MAINT: Prefer PySide6 in testing

.circleci/config.yml

@@ -11,22 +11,14 @@
 
 version: 2.1
 
-_xvfb: &xvfb
-  name: Start Xvfb virtual framebuffer
-  command: |
-    echo "export DISPLAY=:99" >> $BASH_ENV
-    /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1280x1024x24 -ac +extension GLX +render -noreset -nolisten tcp -nolisten unix
-
 jobs:
     build_docs:
       parameters:
         scheduled:
           type: string
           default: "false"
       docker:
-        # Use 18.04 rather than 20.04 because MESA 20.0.8 on 18.04 has working
-        # transparency but 21.0.3 on 20.04 does not!
-        - image: cimg/base:stable-18.04
+        - image: cimg/base:stable-20.04
       steps:
         - restore_cache:
             keys:
@@ -95,23 +87,20 @@ jobs:
             name: Set BASH_ENV
             command: |
               set -e
-              sudo apt update -qq
-              sudo apt install -qq libosmesa6 libglx-mesa0 libopengl0 libglx0 libdbus-1-3 \
-                libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 \
-                libxcb-render-util0 libxcb-shape0 libxcb-xfixes0 libxcb-xinerama0 \
-                graphviz optipng \
-                python3.8-venv python3-venv \
-                xvfb libxft2 ffmpeg
+              ./tools/setup_xvfb.sh
+              sudo apt install -qq graphviz optipng python3.8-venv python3-venv libxft2 ffmpeg
               python3.8 -m venv ~/python_env
               echo "set -e" >> $BASH_ENV
               echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
               echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
               echo "export MNE_FULL_DATE=true" >> $BASH_ENV
               source tools/get_minimal_commands.sh
               echo "export MNE_3D_BACKEND=pyvistaqt" >> $BASH_ENV
+              echo "export MNE_3D_OPTION_MULTI_SAMPLES=1" >> $BASH_ENV
               echo "export MNE_BROWSER_BACKEND=qt" >> $BASH_ENV
               echo "export MNE_BROWSER_PRECOMPUTE=false" >> $BASH_ENV
               echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
+              echo "export DISPLAY=:99" >> $BASH_ENV
               echo "source ~/python_env/bin/activate" >> $BASH_ENV
               mkdir -p ~/.local/bin
               ln -s ~/python_env/bin/python ~/.local/bin/python
@@ -124,9 +113,6 @@ jobs:
             command: |
               neuromag2ft --version
 
-        - run:
-            <<: *xvfb
-
         - run:
             name: Install fonts needed for diagrams
             command: |
@@ -160,8 +146,8 @@ jobs:
               - ~/.local/bin
 
         - run:
-            name: Check PyQt5
-            command: LD_DEBUG=libs python -c "from PyQt5.QtWidgets import QApplication, QWidget; app = QApplication([])"
+            name: Check Qt
+            command: LD_DEBUG=libs python -c "from PySide6.QtWidgets import QApplication, QWidget; app = QApplication([])"
 
