Merge remote-tracking branch 'upstream/master' into resize

* upstream/master: (23 commits)
  MAINT: Add mne.surface to docstring tests (mne-tools#7930)
  MRG: Add smoothing controller to TimeViewer for the notebook backend (mne-tools#7928)
  MRG: TimeViewer matplotlib figure color (mne-tools#7925)
  fix typos (mne-tools#7924)
  MRG, ENH: Add method to project onto max power ori (mne-tools#7883)
  WIP: Warn if untested NIRX device (mne-tools#7905)
  MRG, BUG: Fix bug with volume morph and subject_to!="fsaverage" (mne-tools#7896)
  MRG, MAINT: Clean up use of bool, float, int (mne-tools#7917)
  ENH: Better error message for incompatible Evoked objects (mne-tools#7910)
  try to fix nullcontext (mne-tools#7908)
  WIP: Fix Travis (mne-tools#7906)
  WIP: Prototype of notebook viz (screencast) (mne-tools#7758)
  MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904)
  Proper attribution for Blender tutorial (mne-tools#7900)
  MAINT: Check usage [ci skip] (mne-tools#7902)
  Allow find_bad_channels_maxwell() to return scores (mne-tools#7845)
  Warn if NIRx directory structure has been modified from original format (mne-tools#7898)
  Pin pvyista to 0.24.3 (mne-tools#7899)
  MRG: Add support for reading and writing sufaces to .obj (mne-tools#7824)
  Fix _auto_topomap_coords docstring. (mne-tools#7895)
  ...

Author: larsoner

.circleci/config.yml

@@ -56,7 +56,7 @@ jobs:
             name: Install 3D rendering libraries \ PyQt5 dependencies \ graphviz \ optipng (for optimized images)
             command: |
               sudo apt-get install libosmesa6 libglx-mesa0 libopengl0 libglx0 libdbus-1-3 \
-                  libxkbcommon-x11-0 \
+                  libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-shape0 libxcb-xfixes0 libxcb-xinerama0 \
                   graphviz \
                   optipng
 
@@ -81,7 +81,6 @@ jobs:
             command: |
               python -m pip install --user --upgrade --progress-bar off pip numpy setuptools
               python -m pip install --user --upgrade --progress-bar off -f "https://vtk.org/download" "vtk>=9"
-              python -m pip install --user --upgrade --progress-bar off https://github.com/enthought/mayavi/zipball/master
               python -m pip install --user --upgrade --progress-bar off -r requirements.txt
               python -m pip uninstall -yq pysurfer mayavi
               python -m pip install --user --upgrade --progress-bar off --pre sphinx
@@ -94,6 +93,10 @@ jobs:
             paths:
               - ~/.cache/pip
 
+        - run:
+            name: Check PyQt5
+            command: LD_DEBUG=libs python -c "from PyQt5.QtWidgets import QApplication, QWidget; app = QApplication([])"
+
         # Look at what we have and fail early if there is some library conflict
         - run:
             name: Check installation

.gitignore

@@ -46,6 +46,7 @@ coverage
 .pytest_cache/
 __pycache__/
 prof/
+mne/viz/_brain/tests/.ipynb_checkpoints
 
 dist/
 doc/_build/

.travis.yml

@@ -6,6 +6,7 @@ addons:
   apt:
     packages:
       - libxkbcommon-x11-0
+      - libxcb*
       - libosmesa6
       - libglx-mesa0
       - libopengl0
@@ -52,22 +53,21 @@ before_install:
     - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
         /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
       fi;
-    - if [ -z "$CONDA_ENV" ] && [ -z "$CONDA_DEPENDENCIES" ]; then
-        pip uninstall -yq numpy;
-        pip install -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" --pre numpy;
-        pip install -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" scipy pandas scikit-learn matplotlib h5py Pillow;
-        pip install -f "https://vtk.org/download" "vtk>=9";
-        pip install https://github.com/enthought/mayavi/zipball/master;
-        pip install $PIP_DEPENDENCIES;
-        pip install --upgrade -r requirements.txt;
+    - |
+      if [ -z "$CONDA_ENV" ] && [ -z "$CONDA_DEPENDENCIES" ]; then
+        pip uninstall -yq numpy
+        pip install -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" --pre numpy
+        pip install -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" scipy pandas scikit-learn matplotlib h5py Pillow
+        pip install -f "https://vtk.org/download" "vtk>=9"
+        pip install --upgrade -r requirements.txt
       else
-        git clone https://github.com/astropy/ci-helpers.git;
-        source ci-helpers/travis/setup_conda.sh;
+        git clone https://github.com/astropy/ci-helpers.git
+        source ci-helpers/travis/setup_conda.sh
         if [ ! -z "$CONDA_ENV" ]; then
-          conda activate base;
-          conda env update --file $CONDA_ENV;
-          pip uninstall -yq mne;
-        fi;
+          conda activate base
+          conda env update --file $CONDA_ENV
+          pip uninstall -yq mne
+        fi
       fi
     # Always install these via pip so we get the latest possible versions (testing bugfixes)
     - pip install --upgrade "pytest<5.4" pytest-sugar pytest-cov pytest-mock pytest-timeout pytest-xdist codecov
@@ -141,7 +141,7 @@ script:
         pip install -e .;
         python mne/tests/test_evoked.py;
       fi;
-    - echo pytest -m "${CONDITION}" --cov=mne -n 1 ${USE_DIRS}
+    - echo 'pytest -m "${CONDITION}" --cov=mne -n 1 ${USE_DIRS}'
     - pytest -m "${CONDITION}" --tb=short --cov=mne -n 1 ${USE_DIRS}
     # run the minimal one with the testing data
     - if [ "${DEPS}" == "minimal" ]; then

