Merge remote-tracking branch 'upstream/main' into move-requirements-t…

…o-pyproject.toml * upstream/main: MAINT: Fix CIs (mne-tools#12188) BUG: Fix bug with default alpha and axes (mne-tools#12187) BUG: Fix bug with spectrum warning (mne-tools#12186) Add argument splash to disable splash-screen from Qt-browser (mne-tools#12185) BUG: Fix bug with logging and n_jobs>1 (mne-tools#12154) Use gray logo (works in light and dark modes) (mne-tools#12184) Tweak logo for dark mode (mne-tools#12176) ENH: Improve Covariance.__repr__ (mne-tools#12181) ENH: Enable sensor-specific OPM coregistration in mne coreg (mne-tools#11405) Tweak README.rst (mne-tools#12166)
hoechenberger · Nov 8, 2023 · f62f460 · f62f460
2 parents d29fc04 + fd53fc4
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -223,13 +223,16 @@ jobs:
             - data-cache-fsaverage
       - restore_cache:
           keys:
-            - data-cache-bst-phantom-ctf
+            - data-cache-bst-raw
       - restore_cache:
           keys:
-            - data-cache-bst-raw
+            - data-cache-bst-phantom-ctf
       - restore_cache:
           keys:
             - data-cache-bst-phantom-elekta
+      - restore_cache:
+          keys:
+            - data-cache-bst-phantom-kernel
       - restore_cache:
           keys:
             - data-cache-bst-auditory
@@ -368,18 +371,22 @@ jobs:
           key: data-cache-fsaverage
           paths:
             - ~/mne_data/MNE-fsaverage-data  # (762 M)
-      - save_cache:
-          key: data-cache-bst-phantom-ctf
-          paths:
-            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-raw
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_raw  # (830 M)
+      - save_cache:
+          key: data-cache-bst-phantom-ctf
+          paths:
+            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-phantom-elekta
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_phantom_elekta  # (1.4 G)
+      - save_cache:
+          key: data-cache-bst-phantom-kernel
+          paths:
+            - ~/mne_data/MNE-phantom-kernel-data  # (362 M)
       - save_cache:
           key: data-cache-bst-auditory
           paths:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -106,7 +106,7 @@ jobs:
       - name: 'Install OSMesa VTK variant'
         run: |
           # TODO: As of 2023/02/28, notebook tests need a pinned mesalib
-          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4"
+          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4" "numpy=1.24.4" "numba=0.57.1"
           mamba list
         if: matrix.kind == 'notebook'
       - run: ./tools/github_actions_dependencies.sh

diff --git a/README.rst b/README.rst
@@ -1,87 +1,67 @@
 .. -*- mode: rst -*-
 
-|PyPI|_ |conda-forge|_ |Zenodo|_ |Discourse|_ |Codecov|_ |Bandit|_ |OpenSSF|_
-
 |MNE|_
 
-.. |PyPI| image:: https://img.shields.io/pypi/dm/mne.svg?label=PyPI
-.. _PyPI: https://pypi.org/project/mne/
-
-.. |conda-forge| image:: https://img.shields.io/conda/dn/conda-forge/mne.svg?label=Conda
-.. _conda-forge: https://anaconda.org/conda-forge/mne
-
-.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592483.svg
-.. _Zenodo: https://doi.org/10.5281/zenodo.592483
-
-.. |Discourse| image:: https://img.shields.io/discourse/status?label=Community&server=https%3A%2F%2Fmne.discourse.group%2F
-.. _Discourse: https://mne.discourse.group/
-
-.. |Codecov| image:: https://img.shields.io/codecov/c/github/mne-tools/mne-python?label=Coverage
-.. _Codecov: https://codecov.io/gh/mne-tools/mne-python
-
-.. |Bandit| image:: https://img.shields.io/badge/security-bandit-yellow.svg
-.. _Bandit: https://github.com/PyCQA/bandit
-
-.. |OpenSSF| image:: https://www.bestpractices.dev/projects/7783/badge
-.. _OpenSSF: https://www.bestpractices.dev/projects/7783
-
-.. |MNE| image:: https://mne.tools/stable/_static/mne_logo.svg
-.. _MNE: https://mne.tools/dev/
-
-
 MNE-Python
 ==========
 
-`MNE-Python software`_ is an open-source Python package for exploring,
+MNE-Python is an open-source Python package for exploring,
 visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG,
 ECoG, and more. It includes modules for data input/output, preprocessing,
 visualization, source estimation, time-frequency analysis, connectivity analysis,
-machine learning, and statistics.
+machine learning, statistics, and more.
 
 
 Documentation
 ^^^^^^^^^^^^^
 
-`MNE documentation`_ for MNE-Python is available online.
+`Documentation`_ for MNE-Python encompasses installation instructions, tutorials,
+and examples for a wide variety of topics, contributing guidelines, and an API
+reference.
 
