Merge branch 'main' into doc

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
       - id: ruff
         name: ruff lint mne

azure-pipelines.yml

@@ -111,7 +111,7 @@ 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
+              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 uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -201,7 +201,7 @@ stages:
             displayName: 'PyQt6'
           - bash: |
               set -eo pipefail
-              python -m pip install PySide6
+              python -m pip install "PySide6!=6.8.0,!=6.8.0.1"
               mne sys_info -pd
               mne sys_info -pd | grep "qtpy .* (PySide6=.*)$"
               PYTEST_QT_API=PySide6 pytest ${TEST_OPTIONS}

doc/changes/devel/12901.bugfix.rst

@@ -0,0 +1 @@
+:class:`mne.Report` HDF5 files are now written in ``mode='a'`` (append) to allow users to store other data in the HDF5 files, by `Eric Larson`_.

doc/changes/devel/12901.newfeature.rst

@@ -0,0 +1,8 @@
+Improved reporting and plotting options:
+
+- :meth:`mne.Report.add_projs` can now plot with :func:`mne.viz.plot_projs_joint` rather than :func:`mne.viz.plot_projs_topomap`
+- :class:`mne.Report` now has attributes ``img_max_width`` and ``img_max_res`` that can be used to control image scaling.
+- :class:`mne.Report` now has an attribute ``collapse`` that allows collapsing sections and/or subsections by default.
+- :func:`mne.viz.plot_head_positions` now has a ``totals=True`` option to show the total distance and angle of the head.
+
+Changes by `Eric Larson`_.

doc/changes/devel/12909.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :func:`mne.io.read_raw_gdf` when NumPy >= 2 is used, by `Clemens Brunner`_.

environment.yml

@@ -2,7 +2,7 @@ name: mne
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
+  - python >=3.10
   - pip
   - numpy
   - scipy
@@ -28,25 +28,25 @@ dependencies:
   - psutil
   - numexpr
   - imageio
-  - spyder-kernels>=1.10.0
-  - imageio>=2.6.1
-  - imageio-ffmpeg>=0.4.1
-  - vtk>=9.2
+  - spyder-kernels >=1.10.0
+  - imageio >=2.6.1
+  - imageio-ffmpeg >=0.4.1
+  - vtk >=9.2
   - traitlets
-  - pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0
-  - pyvistaqt>=0.4
-  - qdarkstyle!=3.2.2
+  - pyvista >=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0
+  - pyvistaqt >=0.4
+  - qdarkstyle !=3.2.2
   - darkdetect
   - dipy
   - nibabel
-  - openmeeg>=2.5.5
+  - openmeeg >=2.5.5
   - nilearn
   - python-picard
   - qtpy
-  - pyside6
+  - pyside6 !=6.8.0,!=6.8.0.1
   - mne-base
   - seaborn-base
-  - mffpy>=0.5.7
+  - mffpy >=0.5.7
   - ipyevents
   - ipywidgets
   - ipympl
@@ -59,7 +59,7 @@ dependencies:
   - mne-qt-browser
   - pymatreader
   - eeglabio
-  - edfio>=0.2.1
+  - edfio >=0.2.1
   - pybv
   - mamba
   - lazy_loader

mne/html_templates/report/html.html.jinja

@@ -1,7 +1,6 @@
 <div class="accordion-item {{ div_klass }}" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
   <div class="accordion-header" id="accordion-header-{{id}}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{id}}">
+    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse" data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{id}}">
       <div class="w-100">
         <span class="me-auto"><a href="#{{ id }}" class="text-decoration-none">{{ title }}</a></span>
         {% for tag in tags %}
@@ -12,10 +11,7 @@
       </div>
     </button>
   </div>
-
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
+  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse {{ show }}" aria-labelledby="accordion-header-{{ id }}">
     <div class="accordion-body">
       {{ html | safe }}
     </div>

mne/html_templates/report/image.html.jinja

@@ -1,17 +1,17 @@
 {% extends "section.html.jinja" %}
 {% block html_content %}
-<figure class="figure mx-auto d-block">
-  {% if image_format == 'svg' %}
-  <div class="d-flex justify-content-center">
-    {{ img|safe }}
-  </div>
-  {% else %}
-  <img class="figure-img img-fluid rounded mx-auto my-0 d-block" alt="{{ title }}"
-    src="data:image/{{ image_format }};base64,{{ img }}">
-  {% endif %}
+      <figure class="figure mx-auto d-block">
+        {% if image_format == 'svg' %}
+        <div class="d-flex justify-content-center">
+          {{ img|safe }}
+        </div>
+        {% else %}
+        <img class="figure-img img-fluid rounded mx-auto my-0 d-block" alt="{{ title }}"
+          src="data:image/{{ image_format }};base64,{{ img }}">
+        {% endif %}
 
