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

.circleci/config.yml

@@ -14,10 +14,10 @@ jobs:
               echo "set -e" >> $BASH_ENV
               echo "export DISPLAY=:99" >> $BASH_ENV
               echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+              echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci"  >> $BASH_ENV
               source tools/get_minimal_commands.sh
               echo "source ${PWD}/tools/get_minimal_commands.sh" >> $BASH_ENV
               echo "export MNE_3D_BACKEND=pyvista" >> $BASH_ENV
-              echo "export _MNE_BRAIN_TRACES_AUTO=false" >> $BASH_ENV
               echo "export PATH=~/.local/bin/:${MNE_ROOT}/bin:$PATH" >> $BASH_ENV
               echo "BASH_ENV:"
               cat $BASH_ENV
@@ -73,18 +73,16 @@ jobs:
             command: |
               mkdir -p $HOME/.fonts
               curl https://codeload.github.com/adobe-fonts/source-code-pro/tar.gz/2.030R-ro/1.050R-it | tar xz -C $HOME/.fonts
-              curl https://codeload.github.com/adobe-fonts/source-sans-pro/tar.gz/2.045R-ro/1.095R-it | tar xz -C $HOME/.fonts
+              curl https://codeload.github.com/adobe-fonts/source-sans-pro/tar.gz/3.006R | tar xz -C $HOME/.fonts
               fc-cache -f
 
         - run:
             name: Get Python running
             command: |
               python -m pip install --user --upgrade --progress-bar off pip setuptools
-              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
-              python -m pip install --user --upgrade --progress-bar off ipython sphinx_fontawesome sphinx_bootstrap_theme memory_profiler "https://github.com/sphinx-gallery/sphinx-gallery/archive/master.zip"
-              python -m pip install --user --upgrade seaborn
+              python -m pip install --user --upgrade --progress-bar off -r requirements.txt -r requirements_testing.txt -r requirements_doc.txt
+              python -m pip uninstall -yq pysurfer mayavi
               python -m pip install --user -e .
 
         - save_cache:
@@ -355,7 +353,7 @@ jobs:
             command: |
                set -e;
                python -m pip install --user --progress-bar off numpy scipy matplotlib pillow
-               python -m pip install --user --progress-bar off sphinx numpydoc sphinx_fontawesome sphinx_bootstrap_theme "https://github.com/sphinx-gallery/sphinx-gallery/archive/master.zip" memory_profiler https://github.com/mcmtroffaes/sphinxcontrib-bibtex/archive/29694f215b39d64a31b845aafd9ff2ae9329494f.zip
+               python -m pip install --user --progress-bar off -r requirements_doc.txt
                python -m pip install --user -e .
         - run:
             name: make linkcheck

.travis.yml

@@ -13,12 +13,10 @@ addons:
       - libglx0
       - libdbus-1-3
 env:
-    # TRAVIS_PYTHON_VERSION is only needed for neo's setup.py
     # OPENBLAS_NUM_THREADS=1 avoid slowdowns:
     # https://github.com/xianyi/OpenBLAS/issues/731
     global: PYTHON_VERSION=3.7 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning
-            TRAVIS_PYTHON_VERSION=3.7 CONDA_VERSION=">=4.3.27"
-            OPENBLAS_NUM_THREADS=1
+            CONDA_VERSION=">=4.3.27" OPENBLAS_NUM_THREADS=1 PYTHONUNBUFFERED=1
 