         # Load tiny cache so that ~/.mne does not need to be created below
         - restore_cache:

azure-pipelines.yml

@@ -89,7 +89,9 @@ stages:
       OPENBLAS_NUM_THREADS: '1'
     steps:
     - bash: |
-        sudo apt install libxkbcommon-x11-0 xvfb tcsh libxcb*
+        set -e
+        ./tools/setup_xvfb.sh
+        sudo apt install -yq tcsh
       displayName: 'Install Ubuntu dependencies'
     - bash: |
         source tools/get_minimal_commands.sh
@@ -105,17 +107,17 @@ stages:
         architecture: 'x64'
         addToPath: true
       displayName: 'Get Python'
-    - bash: |
-        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
-      displayName: 'Spin up Xvfb'
     - bash: |
         set -e
         python -m pip install --progress-bar off --upgrade pip setuptools wheel codecov
-        python -m pip install --progress-bar off mne-qt-browser[opengl] vtk scikit-learn pytest-error-for-skips python-picard
+        python -m pip install --progress-bar off mne-qt-browser[opengl] vtk scikit-learn pytest-error-for-skips python-picard PySide6 qtpy
         python -m pip uninstall -yq mne
         python -m pip install --progress-bar off --upgrade -e .[test]
       displayName: 'Install dependencies with pip'
-    - script: mne sys_info -pd
+    - bash: |
+        set -e
+        mne sys_info -pd
+        mne sys_info -pd | grep "qtpy: .*{PySide6=.*}$"
       displayName: Print config
     - bash: source tools/get_testing_version.sh
       displayName: 'Get testing version'
@@ -152,10 +154,7 @@ stages:
       OPENBLAS_NUM_THREADS: '1'
       TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-report=html --cov-append -vv mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/gui"
     steps:
-    - bash: |
-        set -e
-        ./tools/setup_xvfb.sh
-        sudo apt install libegl1
+    - bash: ./tools/setup_xvfb.sh
       displayName: 'Install Ubuntu dependencies'
     - task: UsePythonVersion@0
       inputs:
@@ -191,10 +190,10 @@ stages:
     - bash: |
         set -e
         mne sys_info -pd
-        mne sys_info -pd | grep "^qtpy: .*{PyQt5=.*}$"
+        mne sys_info -pd | grep "qtpy: .*{PySide6=.*}$"
         pytest -m "not slowtest" ${TEST_OPTIONS}
-        python -m pip uninstall -yq PyQt5 PyQt5-sip PyQt5-Qt5
-      displayName: 'PyQt5'
+        python -m pip uninstall -yq PySide6
+      displayName: 'PySide6'
     - bash: |
         set -e
         python -m pip install PyQt6
@@ -211,14 +210,15 @@ stages:
         pytest -m "not slowtest" ${TEST_OPTIONS}
         python -m pip uninstall -yq PySide2
       displayName: 'PySide2'
+    # PyQt5 leaves cruft behind, so run it last
     - bash: |
         set -e
-        python -m pip install PySide6
+        python -m pip install PyQt5
         mne sys_info -pd
-        mne sys_info -pd | grep "qtpy: .*{PySide6=.*}$"
+        mne sys_info -pd | grep "^qtpy: .*{PyQt5=.*}$"
         pytest -m "not slowtest" ${TEST_OPTIONS}
-        python -m pip uninstall -yq PySide6
-      displayName: 'PySide6'
+        python -m pip uninstall -yq PyQt5 PyQt5-sip PyQt5-Qt5
+      displayName: 'PyQt5'
     # Coverage
     - bash: bash <(curl -s https://codecov.io/bash)
       displayName: 'Codecov'
@@ -257,9 +257,9 @@ stages:
           PLATFORM: 'x86-64'
           TEST_MODE: 'conda'
           PYTHON_VERSION: '3.9'
-        3.7 pip:
+        3.9 pip:
           TEST_MODE: 'pip'
-          PYTHON_VERSION: '3.7'
+          PYTHON_VERSION: '3.9'
         3.10 pip pre:
           TEST_MODE: 'pip-pre'
           PYTHON_VERSION: '3.10'

doc/changes/latest.inc

@@ -33,6 +33,8 @@ Bugs
 
 - Fix bug where ``theme`` was not handled properly in :meth:`mne.io.Raw.plot` (:gh:`10487`, :gh:`10500` by `Mathieu Scheltienne`_ and `Eric Larson`_)
 
+- Rendering issues with recent MESA releases can be avoided by setting the new environment variable``MNE_3D_OPTION_MULTI_SAMPLES=1`` or using :func:`mne.viz.set_3d_options` (:gh:`10513` by `Eric Larson`_)
+
 - Fix behavior for the ``pyvista`` 3D renderer's ``quiver3D`` function so that default arguments plot a glyph in ``arrow`` mode (:gh:`10493` by `Alex Rockhill`_)
 
 - Retain epochs metadata when using :func:`mne.channels.combine_channels` (:gh:`10504` by `Clemens Brunner`_)

doc/conf.py

@@ -33,6 +33,7 @@
 os.environ['_MNE_BROWSER_NO_BLOCK'] = 'true'
 os.environ['MNE_BROWSER_OVERVIEW_MODE'] = 'hidden'
 os.environ['MNE_BROWSER_THEME'] = 'light'
+os.environ['MNE_3D_OPTION_THEME'] = 'light'
 
