by `Marijn van Vliet`_.

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/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/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
@@ -273,6 +274,7 @@
 .. _Senwen Deng: https://snwn.de
 .. _Seyed Yahya Shirazi: https://neuromechanist.github.io
 .. _Sheraz Khan: https://github.com/SherazKhan
+.. _Shristi Baral: https://github.com/shristibaral
 .. _Silvia Cotroneo: https://github.com/sfc-neuro
 .. _Simeon Wong: https://github.com/dtxe
 .. _Simon Kern: https://skjerns.de
@@ -283,6 +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

doc/changes/v1.7.rst

@@ -75,12 +75,12 @@ Bugfixes
 - Fix validation of ``ch_type`` in :func:`mne.preprocessing.annotate_muscle_zscore`, by `Mathieu Scheltienne`_. (`#12444 <https://github.com/mne-tools/mne-python/pull/12444>`__)
 - Fix errant redundant use of ``BIDSPath.split`` when writing split raw and epochs data, by `Eric Larson`_. (`#12451 <https://github.com/mne-tools/mne-python/pull/12451>`__)
 - Disable config parser interpolation when reading BrainVision files, which allows using the percent sign as a regular character in channel units, by `Clemens Brunner`_. (`#12456 <https://github.com/mne-tools/mne-python/pull/12456>`__)
-- - Fix the default color of :meth:`mne.viz.Brain.add_text` to properly contrast with the figure background color, by `Marijn van Vliet`_. (`#12470 <https://github.com/mne-tools/mne-python/pull/12470>`__)
-- - Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_ (`#12474 <https://github.com/mne-tools/mne-python/pull/12474>`__)
+- Fix the default color of :meth:`mne.viz.Brain.add_text` to properly contrast with the figure background color, by `Marijn van Vliet`_. (`#12470 <https://github.com/mne-tools/mne-python/pull/12470>`__)
+- Changed default ECoG and sEEG electrode sizes in brain plots to better reflect real world sizes, by `Liberty Hamilton`_ (`#12474 <https://github.com/mne-tools/mne-python/pull/12474>`__)
 - Fixed bugs with handling of rank in :class:`mne.decoding.CSP`, by `Eric Larson`_. (`#12476 <https://github.com/mne-tools/mne-python/pull/12476>`__)
-- - Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. (`#12481 <https://github.com/mne-tools/mne-python/pull/12481>`__)
+- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. (`#12481 <https://github.com/mne-tools/mne-python/pull/12481>`__)
 - Improve compatibility with other Qt-based GUIs by handling theme icons better, by `Eric Larson`_. (`#12483 <https://github.com/mne-tools/mne-python/pull/12483>`__)
-- - Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_ (`#12484 <https://github.com/mne-tools/mne-python/pull/12484>`__)
+- Fix problem caused by onsets with NaN values using :func:`mne.io.read_raw_eeglab` by `Jacob Woessner`_ (`#12484 <https://github.com/mne-tools/mne-python/pull/12484>`__)
 - Fix cleaning of channel names for non vectorview or CTF dataset including whitespaces or dash in their channel names, by `Mathieu Scheltienne`_. (`#12489 <https://github.com/mne-tools/mne-python/pull/12489>`__)
 - Fix bug with :meth:`mne.preprocessing.ICA.plot_sources` for ``evoked`` data where the
   legend contained too many entries, by `Eric Larson`_. (`#12498 <https://github.com/mne-tools/mne-python/pull/12498>`__)

doc/changes/v1.9.rst

@@ -1,12 +1,12 @@
 .. _changes_1_9_0:
 
-1.9.0 (2024-12-18)
-==================
+Version 1.9.0 (2024-12-18)
+==========================
 
 Dependencies
 ------------
 
-- - Minimum supported dependencies were updated in accordance with SPEC0_, most notably Python 3.10+ is now required. (`#12798 <https://github.com/mne-tools/mne-python/pull/12798>`__)
+- Minimum supported dependencies were updated in accordance with SPEC0_, most notably Python 3.10+ is now required. (`#12798 <https://github.com/mne-tools/mne-python/pull/12798>`__)
 - Importing from ``mne.decoding`` now explicitly requires ``scikit-learn`` to be installed,
   by `Eric Larson`_. (`#12834 <https://github.com/mne-tools/mne-python/pull/12834>`__)
 - Compatibility improved for Python 3.13, by `Eric Larson`_. (`#13021 <https://github.com/mne-tools/mne-python/pull/13021>`__)
@@ -63,7 +63,7 @@ New features
 - Add option to :func:`mne.preprocessing.fix_stim_artifact` to use baseline average to flatten TMS pulse artifact by `Fahimeh Mamashli`_ and `Padma Sundaram`_ and `Mohammad Daneshzand`_. (`#6915 <https://github.com/mne-tools/mne-python/pull/6915>`__)
 - Add support for `dict` type argument ``ref_channels`` to :func:`mne.set_eeg_reference`, to allow flexible re-referencing (e.g. ``raw.set_eeg_reference(ref_channels={'A1': ['A2', 'A3']})`` will set the new A1 data to be ``A1 - mean(A2, A3)``), by `Alex Lepauvre`_ and `Qian Chu`_ and `Daniel McCloy`_. (`#12366 <https://github.com/mne-tools/mne-python/pull/12366>`__)
 - Add reader for ANT Neuro files in the ``*.cnt`` format with :func:`~mne.io.read_raw_ant`, by `Mathieu Scheltienne`_, `Eric Larson`_ and `Proloy Das`_. (`#12792 <https://github.com/mne-tools/mne-python/pull/12792>`__)
-- - Add support for a :class:`mne.transforms.Transform` in the argument ``trans`` of the coregistration GUI called with :func:`mne.gui.coregistration`, by `Mathieu Scheltienne`_. (`#12801 <https://github.com/mne-tools/mne-python/pull/12801>`__)
+- Add support for a :class:`mne.transforms.Transform` in the argument ``trans`` of the coregistration GUI called with :func:`mne.gui.coregistration`, by `Mathieu Scheltienne`_. (`#12801 <https://github.com/mne-tools/mne-python/pull/12801>`__)
 - :meth:`~mne.io.Raw` and :meth:`~mne.Epochs.save` now return the path to the saved file(s), by `Victor Ferat`_. (`#12811 <https://github.com/mne-tools/mne-python/pull/12811>`__)
 - :func:`mne.channels.read_custom_montage` may now read a newer version of the ``.elc`` ASA Electrode file format, by `Stefan Appelhoff`_. (`#12830 <https://github.com/mne-tools/mne-python/pull/12830>`__)
 - Added the ``title`` argument to :func:`mne.viz.create_3d_figure`, and