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Merge branch 'main' into add_tfr_weights
2 parents e5eedee + 47ea360 commit 514258d

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‎.circleci/config.yml

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@@ -252,7 +252,7 @@ jobs:
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name: Check sphinx log for warnings (which are treated as errors)
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when: always
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command: |
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! grep "^.* WARNING: .*$" sphinx_log.txt
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! grep "^.* (WARNING|ERROR): .*$" sphinx_log.txt
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- run:
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name: Show profiling output
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when: always

‎.github/workflows/tests.yml

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python-version: ${{ matrix.python }}
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if: startswith(matrix.kind, 'pip')
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# Python (if conda)
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- name: Remove numba and dipy
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run: | # TODO: Remove when numba 0.59 and dipy 1.8 land on conda-forge
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sed -i '/numba/d' environment.yml
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sed -i '/dipy/d' environment.yml
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sed -i 's/- mne$/- mne-base/' environment.yml
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if: matrix.os == 'ubuntu-latest' && startswith(matrix.kind, 'conda') && matrix.python == '3.12'
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- name: Fixes for conda
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run: |
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# For some reason on Linux we get crashes
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if [[ "$RUNNER_OS" == "Linux" ]]; then
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sed -i "/numba/d" environment.yml
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elif [[ "$RUNNER_OS" == "macOS" ]]; then
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sed -i "" "s/ - PySide6 .*/ - PySide6 <6.8/g" environment.yml
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fi
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if: matrix.kind == 'conda' || matrix.kind == 'mamba'
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- uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: ${{ env.CONDA_ENV }}
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environment-name: mne
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create-args: >-
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python=${{ env.PYTHON_VERSION }}
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mamba
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nomkl
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if: ${{ !startswith(matrix.kind, 'pip') }}
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# Make sure we have the right Python
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- run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"
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if: matrix.os == 'macos-14'
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- run: ./tools/github_actions_dependencies.sh
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# Minimal commands on Linux (macOS stalls)
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- run: ./tools/get_minimal_commands.sh

‎.pre-commit-config.yaml

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repos:
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# Ruff mne
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.8.4
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rev: v0.8.6
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hooks:
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- id: ruff
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name: ruff lint mne
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# zizmor
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- repo: https://github.com/woodruffw/zizmor-pre-commit
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rev: v0.10.0
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rev: v1.0.0
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hooks:
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- id: zizmor
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‎doc/changes/devel/13048.bugfix.rst

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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/v1.7.rst

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@@ -75,12 +75,12 @@ Bugfixes
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- 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>`__)
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- 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>`__)
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- 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>`__)
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- - 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>`__)
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- - 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>`__)
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- 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>`__)
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- 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>`__)
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- Fixed bugs with handling of rank in :class:`mne.decoding.CSP`, by `Eric Larson`_. (`#12476 <https://github.com/mne-tools/mne-python/pull/12476>`__)
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- - Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. (`#12481 <https://github.com/mne-tools/mne-python/pull/12481>`__)
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- Fix reading segmented recordings with :func:`mne.io.read_raw_eyelink` by `Dominik Welke`_. (`#12481 <https://github.com/mne-tools/mne-python/pull/12481>`__)
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- 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>`__)
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- - 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>`__)
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- 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>`__)
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- 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>`__)
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- Fix bug with :meth:`mne.preprocessing.ICA.plot_sources` for ``evoked`` data where the
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legend contained too many entries, by `Eric Larson`_. (`#12498 <https://github.com/mne-tools/mne-python/pull/12498>`__)

‎doc/changes/v1.9.rst

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.. _changes_1_9_0:
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1.9.0 (2024-12-18)
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==================
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Version 1.9.0 (2024-12-18)
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==========================
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Dependencies
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------------
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- - 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>`__)
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- 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>`__)
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- Importing from ``mne.decoding`` now explicitly requires ``scikit-learn`` to be installed,
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by `Eric Larson`_. (`#12834 <https://github.com/mne-tools/mne-python/pull/12834>`__)
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- Compatibility improved for Python 3.13, by `Eric Larson`_. (`#13021 <https://github.com/mne-tools/mne-python/pull/13021>`__)
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- 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>`__)
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- 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>`__)
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- 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>`__)
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- - 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>`__)
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- 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>`__)
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- :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>`__)
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- :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>`__)
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- Added the ``title`` argument to :func:`mne.viz.create_3d_figure`, and

‎doc/conf.py

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r"https://scholar.google.com/scholar\?cites=12188330066413208874&as_ylo=2014",
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r"https://scholar.google.com/scholar\?cites=1521584321377182930&as_ylo=2013",
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"https://www.research.chop.edu/imaging",
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"http://prdownloads.sourceforge.net/optipng/optipng-0.7.8-win64.zip?download",
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"https://sourceforge.net/projects/aespa/files/",
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"https://sourceforge.net/projects/ezwinports/files/",
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"https://www.mathworks.com/products/compiler/matlab-runtime.html",
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# 500 server error
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"https://openwetware.org/wiki/Beauchamp:FreeSurfer",
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# 503 Server error
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# SSL problems sometimes
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"http://ilabs.washington.edu",
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"https://psychophysiology.cpmc.columbia.edu",
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"https://erc.easme-web.eu",
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]
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linkcheck_anchors = False # saves a bit of time
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linkcheck_timeout = 15 < 179B span class=pl-c># some can be quite slow

‎doc/development/contributing.rst

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.. optipng
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.. _optipng: http://optipng.sourceforge.net/
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.. _optipng for Windows: http://prdownloads.sourceforge.net/optipng/optipng-0.7.7-win32.zip?download
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.. _optipng for Windows: http://prdownloads.sourceforge.net/optipng/optipng-0.7.8-win64.zip?download
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.. include:: ../links.inc

‎doc/install/installers.rst

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.. We have to use a button-link here because button-ref doesn't properly nested parse the inline code
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.. button-link:: ./ides.html
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.. button-link:: ides.html
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:ref-type: ref
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:color: success
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:shadow:

‎environment.yml

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- joblib
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- jupyter
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- lazy_loader >=0.3
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- mamba
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- matplotlib >=3.7
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- mffpy >=0.5.7
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- mne-qt-browser
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- nibabel
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- nilearn
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- nomkl
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- numba
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- numpy >=1.25,<3
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- openmeeg >=2.5.5

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