 # -- Path setup --------------------------------------------------------------
 
@@ -311,9 +312,9 @@ def __call__(self, gallery_conf, fname, when):
         except ImportError:
             vtkPolyData = None  # noqa
         try:
-            from mne_qt_browser._pg_figure import PyQtGraphBrowser
+            from mne_qt_browser._pg_figure import MNEQtBrowser
         except ImportError:
-            PyQtGraphBrowser = None
+            MNEQtBrowser = None
         from mne.viz.backends.renderer import backend
         _Renderer = backend._Renderer if backend is not None else None
         reset_warnings(gallery_conf, fname)
@@ -332,7 +333,7 @@ def __call__(self, gallery_conf, fname, when):
         when = f'mne/conf.py:Resetter.__call__:{when}:{fname}'
         # Support stuff like
         # MNE_SKIP_INSTANCE_ASSERTIONS="Brain,Plotter,BackgroundPlotter,vtkPolyData,_Renderer" make html_dev-memory  # noqa: E501
-        # to just test PyQtGraphBrowser
+        # to just test MNEQtBrowser
         skips = os.getenv('MNE_SKIP_INSTANCE_ASSERTIONS', '').lower()
         prefix = ''
         if skips not in ('true', '1', 'all'):
@@ -349,15 +350,15 @@ def __call__(self, gallery_conf, fname, when):
                 _assert_no_instances(vtkPolyData, when)
             if '_renderer' not in skips:
                 _assert_no_instances(_Renderer, when)
-            if PyQtGraphBrowser is not None and \
-                    'pyqtgraphbrowser' not in skips:
+            if MNEQtBrowser is not None and \
+                    'mneqtbrowser' not in skips:
                 # Ensure any manual fig.close() events get properly handled
                 from mne_qt_browser._pg_figure import QApplication
                 inst = QApplication.instance()
                 if inst is not None:
                     for _ in range(2):
                         inst.processEvents()
-                _assert_no_instances(PyQtGraphBrowser, when)
+                _assert_no_instances(MNEQtBrowser, when)
         # This will overwrite some Sphinx printing but it's useful
         # for memory timestamps
         if os.getenv('SG_STAMP_STARTS', '').lower() == 'true':
@@ -394,7 +395,7 @@ def __call__(self, gallery_conf, fname, when):
     import mne_qt_browser
     _min_ver = _compare_version(mne_qt_browser.__version__, '>=', '0.2')
     if mne.viz.get_browser_backend() == 'qt' and _min_ver:
-        scrapers += (mne.viz._scraper._PyQtGraphScraper(),)
+        scrapers += (mne.viz._scraper._MNEQtBrowserScraper(),)
 except ImportError:
     pass
 
@@ -892,6 +893,9 @@ def reset_warnings(gallery_conf, fname):
     warnings.filterwarnings(
         'ignore', message=r'numpy\.ndarray size changed.*',
         category=RuntimeWarning)
+    warnings.filterwarnings(
+        'ignore', message=r'.*Setting theme=.*6 in qdarkstyle.*',
+        category=RuntimeWarning)
 
     # In case we use np.set_printoptions in any tutorials, we only
     # want it to affect those:

doc/install/advanced.rst

@@ -191,6 +191,12 @@ to force MESA to use modern OpenGL by using this before executing
 
 Also, it's possible that different software rending backends might perform
 better than others, such as using the ``llvmpipe`` backend rather than ``swr``.
+In newer MESA (21+), rendering can be incorrect when using MSAA, so consider
+setting:
+
+.. code-block:: console
+
+    export MNE_3D_OPTION_MULTI_SAMPLES=1
 
 MESA also can have trouble with full-screen antialiasing, which you can
 disable with:

doc/install/check_installation.rst

@@ -27,7 +27,7 @@ MNE-Python and its dependencies. Typical output looks like this::
     mne:           0.21.dev0
     numpy:         1.19.0.dev0+8dfaa4a {blas=openblas, lapack=openblas}
     scipy:         1.5.0.dev0+f614064
-    matplotlib:    3.2.1 {backend=Qt5Agg}
+    matplotlib:    3.2.1 {backend=QtAgg}
 
     sklearn:       0.22.2.post1
     numba:         0.49.0
@@ -37,7 +37,7 @@ MNE-Python and its dependencies. Typical output looks like this::
     dipy:          1.1.1
     pyvista:       0.25.2 {pyvistaqt=0.1.0}
     vtk:           9.0.0
-    qtpy:          2.0.1 {PyQt5=5.14.1}
+    qtpy:          2.0.1 {PySide6=6.2.4}
 
 
 .. collapse:: |hand-paper| If you get an error...

