Merge branch 'main' into remove_depr_subplot_param

tsbinns · Dec 21, 2024 · 0a44c93 · 0a44c93
2 parents 08b8393 + 5095aeb
commit 0a44c93
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -76,13 +76,11 @@ jobs:
 
       - run:
           name: Get Python running and install dependencies
-          # Install mne-bids dev version: https://github.com/mne-tools/mne-connectivity/pull/237
           command: |
             pip install git+https://github.com/mne-tools/mne-python@main
             curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/circleci_dependencies.sh -o circleci_dependencies.sh
             chmod +x circleci_dependencies.sh
             ./circleci_dependencies.sh
-            pip install .[doc] git+https://github.com/mne-tools/mne-bids@main
 
       - save_cache:
           key: pip-cache

diff --git a/.github/workflows/linux_conda.yml b/.github/workflows/linux_conda.yml
@@ -32,8 +32,6 @@ jobs:
           pyvista: false
       - uses: mamba-org/setup-micromamba@v2
         with:
-          # https://github.com/mamba-org/setup-micromamba/issues/225
-          micromamba-version: 1.5.10-0
           environment-file: environment.yml
           create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
             python=${{ env.PYTHON_VERSION }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Ruff mne_connectivity
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: ruff lint mne_connectivity
@@ -10,7 +10,7 @@ repos:
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.3
     hooks:
       - id: ruff
         name: ruff lint tutorials and examples

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -31,7 +31,6 @@ jobs:
           versionSpec: $(PYTHON_VERSION)
           architecture: $(PYTHON_ARCH)
           addToPath: true
-        condition: eq(variables['TEST_MODE'], 'pip')
       - bash: |
           set -e
           pip install --upgrade --pre numpy scipy matplotlib "h5py<3.7"

diff --git a/doc/_static/style.css b/doc/_static/style.css
@@ -4,9 +4,10 @@
     --pst-font-family-monospace: 'Source Code Pro', var(--pst-font-family-monospace-system);
 }
 
-a[class^="sphx-glr-backref-module-mne_hfo"] {
-  /* make all MNE-BIDS backrefs bold */
+a[class^="sphx-glr-backref-module-mne_connectivity"] {
+  /* make all MNE-Connectivity backrefs bold */
   font-weight: 800;
+  color: var(--pst-color-link);
 }
 
 span.option {
@@ -19,7 +20,7 @@ html[data-theme="light"] {
     --sg-download-a-background-color: var(--pst-color-primary);
     --sg-download-a-background-image: unset;
     --sg-download-a-border-color: var(--pst-color-border);
-    --sg-download-a-color: #fff;
+    --sg-download-a-color: var(--sd-color-primary-text);
     --sg-download-a-hover-background-color: var(--pst-color-primary-highlight);
     --sg-download-a-hover-box-shadow-1: none;
     --sg-download-a-hover-box-shadow-2: none;
@@ -29,21 +30,24 @@ html[data-theme="dark"] {
     --sg-download-a-background-color: var(--pst-color-primary);
     --sg-download-a-background-image: unset;
     --sg-download-a-border-color: var(--pst-color-border);
-    --sg-download-a-color: #000;
+    --sg-download-a-color: var(--sd-color-primary-text);
     --sg-download-a-hover-background-color: var(--pst-color-primary-highlight);
     --sg-download-a-hover-box-shadow-1: none;
     --sg-download-a-hover-box-shadow-2: none;
 }
 
 /* script/notebook download buttons */
-div.sphx-glr-download a {
+.sphx-glr-download a.download {
     border-radius: 0.5rem;
     /* ↓↓↓↓↓↓↓ these two rules copied from sphinx-design */
     box-shadow: 0 .125rem .25rem var(--sd-color-shadow) !important;
+    text-decoration: none;
     transition: color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out;
 }
-
-div.sphx-glr-download a code {
+.sphx-glr-download a.download::before {
+    color: var(--sg-download-a-color);
+}
+.sphx-glr-download a.download code {
     color: var(--sg-download-a-color);
 }
 /* ************************************************* truncate version string */

diff --git a/doc/api.rst b/doc/api.rst
@@ -111,4 +111,5 @@ Dataset functions
 .. autosummary::
    :toctree: generated/
 
-   make_signals_in_freq_bands
+   make_signals_in_freq_bands
+   make_surrogate_data
diff --git a/doc/authors.inc b/doc/authors.inc
@@ -16,3 +16,4 @@
 .. _Richard Köhler: https://github.com/richardkoehler
 .. _Mohammad Orabe: https://github.com/orabe
 .. _Mina Jamshidi: https://github.com/minajamshidi
+.. _Marijn van Vliet: https://github.com/wmvanvliet
diff --git a/doc/conf.py b/doc/conf.py
@@ -259,6 +259,10 @@
 templates_path = ["_templates"]
 html_static_path = ["_static"]
 html_css_files = ["style.css"]
+html_sidebars = {
+    "whats_new": [],
+    "install": [],
+}
 
 switcher_version_match = "dev" if "dev" in release else version
 
@@ -281,6 +285,7 @@
         "json_url": "https://mne.tools/mne-connectivity/dev/_static/versions.json",
         "version_match": switcher_version_match,
     },
+    "back_to_top_button": False,
 }
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
@@ -346,6 +351,7 @@
     "compress_images": ("images", "thumbnails"),
     "image_scrapers": scrapers,
     "expected_failing_examples": ["../examples/granger_causality.py"],
+    "show_signature": False,
 }
 