 
 Forum
 ^^^^^^
 
-Our user forum is https://mne.discourse.group and is the best place to ask
-questions about MNE-Python usage or about the contribution process. It also
-includes job opportunities and other announcements.
+The `user forum`_ is the best place to ask questions about MNE-Python usage or
+the contribution process. The forum also features job opportunities and other
+announcements.
+
+If you find a bug or have an idea for a new feature that should be added to
+MNE-Python, please use the
+`issue tracker <https://github.com/mne-tools/mne-python/issues/new/choose>`__ of
+our GitHub repository.
 
 
-Installing MNE-Python
-^^^^^^^^^^^^^^^^^^^^^
+Installation
+^^^^^^^^^^^^
 
-To install the latest stable version of MNE-Python, you can use pip_ in a terminal:
+To install the latest stable version of MNE-Python with minimal dependencies
+only, use pip_ in a terminal:
 
 .. code-block:: console
 
     $ pip install --upgrade mne
 
-- MNE-Python 0.17 was the last release to support Python 2.7
-- MNE-Python 0.18 requires Python 3.5 or higher
-- MNE-Python 0.21 requires Python 3.6 or higher
-- MNE-Python 0.24 requires Python 3.7 or higher
-- MNE-Python 1.4 requires Python 3.8 or higher
+The current MNE-Python release requires Python 3.8 or higher. MNE-Python 0.17
+was the last release to support Python 2.7.
 
-For more complete instructions and more advanced installation methods (e.g. for
-the latest development version), see the `installation guide`_.
+For more complete instructions, including our standalone installers and more
+advanced installation methods, please refer to the `installation guide`_.
 
 
-Get the latest code
-^^^^^^^^^^^^^^^^^^^
+Get the development version
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-To install the latest version of the code using pip_ open a terminal and type:
+To install the latest development version of MNE-Python using pip_, open a
+terminal and type:
 
 .. code-block:: console
 
     $ pip install --upgrade git+https://github.com/mne-tools/mne-python@main
 
-To get the latest code using `git <https://git-scm.com/>`__, open a terminal and type:
+To clone the repository with `git <https://git-scm.com/>`__, open a terminal
+and type:
 
 .. code-block:: console
 
@@ -93,55 +73,68 @@ Dependencies
 
 The minimum required dependencies to run MNE-Python are:
 
-- Python >= 3.8
-- NumPy >= 1.21.2
-- SciPy >= 1.7.1
-- Matplotlib >= 3.5.0
-- pooch >= 1.5
-- tqdm
-- Jinja2
-- decorator
-- lazy_loader
+- `Python <https://www.python.org>`__ ≥ 3.8
+- `NumPy <https://numpy.org>`__ ≥ 1.21.2
+- `SciPy <https://scipy.org>`__ ≥ 1.7.1
+- `Matplotlib <https://matplotlib.org>`__ ≥ 3.5.0
+- `Pooch <https://www.fatiando.org/pooch/latest/>`__ ≥ 1.5
+- `tqdm <https://tqdm.github.io>`__
+- `Jinja2 <https://palletsprojects.com/p/jinja/>`__
+- `decorator <https://github.com/micheles/decorator>`__
+- `lazy_loader <https://pypi.org/project/lazy_loader/>`__
 
 For full functionality, some functions require:
 
-- Scikit-learn >= 1.0
-- joblib >= 0.15 (for parallelization control)
-- mne-qt-browser >= 0.1 (for fast raw data visualization)
-- Qt5 >= 5.12 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
-
-  - PyQt6 >= 6.0
-  - PySide6 >= 6.0
-  - PyQt5 >= 5.12
-  - PySide2 >= 5.12
+- `scikit-learn <https://scikit-learn.org/stable/>`__ ≥ 1.0
+- `Joblib <https://joblib.readthedocs.io/en/latest/index.html>`__ ≥ 0.15 (for parallelization)
+- `mne-qt-browser <https://github.com/mne-tools/mne-qt-browser>`__ ≥ 0.1 (for fast raw data visualization)
+- `Qt <https://www.qt.io>`__ ≥ 5.12 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
+
+  - `PyQt6 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 6.0
+  - `PySide6 <https://doc.qt.io/qtforpython-6/>`__ ≥ 6.0
+  - `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`__ ≥ 5.12
+  - `PySide2 <https://doc.qt.io/qtforpython-6/gettingstarted/porting_from2.html>`__ ≥ 5.12
+
+- `Numba <https://numba.pydata.org>`__ ≥ 0.54.0
+- `NiBabel <https://nipy.org/nibabel/>`__ ≥ 3.2.1
+- `OpenMEEG <https://openmeeg.github.io>`__ ≥ 2.5.6
+- `pandas <https://pandas.pydata.org>`__ ≥ 1.3.2
+- `Picard <https://pierreablin.github.io/picard/>`__ ≥ 0.3
+- `CuPy <https://cupy.dev>`__ ≥ 9.0.0 (for NVIDIA CUDA acceleration)
+- `DIPY <https://dipy.org>`__ ≥ 1.4.0
+- `imageio <https://imageio.readthedocs.io/en/stable/>`__ ≥ 2.8.0
+- `PyVista <https://pyvista.org>`__ ≥ 0.32 (for 3D visualization)
+- `PyVistaQt <https://qtdocs.pyvista.org>`__ ≥ 0.4 (for 3D visualization)
+- `mffpy <https://github.com/BEL-Public/mffpy>`__ ≥ 0.5.7
+- `h5py <https://www.h5py.org>`__
+- `h5io <https://github.com/h5io/h5io>`__
+- `pymatreader <https://pymatreader.readthedocs.io/en/latest/>`__
+
+
+Contributing
+^^^^^^^^^^^^
 