 matrix:
     include:
@@ -63,13 +61,13 @@ before_install:
         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 $CONDA_ENV
+          conda activate mne
           pip uninstall -yq mne
         fi
       fi
     # Always install these via pip so we get the latest possible versions (testing bugfixes)
-    - pip install --upgrade "pytest<5.4" pytest-sugar pytest-cov pytest-mock pytest-timeout pytest-xdist codecov
+    - pip install --upgrade -r requirements_testing.txt codecov
     - if [ "${DEPS}" != "minimal" ]; then
         pip install nitime;
       fi
@@ -134,21 +132,25 @@ script:
           fi;
         done;
       fi;
+    # Remove numpydoc tests on older Python (builtin docstrings not as good)
+    - if [ "${PYTHON_VERSION}" == "3.6" ]; then
+        pip uninstall -yq numpydoc;
+      fi;
     # Test run_tests_if_main
     - if [ "${DEPS}" == "minimal" ]; then
         pip uninstall -yq mne;
         pip install -e .;
         python mne/tests/test_evoked.py;
       fi;
-    - echo 'pytest -m "${CONDITION}" --cov=mne -n 1 ${USE_DIRS}'
-    - pytest -m "${CONDITION}" --tb=short --cov=mne -n 1 ${USE_DIRS}
+    - echo 'pytest -m "${CONDITION}" --tb=short --cov=mne -vv ${USE_DIRS}'
+    - pytest -m "${CONDITION}" --tb=short --cov=mne -vv ${USE_DIRS}
     # run the minimal one with the testing data
     - if [ "${DEPS}" == "minimal" ]; then
         export MNE_SKIP_TESTING_DATASET_TESTS=false;
         python -c 'import mne; mne.datasets.testing.data_path(verbose=True)';
       fi;
     - if [ "${DEPS}" == "minimal" ]; then
-        pytest -m "${CONDITION}" --tb=short --cov=mne -n 1 ${USE_DIRS};
+        pytest -m "${CONDITION}" --tb=short --cov=mne -vv ${USE_DIRS};
       fi;
 
 after_script:

MANIFEST.in

@@ -1,6 +1,8 @@
 include *.rst
 include LICENSE.txt
 include requirements.txt
+include requirements_testing.txt
+include requirements_doc.txt
 include mne/__init__.py
 