 # sphinxcontrib-bibtex

diff --git a/doc/references.bib b/doc/references.bib
@@ -61,6 +61,16 @@ @article{Dawson_2016
  year = {2016}
 }
 
+@article{DowdingHaufe2018,
+  title={Powerful statistical inference for nested data using sufficient summary statistics},
+  author={Dowding, Irene and Haufe, Stefan},
+  doi={10.3389/fnhum.2018.00103},
+  journal={Frontiers in Human Neuroscience},
+  volume={12},
+  pages={103},
+  year={2018}
+}
+
 @article{EwaldEtAl2012,
  author = {Ewald, Arne and Marzetti, Laura and Zappasodi, Filippo and Meinecke, Frank C. and Nolte, Guido},
  doi = {10.1016/j.neuroimage.2011.11.084},
@@ -185,6 +195,17 @@ @book{OppenheimEtAl1999
  year = {1999}
 }
 
+@article{PellegriniEtAl2023,
+  title={Identifying good practices for detecting inter-regional linear functional connectivity from {EEG}},
+  author={Pellegrini, Franziska and Delorme, Arnaud and Nikulin, Vadim and Haufe, Stefan},
+  doi={10.1016/j.neuroimage.2023.120218},
+  journal={NeuroImage},
+  volume={277},
+  pages={120218},
+  year={2023},
+  publisher={Elsevier}
+}
+
 @book{SekiharaNagarajan2008,
  author = {Sekihara, Kensuke and Nagarajan, Srikantan S.},
  doi = {10.1007/978-3-540-79370-0},

diff --git a/doc/whats_new.rst b/doc/whats_new.rst
@@ -1,5 +1,3 @@
-:orphan:
-
 .. _whats_new:
 
 
@@ -19,20 +17,36 @@ Here we list a changelog of MNE-connectivity.
 Version 0.8 (in dev)
 --------------------
 
+Minimum supported Python version is now 3.10.
+
 Enhancements
 ~~~~~~~~~~~~
 
-
+- Add a new :class:`~mne_connectivity.decoding.CoherencyDecomposition` class for decomposing connectivity sources using multivariate coherency-based methods, by `Thomas Binns`_ (:pr:`193`).
+- Add new plotting methods :meth:`CoherencyDecomposition.plot_filters() <mne_connectivity.decoding.CoherencyDecomposition.plot_filters>` and :meth:`CoherencyDecomposition.plot_patterns() <mne_connectivity.decoding.CoherencyDecomposition.plot_patterns>` for visualising the decomposed connectivity sources, by `Thomas Binns`_ (:pr:`208`).
+- Add support for computing multiple components of multivariate connectivity in the :func:`~mne_connectivity.spectral_connectivity_epochs` and :func:`~mne_connectivity.spectral_connectivity_time` functions and :class:`~mne_connectivity.decoding.CoherencyDecomposition` class, and add support for storing data with a components dimension in all :class:`~mne_connectivity.Connectivity` classes, by `Thomas Binns`_ and `Eric Larson`_ (:pr:`213`).
+- Add support for :class:`mne.time_frequency.EpochsSpectrum` objects to be passed as data to the :func:`~mne_connectivity.spectral_connectivity_epochs` function, by `Thomas Binns`_ and `Eric Larson`_ (:pr:`220`).
+- Update the cross-references for relevant functions and classes and make data types more explicit throughout the documentation, by `Thomas Binns`_ (:pr:`214`).
 
 Bug
 ~~~
 
+- Improve the documentation of the ``fmin`` and ``cwt_freqs`` parameters in the :func:`~mne_connectivity.spectral_connectivity_epochs` function, by `Richard Köhler`_ and `Daniel McCloy`_ (:pr:`242`).
 
+API
+~~~
+
+- Add a new ``min_distance`` parameter to the :func:`~mne_connectivity.viz.plot_sensors_connectivity` function which offers greater control over the minimum distance required between sensors to plot a connection between them, by `Thomas Binns`_ and `Eric Larson`_ (:pr:`221`).
 
 Authors
 ~~~~~~~
 
-
+* `Thomas Binns`_
+* `Richard Köhler`_
+* `Adam Li`_
+* `Marijn van Vliet`_
+* `Eric Larson`_
+* `Daniel McCloy`_
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`