MANIFEST.in

@@ -32,6 +32,7 @@ recursive-include mne mne/datasets *.csv
 include mne/io/edf/gdf_encodes.txt
 include mne/datasets/sleep_physionet/SHA1SUMS
 include mne/externals/tqdm/_tqdm/tqdm.1
+include mne/viz/_brain/tests/test.ipynb
 
 ### Exclude
 

Makefile

@@ -105,10 +105,10 @@ flake:
 	@echo "flake8 passed"
 
 codespell:  # running manually
-	@codespell --builtin clear,rare,informal,names -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
+	@codespell --builtin clear,rare,informal,names,usage -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
 
 codespell-error:  # running on travis
-	@codespell --builtin clear,rare,informal,names -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
+	@codespell --builtin clear,rare,informal,names,usage -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
 
 pydocstyle:
 	@echo "Running pydocstyle"

azure-pipelines.yml

@@ -15,11 +15,9 @@ jobs:
 - job: Style
   pool:
     vmImage: 'ubuntu-18.04'
-  strategy:
-    matrix:
-      Python37-64bit-fast:
-        PYTHON_VERSION: '3.7'
-        PYTHON_ARCH: 'x64'
+  variables:
+    PYTHON_VERSION: '3.8'
+    PYTHON_ARCH: 'x64'
   steps:
   - task: UsePythonVersion@0
     inputs:
@@ -28,6 +26,7 @@ jobs:
       addToPath: true
     displayName: 'Get Python'
   - bash: |
+      set -e
       python -m pip install --upgrade pip setuptools
       python -m pip install numpy scipy matplotlib sphinx pytest pytest-cov pytest-timeout pytest-sugar flake8
     displayName: Install dependencies
@@ -89,7 +88,7 @@ jobs:
     OPENBLAS_NUM_THREADS: '1'
   steps:
   - bash: |
-      sudo apt install libxkbcommon-x11-0 xvfb tcsh
+      sudo apt install libxkbcommon-x11-0 xvfb tcsh libxcb*
     displayName: 'Install Ubuntu dependencies'
   - bash: |
       source tools/get_minimal_commands.sh
@@ -124,16 +123,55 @@ jobs:
     displayName: 'Get test data'
   - script: pytest -m "ultraslowtest" --tb=short --cov=mne -n 1 mne
     displayName: 'Run ultraslow tests'
-  - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
+  - script: codecov --root $BUILD_REPOSITORY_LOCALPATH -t $CODECOV_TOKEN
     displayName: 'Codecov'
     env:
       CODECOV_TOKEN: $(CODECOV_TOKEN)
-    condition: always()
+    condition: succeededOrFailed()
   - task: PublishTestResults@2
     inputs:
       testResultsFiles: 'junit-*.xml'
-      testRunTitle: 'Publish test results for Python $(python.version)'
-    condition: always()
+      testRunTitle: 'Publish test results for $(Agent.JobName)'
+      failTaskOnFailedTests: true
+    condition: succeededOrFailed()
+
+
+- job: Notebook
+  pool:
+    vmImage: 'ubuntu-18.04'
+  variables:
+    CONDA_ENV: 'server_environment.yml'
+  steps:
+  - bash: |
+      set -e
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh --progress=dot:mega
+      bash miniconda.sh -b -p ~/miniconda
+      source ~/miniconda/etc/profile.d/conda.sh
+      conda activate base
+      conda env update --file $CONDA_ENV
+      pip uninstall -yq mne
+      pip install -ve .
+      pip install pytest pytest-cov pytest-timeout pytest-sugar pytest-xdist flake8 codecov
+      echo "##vso[task.setvariable variable=PATH]${PATH}"
+      echo "##vso[task.setvariable variable=LD_LIBRARY_PATH]${LD_LIBRARY_PATH}"
+    displayName: 'Install dependencies'
+  - script: mne sys_info
+    displayName: 'Print config and test access to commands'
+  - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
+    displayName: 'Get test data'
+  - script: pytest --tb=short --cov=mne mne/viz
+    displayName: 'Run viz tests'
+  - script: codecov --root $BUILD_REPOSITORY_LOCALPATH -t $CODECOV_TOKEN
+    displayName: 'Codecov'
+    env:
+      CODECOV_TOKEN: $(CODECOV_TOKEN)
+    condition: succeededOrFailed()
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFiles: 'junit-*.xml'
+      testRunTitle: 'Publish test results for $(Agent.JobName)'
+      failTaskOnFailedTests: true
+    condition: succeededOrFailed()
 
 
 - job: Windows
@@ -220,15 +258,16 @@ jobs:
     displayName: Print NumPy config
   - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
     displayName: 'Get test data'
-  - script: pytest -m "not ultraslowtest" --tb=short --cov=mne -n 1 mne
+  - script: pytest -m "not slowtest" --tb=short --cov=mne -n 1 mne
     displayName: 'Run tests'
   - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
     displayName: 'Codecov'
     env:
       CODECOV_TOKEN: $(CODECOV_TOKEN)
-    condition: always()
+    condition: succeededOrFailed()
   - task: PublishTestResults@2
     inputs:
       testResultsFiles: 'junit-*.xml'
-      testRunTitle: 'Publish test results for Python $(python.version)'
-    condition: always()
+      testRunTitle: 'Publish test results for $(Agent.JobName) $(TEST_MODE) $(PYTHON_VERSION)'
+      failTaskOnFailedTests: true
+    condition: succeededOrFailed()

doc/_static/blender_import_obj/blender_import_obj1.jpg

@@ -64,7 +64,7 @@
 {% endblock %}
 
 {# put the sidebar before the body #}
-{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar1 %}{% endblock %}
 {% block sidebar2 %}{% endblock %}
 
 {%- block footer %}