Merge branch 'main' into add_tfr_weights

mne-tools · Dec 9, 2024 · 5ad9bd5 · 5ad9bd5
2 parents 8d645bb + 4967ecd
commit 5ad9bd5
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diff --git a/.github/workflows/autofix.yml b/.github/workflows/autofix.yml
@@ -19,4 +19,4 @@ 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@dd55f44df8f7cdb7a6bf74c78677eb8acd40cd0a
+      - uses: autofix-ci/action@ff86a557419858bb967097bfc916833f5647fa8c
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -40,8 +40,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 70
-    continue-on-error: true
+    timeout-minutes: 80
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -54,6 +53,7 @@ jobs:
       MNE_CI_KIND: '${{ matrix.kind }}'
       CI_OS_NAME: '${{ matrix.os }}'
     strategy:
+      fail-fast: false
       matrix:
         include:
           - os: ubuntu-latest
@@ -83,7 +83,7 @@ jobs:
           fetch-depth: 0
       - run: ./tools/github_actions_env_vars.sh
       # Xvfb/OpenGL
-      - uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@v3
         with:
           qt: true
           pyvista: false
@@ -129,7 +129,7 @@ jobs:
           path: ~/mne_data
       - run: ./tools/github_actions_download.sh
       - run: ./tools/github_actions_test.sh
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-        if: always()
+        if: success() || failure()
diff --git a/.mailmap b/.mailmap
@@ -118,6 +118,7 @@ Fu-Te Wong <[email protected]> zuxfoucault <[email protected]>
 Félix Raimundo <[email protected]> Felix Raimundo <[email protected]>
 Gansheng Tan <[email protected]> Gansheng TAN <[email protected]>
 Gennadiy Belonosov <[email protected]> Gennadiy <[email protected]>
+Gennadiy Belonosov <[email protected]> Genuster <[email protected]>
 Giorgio Marinato <[email protected]> neurogima <[email protected]>
 Giulio Gabrieli <[email protected]>
 Guillaume Dumas <[email protected]> deep-introspection <[email protected]>
@@ -135,6 +136,7 @@ Ivo de Jong <[email protected]> ivopascal <[email protected]>
 Jaakko Leppakangas <[email protected]> Jaakko Leppakangas <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
+Jacob Phelan <[email protected]>
 Jair Montoya <[email protected]> jmontoyam <[email protected]>
 Jan Ebert <[email protected]> janEbert <[email protected]>
 Jan Sedivy <[email protected]>
@@ -354,3 +356,4 @@ Yousra Bekhti <[email protected]> Yousra BEKHTI <[email protected]>
 Yousra Bekhti <[email protected]> yousrabk <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>
 Zhi Zhang <[email protected]> ZHANG Zhi <[email protected]>
+Ziyi ZENG <[email protected]>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.1
+    rev: v0.8.0
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -58,7 +58,7 @@ repos:
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.23.1
+    rev: v0.24.2
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -263,8 +263,8 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -eo pipefail
-              git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-              powershell gl-ci-helpers/appveyor/install_opengl.ps1
+              git clone --depth 1 https://github.com/pyvista/setup-headless-display-action.git
+              MESA3D_VERSION=24.3.0 bash setup-headless-display-action/windows/install_opengl.sh
             displayName: Install OpenGL
           - bash: ./tools/azure_dependencies.sh
             displayName: Install dependencies with pip

diff --git a/doc/_static/js/set_installer_tab.js b/doc/_static/js/set_installer_tab.js
@@ -42,4 +42,14 @@ function setTabs() {
     uninstall_input.checked = true;
 }
 
+function setAlert() {
+    for (let button of document.querySelectorAll('.install-download-button')) {
+        button.addEventListener('click', function() {
+            alert = document.querySelectorAll('.install-download-alert')[0];
+            alert.style.display = 'block';
+        });
+    }
+}
+
 documentReady(setTabs);
+documentReady(setAlert);
diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
@@ -1,7 +1,7 @@
 {%- extends 'pydata_sphinx_theme/layout.html' %}
 
 {% block extrahead %}
-    <link rel="canonical" href="https://mne.tools/stable/index.html" />
+    <link rel="canonical" href="https://mne.tools/stable/{{ pagename }}.html" />
     {{ super() }}
 {% endblock %}
 

diff --git a/doc/api/preprocessing.rst b/doc/api/preprocessing.rst
@@ -48,6 +48,7 @@ Projections:
    read_dig_localite
    make_standard_montage
    read_custom_montage
+   transform_to_head
    compute_dev_head_t
    read_layout
    find_layout