mne/conftest.py

@@ -440,8 +440,7 @@ def _check_pyqtgraph(request):
         pytest.skip('Requires mne_qt_browser')
     else:
         ver = mne_qt_browser.__version__
-        req_pyqt5 = _compare_version(ver, '<=', '0.2.6')
-        if api != 'PyQt5' and req_pyqt5:
+        if api != 'PyQt5' and _compare_version(ver, '<=', '0.2.6'):
             pytest.skip(f'mne_qt_browser {ver} requires PyQt5, API is {api}')
 
 

mne/utils/config.py

@@ -70,6 +70,7 @@ def set_memmap_min_size(memmap_min_size):
 known_config_types = (
     'MNE_3D_OPTION_ANTIALIAS',
     'MNE_3D_OPTION_DEPTH_PEELING',
+    'MNE_3D_OPTION_MULTI_SAMPLES',
     'MNE_3D_OPTION_SMOOTH_SHADING',
     'MNE_3D_OPTION_THEME',
     'MNE_BROWSE_RAW_SIZE',

mne/utils/misc.py

@@ -366,6 +366,12 @@ def _assert_no_instances(cls, when=''):
                         del r_
                     else:
                         rep = repr(r)[:100].replace('\n', ' ')
+                        # If it's a __closure__, get more information
+                        if rep.startswith('<cell at '):
+                            try:
+                                rep += f' ({repr(r.cell_contents)[:100]})'
+                            except Exception:
+                                pass
                     name = _fullname(r)
                     ref.append(f'{name}: {rep}')
                     count += 1

mne/viz/_3d.py

@@ -3292,24 +3292,28 @@ def plot_brain_colorbar(ax, clim, colormap='auto', transparent=True,
 
 @dataclass()
 class _3d_Options:
-    antialias: Optional[str]
-    depth_peeling: Optional[str]
-    smooth_shading: Optional[str]
+    antialias: Optional[bool]
+    depth_peeling: Optional[bool]
+    smooth_shading: Optional[bool]
+    multi_samples: Optional[int]
 
 
 _3d_options = _3d_Options(
     antialias=None,
     depth_peeling=None,
     smooth_shading=None,
+    multi_samples=None,
 )
 _3d_default = _3d_Options(
     antialias='true',
     depth_peeling='true',
     smooth_shading='true',
+    multi_samples='4',
 )
 
 
-def set_3d_options(antialias=None, depth_peeling=None, smooth_shading=None):
+def set_3d_options(antialias=None, depth_peeling=None, smooth_shading=None, *,
+                   multi_samples=None):
     """Set 3D rendering options.
 
     Parameters
@@ -3332,25 +3336,34 @@ def set_3d_options(antialias=None, depth_peeling=None, smooth_shading=None):
         where this type of shading is not supported or for performance
         reasons. This option can also be controlled using an environment
         variable, e.g., ``MNE_3D_OPTION_SMOOTH_SHADING=false``.
+    multi_samples : int
+        Number of multi-samples. Should be 1 for MESA for volumetric rendering
+        to work properly.
+
+        .. versionadded:: 1.1
 
     Notes
     -----
     .. versionadded:: 0.21.0
     """
     if antialias is not None:
-        _3d_options.antialias = str(bool(antialias)).lower()
+        _3d_options.antialias = bool(antialias)
     if depth_peeling is not None:
-        _3d_options.depth_peeling = str(bool(depth_peeling)).lower()
+        _3d_options.depth_peeling = bool(depth_peeling)
     if smooth_shading is not None:
-        _3d_options.smooth_shading = str(bool(smooth_shading)).lower()
+        _3d_options.smooth_shading = bool(smooth_shading)
+    if multi_samples is not None:
+        _3d_options.multi_samples = int(multi_samples)
 
 
 def _get_3d_option(key):
     _validate_type(key, 'str', 'key')
     opt = getattr(_3d_options, key)
-    if opt is None:
+    if opt is None:  # parse get_config (and defaults)
         default_value = getattr(_3d_default, key)
         opt = get_config(f'MNE_3D_OPTION_{key.upper()}', default_value)
-    opt = opt.lower()
-    _check_option(f'3D option {key}', opt, ('true', 'false'))
-    return opt == 'true'
+        if key == 'multi_samples':
+            opt = int(opt)
+        else:
+            opt = opt.lower() == 'true'
+    return opt