-  {% if caption is not none %}
-  <figcaption class="figure-caption text-center">{{ caption }}</figcaption>
-  {% endif %}
-</figure>
+        {% if caption is not none %}
+        <figcaption class="figure-caption text-center">{{ caption }}</figcaption>
+        {% endif %}
+      </figure>
 {% endblock html_content %}

mne/html_templates/report/section.html.jinja

@@ -1,7 +1,6 @@
 <div class="accordion-item {{ div_klass }}" id="{{ id }}" data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
   <div class="accordion-header" id="accordion-header-{{id}}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{id}}">
+    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse" data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{id}}">
       <div class="w-100">
         <span class="me-auto"><a href="#{{ id }}" class="text-decoration-none">{{ title }}</a></span>
         {% for tag in tags %}
@@ -12,10 +11,7 @@
       </div>
     </button>
   </div>
-
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
+  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse {{ show }}" aria-labelledby="accordion-header-{{ id }}">
     <div class="accordion-body">
       {% block html_content %}
       {% for html in htmls %}

mne/html_templates/report/slider.html.jinja

@@ -1,8 +1,7 @@
 <div class="accordion-item slider {{ klass }}" id="{{ id }}"
   data-mne-tags="{% for tag in tags %} {{ tag }} {% endfor %}">
   <div class="accordion-header" id="accordion-header-{{ id }}">
-    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse"
-      data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
+    <button class="accordion-button pt-1 pb-1" type="button" data-bs-toggle="collapse" data-bs-target="#accordion-collapse-{{ id }}" aria-expanded="true" aria-controls="accordion-collapse-{{ id }}">
       <div class="w-100">
         <span class="me-auto"><a href="#{{ id }}" class="text-decoration-none">{{ title }}</a></span>
         {% for tag in tags %}
@@ -13,9 +12,7 @@
       </div>
     </button>
   </div>
-
-  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse show"
-    aria-labelledby="accordion-header-{{ id }}">
+  <div id="accordion-collapse-{{ id }}" class="accordion-collapse collapse {{ show }}" aria-labelledby="accordion-header-{{ id }}">
     <div class=" accordion-body">
       <div class="mx-auto d-block w-75">
         <label for="slider-{{ id }}" class="form-label small">
@@ -24,9 +21,7 @@
         <input type="range" class="form-range" min="0" max="{{ images|length - 1 }}" value="{{ start_idx }}"
           id="slider-{{id}}">
       </div>
-
-      <div id="corousel-{{ id }}" class="carousel carousel-dark" data-bs-interval="false" data-bs-wrap="false"
-        data-bs-keyboard="true">
+      <div id="corousel-{{ id }}" class="carousel carousel-dark" data-bs-interval="false" data-bs-wrap="false" data-bs-keyboard="true">
         <div class="carousel-inner">
           {% for idx, img, caption in range(images|length)|zip(images, captions) %}
           <div class="carousel-item {% if idx == start_idx %}active{% endif %}">
@@ -40,7 +35,6 @@
           </div>
           {% endfor %}
         </div>
-
         {# <button class="carousel-control-prev" type="button" data-bs-target="#corousel-{{id}}" data-bs-slide="prev">
           <span class="carousel-control-prev-icon" aria-hidden="true"></span>
           <span class="visually-hidden">Previous</span>

mne/io/edf/edf.py

@@ -1443,7 +1443,7 @@ def _read_gdf_header(fname, exclude, include=None):
                     ne = np.fromfile(fid, UINT8, 3)
                     n_events = ne[0]
                     for i in range(1, len(ne)):
-                        n_events = n_events + ne[i] * 2 ** (i * 8)
+                        n_events = n_events + int(ne[i]) * 2 ** (i * 8)
                     event_sr = np.fromfile(fid, FLOAT32, 1)[0]
 
                 pos = np.fromfile(fid, UINT32, n_events) - 1  # 1-based inds