diff --git a/doc/changes/devel/12896.other.rst b/doc/changes/devel/12896.other.rst
@@ -0,0 +1 @@
+Update governance model, by `Daniel McCloy`_.
diff --git a/doc/changes/devel/12924.bugfix.rst b/doc/changes/devel/12924.bugfix.rst
@@ -0,0 +1 @@
+Fix typos in the Spatio-Spectral Decomposition example, by :newcontrib:`Simon M. Hofmann`.
diff --git a/doc/changes/devel/12931.bugfix.rst b/doc/changes/devel/12931.bugfix.rst
@@ -0,0 +1,3 @@
+Fix a bug in :func:`mne.epochs.make_metadata`, where missing values in the columns
+generated for ``keep_first`` and ``keep_last`` events were represented by empty strings,
+while it should have been ``NA`` values, by `Richard Höchenberger`_.
diff --git a/doc/changes/devel/12931.other.rst b/doc/changes/devel/12931.other.rst
@@ -0,0 +1 @@
+Improve the :ref:`tut-autogenerate-metadata`, by `Clemens Brunner`_ and `Richard Höchenberger`_.
diff --git a/doc/changes/devel/12936.bugfix.rst b/doc/changes/devel/12936.bugfix.rst
@@ -0,0 +1 @@
+Fix decimal places of :class:`float` ``mne.Evoked.nave`` in :meth:`mne.Evoked.plot` and :meth:`mne.Evoked.plot_image`, by `Gennadiy Belonosov`_.
diff --git a/doc/changes/devel/12955.bugfix.rst b/doc/changes/devel/12955.bugfix.rst
@@ -0,0 +1 @@
+Fix duration calculation for the textual (``__repr__``) and html (``_repr_html_``, used by e.g. Jupyter) display of :class:`mne.io.Raw` instances. For example a duration of 1h is now displayed as ``00:01:00`` rather than ``00:59:60``.  By :newcontrib:`Leonardo Rochael Almeida`.
diff --git a/doc/changes/devel/12955.newfeature.rst b/doc/changes/devel/12955.newfeature.rst
@@ -0,0 +1 @@
+Add convenience :attr:`mne.io.Raw.duration` property to centralize duration calculation for the textual (``__repr__``) and html (``_repr_html_``, used by e.g. Jupyter) display of :class:`mne.io.Raw` instances, by :newcontrib:`Leonardo Rochael Almeida`.
diff --git a/doc/changes/devel/12960.other.rst b/doc/changes/devel/12960.other.rst
@@ -0,0 +1 @@
+Mention some gotchas that arise from the fact that by default, we pool across dipole orientations when performing source estimation, by `Marijn van Vliet`_
diff --git a/doc/changes/devel/12962.bugfix.rst b/doc/changes/devel/12962.bugfix.rst
@@ -0,0 +1 @@
+Fix displayed units in representations of classes such as :class:`mne.io.Raw` to correctly use KiB, MiB, GiB, and so on, by `Clemens Brunner`_.
diff --git a/doc/changes/devel/12966.newfeature.rst b/doc/changes/devel/12966.newfeature.rst
@@ -0,0 +1 @@
+Add ability to use :func:`mne.preprocessing.compute_fine_calibration` with non-Neuromag-style systems, as well as options to control the bad-angle and error tolerances, by `Eric Larson`_.
diff --git a/doc/changes/devel/12968.bugfix.rst b/doc/changes/devel/12968.bugfix.rst
@@ -0,0 +1 @@
+Gracefully handle invalid patient info when reading EDF files by `Scott Huberty`_.
diff --git a/doc/changes/devel/12971.newfeature.rst b/doc/changes/devel/12971.newfeature.rst
@@ -0,0 +1 @@
+Add support for ``uint16_codec`` argument in :func:`mne.io.read_raw_eeglab` when ``pymatreader`` (which already supported this argument previously) is not installed, by `Clemens Brunner`_.
diff --git a/doc/changes/devel/12978.other.rst b/doc/changes/devel/12978.other.rst
@@ -0,0 +1 @@
+Fix a mistake in :ref:`tut-artifact-regression` where the wrong regression coefficients were applied, by :newcontrib:`Jacob Phelan`.
diff --git a/doc/changes/devel/12986.bugfix.rst b/doc/changes/devel/12986.bugfix.rst
@@ -0,0 +1 @@
+Fix IndexError when loading CNT file does not have annotations, by :newcontrib:`Ziyi ZENG`.
diff --git a/doc/changes/devel/13003.newfeature.rst b/doc/changes/devel/13003.newfeature.rst
@@ -0,0 +1 @@
+Added support for saving and loading channel names from FIF in :meth:`mne.channels.DigMontage.save` and :meth:`mne.channels.read_dig_fif` and added the convention that they should be saved as ``-dig.fif``, by `Eric Larson`_.
diff --git a/doc/changes/devel/13007.bugfix.rst b/doc/changes/devel/13007.bugfix.rst
@@ -0,0 +1 @@
+Correct :func:`mne.io.read_raw_cnt` to read responses and fix exceptions by `Jacob Woessner`_. 
diff --git a/doc/changes/names.inc b/doc/changes/names.inc
@@ -119,6 +119,7 @@
 .. _Ivo de Jong: https://github.com/ivopascal
 .. _Jaakko Leppakangas: https://github.com/jaeilepp