-- Numba >= 0.54.0
-- NiBabel >= 3.2.1
-- OpenMEEG >= 2.5.6
-- Pandas >= 1.3.2
-- Picard >= 0.3
-- CuPy >= 9.0.0 (for NVIDIA CUDA acceleration)
-- DIPY >= 1.4.0
-- Imageio >= 2.8.0
-- PyVista >= 0.32 (for 3D visualization)
-- pyvistaqt >= 0.4 (for 3D visualization)
-- mffpy >= 0.5.7
-- h5py
-- h5io
-- pymatreader
+Please see the `contributing guidelines <https://mne.tools/dev/development/contributing.html>`__ on our documentation website.
 
-Contributing to MNE-Python
-^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Please see the documentation on the MNE-Python homepage:
+About
+^^^^^
 
-https://mne.tools/dev/install/contributing.html
++---------+------------+----------------+
+| CI      | |Codecov|_ | |Bandit|_      |
++---------+------------+----------------+
+| Package | |PyPI|_    | |conda-forge|_ |
++---------+------------+----------------+
+| Docs    | |Docs|_    | |Discourse|_   |
++---------+------------+----------------+
+| Meta    | |Zenodo|_  | |OpenSSF|_     |
++---------+------------+----------------+
 
 
-Licensing
-^^^^^^^^^
+License
+^^^^^^^
 
-MNE-Python is **BSD-licenced** (BSD-3-Clause):
+MNE-Python is **BSD-licensed** (BSD-3-Clause):
 
     This software is OSI Certified Open Source Software.
     OSI Certified is a certification mark of the Open Source Initiative.
@@ -177,7 +170,34 @@ MNE-Python is **BSD-licenced** (BSD-3-Clause):
     damage.**
 
 
-.. _MNE-Python software: https://mne.tools/dev/
-.. _MNE documentation: https://mne.tools/dev/overview/index.html
+.. _Documentation: https://mne.tools/dev/
+.. _user forum: https://mne.discourse.group
 .. _installation guide: https://mne.tools/dev/install/index.html
 .. _pip: https://pip.pypa.io/en/stable/
+
+.. |PyPI| image:: https://img.shields.io/pypi/dm/mne.svg?label=PyPI
+.. _PyPI: https://pypi.org/project/mne/
+
+.. |conda-forge| image:: https://img.shields.io/conda/dn/conda-forge/mne.svg?label=Conda
+.. _conda-forge: https://anaconda.org/conda-forge/mne
+
+.. |Docs| image:: https://img.shields.io/badge/Docs-online-green?label=Documentation
+.. _Docs: https://mne.tools/dev/
+
+.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592483.svg
+.. _Zenodo: https://doi.org/10.5281/zenodo.592483
+
+.. |Discourse| image:: https://img.shields.io/discourse/status?label=Forum&server=https%3A%2F%2Fmne.discourse.group%2F
+.. _Discourse: https://mne.discourse.group/
+
+.. |Codecov| image:: https://img.shields.io/codecov/c/github/mne-tools/mne-python?label=Coverage
+.. _Codecov: https://codecov.io/gh/mne-tools/mne-python
+
+.. |Bandit| image:: https://img.shields.io/badge/Security-Bandit-yellow.svg
+.. _Bandit: https://github.com/PyCQA/bandit
+
+.. |OpenSSF| image:: https://www.bestpractices.dev/projects/7783/badge
+.. _OpenSSF: https://www.bestpractices.dev/projects/7783
+
+.. |MNE| image:: https://mne.tools/dev/_static/mne_logo_gray.svg
+.. _MNE: https://mne.tools/dev/