Merge remote-tracking branch 'upstream/main' into enh/crop_by_annot

* upstream/main: (52 commits)
  MAINT: Extra test for coreg (mne-tools#10549)
  BUG: Fix annot meas_date / crop (mne-tools#10491)
  Update latest.inc
  Use liblinear solver instead of lbgfs in all decodung examples [skip azp][skip actions] (mne-tools#10552)
  STY: Hotfix for HTML [ci skip]
  Allow making inverse solutions from fixed-orientation discrete forward models, enabling multi-dipole modeling (mne-tools#10464)
  Correct documented default number of CV splits [skip azp][skip actions] (mne-tools#10548)
  MRG: Add error checking to prevent the creation of montage with invalid [x, y, z] (mne-tools#10547)
  MRG: Add "verbose" parameter to pick_channels() method (mne-tools#10544)
  CI: Avoid bad PySide6 (mne-tools#10545)
  FIX: Flake (mne-tools#10540)
  FIX: Correct link (mne-tools#10536)
  DOC: Update installers (mne-tools#10535)
  ENH: Add dark mode to website (mne-tools#10523)
  WIP: Copy BEM surfaces by default (don't symlink) (mne-tools#10531)
  Avoid lowpass=0 in brainvision data (mne-tools#10517)
  DOC: Update installers [skip azp] [skip actions] (mne-tools#10528)
  FIX: Fix for old build (mne-tools#10527)
  Fix line noise at wrong frequencies (mne-tools#10525)
  FIX : read fids in eeglab (mne-tools#10521)
  ...

Author: larsoner

.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:

.github/workflows/circle_artifacts.yml

@@ -9,5 +9,5 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           artifact-path: 0/dev/index.html
-          circleci-jobs: build_docs_pr,build_docs_nightly
+          circleci-jobs: build_docs,build_docs_main
           job-title: Check the rendered docs here!

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
@@ -101,21 +103,21 @@ stages:
       displayName: 'Test minimal commands'
     - task: UsePythonVersion@0
       inputs:
-        versionSpec: '3.8'
+        versionSpec: '3.9'
         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]
+        python -m pip install --progress-bar off mne-qt-browser[opengl] vtk scikit-learn pytest-error-for-skips python-picard "PySide6!=6.3.0" 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'
@@ -126,8 +128,98 @@ stages:
       displayName: 'Cache testing data'
     - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
       displayName: 'Get test data'
-    - script: pytest -m "ultraslowtest or pgtest" --tb=short --cov=mne --cov-report=xml --cov-report=html -vv mne
-      displayName: 'Run ultraslow and mne-qt-browser tests'
+    - script: pytest --error-for-skips -m "ultraslowtest or pgtest" --tb=short --cov=mne --cov-report=xml --cov-report=html -vv mne
+      displayName: 'slow and mne-qt-browser tests'
+    # Coverage
+    - bash: bash <(curl -s https://codecov.io/bash)
+      displayName: 'Codecov'
+      condition: succeededOrFailed()
+    - task: PublishTestResults@2
+      inputs:
+        testResultsFiles: '**/junit-*.xml'
+        testRunTitle: 'Publish test results for $(Agent.JobName)'
+        failTaskOnFailedTests: true
+      condition: succeededOrFailed()
+    - task: PublishCodeCoverageResults@1
+      inputs:
+        codeCoverageTool: Cobertura
+        summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml'
+        reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov'
+
+  - job: Qt
+    pool:
+      vmImage: 'ubuntu-20.04'
+    variables:
+      DISPLAY: ':99'
+      OPENBLAS_NUM_THREADS: '1'
+      TEST_OPTIONS: "--tb=short --cov=mne --cov-report=xml --cov-report=html --cov-append -vv mne/viz/_brain mne/viz/backends mne/viz/tests/test_evoked.py mne/gui"
+    steps:
+    - bash: ./tools/setup_xvfb.sh
+      displayName: 'Install Ubuntu dependencies'
+    - task: UsePythonVersion@0
+      inputs:
+        versionSpec: '3.10'
+        architecture: 'x64'
+        addToPath: true
+      displayName: 'Get Python'
+    - bash: |
+        set -e
+        python -m pip install --progress-bar off --upgrade pip setuptools wheel
+        python -m pip install --progress-bar off --upgrade --only-binary=\"numpy,scipy,matplotlib\" numpy scipy matplotlib
+        wget -q https://osf.io/ajder/download -O vtk-9.1.20220406.dev0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+        python -m pip install --pre --only-binary ":all:" vtk-9.1.20220406.dev0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+        python -c "import vtk"
+        python -m pip install --progress-bar off --upgrade -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt codecov
+        python -m pip install -e .
+      displayName: 'Install dependencies with pip'
+    - bash: |
+        set -e
+        which mne
+        mne sys_info -pd
+        mne sys_info -pd | grep "^mne: .*dev0.*$"
+      displayName: Print config
+    - bash: source tools/get_testing_version.sh
+      displayName: 'Get testing version'
+    - task: Cache@2
+      inputs:
+        key: $(testing_version)
+        path: /home/vsts/mne_data
+      displayName: 'Cache testing data'
+    - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
+      displayName: 'Get test data'
+    - bash: |
+        set -e
+        mne sys_info -pd
+        mne sys_info -pd | grep "qtpy: .*{PySide6=.*}$"
+        pytest -m "not slowtest" ${TEST_OPTIONS}
+        python -m pip uninstall -yq PySide6
+      displayName: 'PySide6'
+    - bash: |
+        set -e
+        python -m pip install PyQt6
+        mne sys_info -pd
+        mne sys_info -pd | grep "^qtpy: .*{PyQt6=.*}$"
+        pytest -m "not slowtest" ${TEST_OPTIONS}
+        python -m pip uninstall -yq PyQt6 PyQt6-sip PyQt6-Qt6
+      displayName: 'PyQt6'
+    - bash: |
+        set -e
+        python -m pip install PySide2
+        mne sys_info -pd
+        mne sys_info -pd | grep "^qtpy: .*{PySide2=.*}$"
+        pytest -m "not slowtest" ${TEST_OPTIONS}
+        python -m pip uninstall -yq PySide2
+      displayName: 'PySide2'
+    # PyQt5 leaves cruft behind, so run it last
+    - bash: |
+        set -e
+        python -m pip install PyQt5
+        mne sys_info -pd
+        mne sys_info -pd | grep "^qtpy: .*{PyQt5=.*}$"
+        pytest -m "not slowtest" ${TEST_OPTIONS}
+        python -m pip uninstall -yq PyQt5 PyQt5-sip PyQt5-Qt5
+      displayName: 'PyQt5'
+    # Coverage
     - bash: bash <(curl -s https://codecov.io/bash)
       displayName: 'Codecov'
       condition: succeededOrFailed()
@@ -165,9 +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'