 .. _Jack Zhang: https://github.com/jackz314
+.. _Jacob Phelan: https://github.com/JacPhe
 .. _Jacob Woessner: https://github.com/withmywoessner
 .. _Jair Montoya Martinez: https://github.com/jmontoyam
 .. _Jan Ebert: https://www.jan-ebert.com/
@@ -161,6 +162,7 @@
 .. _Lau Møller Andersen: https://github.com/ualsbombe
 .. _Laura Gwilliams: https://lauragwilliams.github.io
 .. _Leonardo Barbosa: https://github.com/noreun
+.. _Leonardo Rochael Almeida: https://github.com/leorochael
 .. _Liberty Hamilton: https://github.com/libertyh
 .. _Lorenzo Desantis: https://github.com/lorenzo-desantis/
 .. _Lukas Breuer: https://www.researchgate.net/profile/Lukas-Breuer-2
@@ -275,6 +277,7 @@
 .. _Simeon Wong: https://github.com/dtxe
 .. _Simon Kern: https://skjerns.de
 .. _Simon Kornblith: https://simonster.com
+.. _Simon M. Hofmann: https://github.com/SHEscher
 .. _Sondre Foslien: https://github.com/sondrfos
 .. _Sophie Herbst: https://github.com/SophieHerbst
 .. _Stanislas Chambon: https://github.com/Slasnista
@@ -315,4 +318,5 @@
 .. _Yousra Bekhti: https://www.linkedin.com/pub/yousra-bekhti/56/886/421
 .. _Yu-Han Luo: https://github.com/yh-luo
 .. _Zhi Zhang: https://github.com/tczhangzhi/
+.. _Ziyi ZENG: https://github.com/ZiyiTsang
 .. _Zvi Baratz: https://github.com/ZviBaratz
diff --git a/doc/conf.py b/doc/conf.py
@@ -732,10 +732,12 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     ("py:.*", r"mne\.io\..*\.Raw.*"),  # RawEDF etc.
     ("py:.*", r"mne\.epochs\.EpochsFIF.*"),
     ("py:.*", r"mne\.io\..*\.Epochs.*"),  # EpochsKIT etc.
-    (
+    (  # BaseRaw attributes are documented in Raw
         "py:obj",
-        "(filename|metadata|proj|times|tmax|tmin|annotations|ch_names|compensation_grade|filenames|first_samp|first_time|last_samp|n_times|proj|times|tmax|tmin)",
-    ),  # noqa: E501
+        "(filename|metadata|proj|times|tmax|tmin|annotations|ch_names"
+        "|compensation_grade|duration|filenames|first_samp|first_time"
+        "|last_samp|n_times|proj|times|tmax|tmin)",
+    ),
 ]
 suppress_warnings = [
     "image.nonlocal_uri",  # we intentionally link outside
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix typos in the Spatio-Spectral Decomposition example, by :newcontrib:`Simon M. Hofmann`.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Improve the :ref:`tut-autogenerate-metadata`, by `Clemens Brunner`_ and `Richard Höchenberger`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix decimal places of :class:`float` ``mne.Evoked.nave`` in :meth:`mne.Evoked.plot` and :meth:`mne.Evoked.plot_image`, by `Gennadiy Belonosov`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix duration calculation for the textual (``__repr__``) and html (``_repr_html_``, used by e.g. Jupyter) display of :class:`mne.io.Raw` instances. For example a duration of 1h is now displayed as ``00:01:00`` rather than ``00:59:60``. By :newcontrib:`Leonardo Rochael Almeida`.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Add convenience :attr:`mne.io.Raw.duration` property to centralize duration calculation for the textual (``__repr__``) and html (``_repr_html_``, used by e.g. Jupyter) display of :class:`mne.io.Raw` instances, by :newcontrib:`Leonardo Rochael Almeida`.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Mention some gotchas that arise from the fact that by default, we pool across dipole orientations when performing source estimation, by `Marijn van Vliet`_
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Fix displayed units in representations of classes such as :class:`mne.io.Raw` to correctly use KiB, MiB, GiB, and so on, by `Clemens Brunner`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Add ability to use :func:`mne.preprocessing.compute_fine_calibration` with non-Neuromag-style systems, as well as options to control the bad-angle and error tolerances, by `Eric Larson`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Gracefully handle invalid patient info when reading EDF files by `Scott Huberty`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Add support for ``uint16_codec`` argument in :func:`mne.io.read_raw_eeglab` when ``pymatreader`` (which already supported this argument previously) is not installed, by `Clemens Brunner`_.