 recursive-include examples *.py

azure-pipelines.yml

@@ -28,52 +28,32 @@ jobs:
   - 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
+      python -m pip install numpy scipy matplotlib -r requirements_testing.txt
     displayName: Install dependencies
     condition: always()
   - bash: |
       make flake
     displayName: make flake
     condition: always()
-  - bash: |
-      pip install pydocstyle
-    displayName: Install pydocstyle
-    condition: always()
   - bash: |
       make pydocstyle
     displayName: make pydocstyle
     condition: always()
-  - bash: |
-      pip install https://github.com/codespell-project/codespell/zipball/master
-    displayName: Install latest codespell
-    condition: always()
   - bash: |
       make codespell-error
     displayName: make codespell-error
     condition: always()
-  - bash: |
-      pip install https://github.com/numpy/numpydoc/archive/master.zip pytest pytest-cov pytest-timeout pytest-sugar
-    displayName: Install NumpyDoc validation
-    condition: always()
   - bash: |
       make docstring
     displayName: make docstring
   - bash: |
       make nesting
     displayName: make nesting
     condition: always()
-  - bash: |
-      pip install check-manifest
-    displayName: Install manifest checker
-    condition: always()
   - bash: |
       make check-manifest
     displayName: make check-manifest
     condition: always()
-  - bash: |
-      pip install twine wheel
-    displayName: Install twine
-    condition: always()
   - bash: |
       make check-readme
     displayName: make check-readme
@@ -115,13 +95,12 @@ jobs:
     displayName: 'Spin up Xvfb'
   - bash: |
       set -e
-      pip install --upgrade numpy scipy vtk
-      pip install --upgrade -r requirements.txt
-      pip install codecov
+      python -m pip install --upgrade pip setuptools
+      python -m pip install --upgrade numpy scipy vtk -r requirements.txt -r requirements_testing.txt codecov
     displayName: 'Install dependencies with pip'
   - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
     displayName: 'Get test data'
-  - script: pytest -m "ultraslowtest" --tb=short --cov=mne -n 1 mne
+  - script: pytest -m "ultraslowtest" --tb=short --cov=mne -vv mne
     displayName: 'Run ultraslow tests'
   - script: codecov --root $BUILD_REPOSITORY_LOCALPATH -t $CODECOV_TOKEN
     displayName: 'Codecov'
@@ -159,7 +138,7 @@ jobs:
     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
+  - script: pytest --tb=short --cov=mne -vv mne/viz
     displayName: 'Run viz tests'
   - script: codecov --root $BUILD_REPOSITORY_LOCALPATH -t $CODECOV_TOKEN
     displayName: 'Codecov'
@@ -181,6 +160,8 @@ jobs:
     MNE_LOGGING_LEVEL: 'warning'
     MNE_FORCE_SERIAL: 'true'
     OPENBLAS_NUM_THREADS: 1
+    PYTHONUNBUFFERED: 1
+    PYTHONIOENCODING: 'utf-8'
     MKL_NUM_THREADS: 1
     AZURE_CI_WINDOWS: 'true'
     CONDA_VERSION: '>=4.3.27'
@@ -201,6 +182,7 @@ jobs:
         PYTHON_ARCH: 'x64'
         TEST_MODE: 'pre-pip'
         PYTHON_VERSION: '3.8'
+        OPENBLAS_CORETYPE: 'prescott'  # workaround for https://github.com/numpy/numpy/issues/16913
   steps:
   - task: UsePythonVersion@0
     inputs:
@@ -216,10 +198,11 @@ jobs:
     displayName: Install OpenGL
   - bash: |
       set -e
-      pip install --upgrade numpy scipy vtk
-      pip install --upgrade -r requirements.txt
-      pip install codecov
-      pip uninstall -yq pysurfer mayavi
+      python -m pip install --upgrade pip setuptools
+      python -m pip install --upgrade numpy scipy vtk
+      python -m pip install --upgrade -r requirements.txt -r requirements_testing.txt
+      python -m pip install codecov
+      python -m pip uninstall -yq pysurfer mayavi
     condition: eq(variables['TEST_MODE'], 'pip')
     displayName: 'Install dependencies with pip'
   - bash: |
@@ -228,9 +211,7 @@ jobs:
       python -m pip install --upgrade --pre --only-binary ":all:" -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy
       python -m pip install --upgrade --pre --only-binary ":all:" -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" scipy pandas scikit-learn matplotlib h5py Pillow
       python -m pip install --upgrade --only-binary vtk vtk;
-      python -m pip install https://github.com/enthought/mayavi/zipball/master
-      python -m pip install -r requirements.txt
-      python -m pip install codecov
+      python -m pip install -r requirements.txt -r requirements_testing.txt codecov
     condition: eq(variables['TEST_MODE'], 'pre-pip')
     displayName: 'Install dependencies with pip --pre'
   - powershell: |
@@ -243,9 +224,9 @@ jobs:
       $env:PATH = $env:PYTHON + ";" + $env:PYTHON + "\Scripts;" + $env:PYTHON + "\Library\bin;" + $env:PATH
       conda env list
       conda install numpy scipy matplotlib scikit-learn
-      conda env update --file $env:CONDA_ENV
+      conda env update --name base --file $env:CONDA_ENV
       pip uninstall -yq mne
-      pip install codecov
+      pip install -r requirements_testing.txt codecov
       pip uninstall -yq pysurfer mayavi
       Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)
     condition: eq(variables['TEST_MODE'], 'conda')
@@ -258,7 +239,7 @@ 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 slowtest" --tb=short --cov=mne -n 1 mne
+  - script: pytest -m "not slowtest" --tb=short --cov=mne -vv mne
     displayName: 'Run tests'
   - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
     displayName: 'Codecov'

doc/Makefile

@@ -64,7 +64,7 @@ html-noplot:
 	@echo "Build finished. The HTML pages are in _build/html_stable."
 
 html_dev-front:
-	@PATTERN="\(plot_mne_dspm_source_localization.py\|plot_receptive_field.py\|plot_mne_inverse_label_connectivity.py\|plot_sensors_decoding.py\|plot_stats_cluster_spatio_temporal.py\|plot_visualize_evoked.py\)" make html_dev-pattern;
+	@PATTERN="\(plot_mne_dspm_source_localization.py\|plot_receptive_field.py\|plot_mne_inverse_label_connectivity.py\|plot_sensors_decoding.py\|plot_stats_cluster_spatio_temporal.py\|plot_20_visualize_evoked.py\)" make html_dev-pattern;
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml

doc/_static/style.css

@@ -555,3 +555,7 @@ div[id^="mne-"] h1 {
 div[id^="examples-using-"] h2 {
   word-break: break-word;
 }
+/* Avoid awkward extra spacing in .. contents:: */
+div.contents ul li p {
+  margin: 0 0 0px;
+}