.circleci/artifact_path

+0/dev/index.html

.circleci/config.yml

@@ -65,9 +65,17 @@ jobs:
             command: |
               sudo apt-get install qt5-default
 
+        - run:
+            name: Install graphviz and fonts needed for diagrams
+            command: |
+              sudo apt-get install graphviz
+              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
+              fc-cache -f
+
         - run:
             name: Get Python running
-            # pip install --user --upgrade --progress-bar off https://api.github.com/repos/larsoner/numpydoc/zipball/xref-param-type
             command: |
               pip install --user --upgrade --progress-bar off pip numpy vtk
               pip install --user --upgrade --progress-bar off -r requirements.txt
@@ -85,6 +93,7 @@ jobs:
                which python
                python -c "import mne; mne.sys_info()"
                LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
+               python -c "import mne; mne.set_config('MNE_USE_CUDA', 'false')"  # this is needed for the config tutorial
                python -c "import mne; mne.set_config('MNE_LOGGING_LEVEL', 'info')"
                python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"
 
@@ -101,7 +110,7 @@ jobs:
               if [ "$CIRCLE_BRANCH" == "master" ] || [[ $(cat gitlog.txt) == *"[circle full]"* ]]; then
                 echo html_dev > build.txt;
                 python -c "import mne; mne.datasets._download_all_example_data()";
-              elif [ "$CIRCLE_BRANCH" == "maint/0.18" ]; then
+              elif [ "$CIRCLE_BRANCH" == "maint/0.19" ]; then
                 echo html_stable > build.txt;
                 python -c "import mne; mne.datasets._download_all_example_data()";
               else
@@ -128,7 +137,10 @@ jobs:
                       python -c "import mne; print(mne.datasets.somato.data_path(update_path=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*datasets.*eegbci.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.eegbci.load_data(1, [6, 10, 14], update_path=True))";
+                      python -c "import mne; print(mne.datasets.eegbci.load_data(1, [3, 6, 10, 14], update_path=True))";
+                      python -c "import mne; print(mne.datasets.eegbci.load_data(2, [3], update_path=True))";
+                      python -c "import mne; print(mne.datasets.eegbci.load_data(3, [3], update_path=True))";
+                      python -c "import mne; print(mne.datasets.eegbci.load_data(4, [3], update_path=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*datasets.*sleep_physionet.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.sleep_physionet.age.fetch_data([0, 1], recording=[1], update_path=True))";
@@ -151,10 +163,6 @@ jobs:
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_elekta.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_elekta.data_path(update_path=True))" --accept-brainstorm-license;
                     fi;
-                    if [[ $(cat $FNAME | grep -x ".*datasets.*megsim.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.megsim.load_data(condition='visual', data_format='single-trial', data_type='simulation', update_path=True))";
-                      python -c "import mne; print(mne.datasets.megsim.load_data(condition='visual', data_format='raw', data_type='experimental', update_path=True))";
-                    fi;
                     if [[ $(cat $FNAME | grep -x ".*datasets.*hcp_mmp_parcellation.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.sample.data_path(update_path=True))";
                       python -c "import mne; print(mne.datasets.fetch_hcp_mmp_parcellation())" --accept-hcpmmp-license;
@@ -183,6 +191,9 @@ jobs:
                     if [[ $(cat $FNAME | grep -x ".*datasets.*phantom_4dbti.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.phantom_4dbti.data_path(update_path=True))";
                     fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*limo.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.limo.data_path(subject=2, update_path=True))";
+                    fi;
                   fi;
                 done;
                 echo PATTERN="$PATTERN";
@@ -222,6 +233,15 @@ jobs:
             command: |
               python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"
 
+        # Reduce upload time of artifacts we will (almost) never look at
+        - run:
+            name: Reduce artifact upload time
+            command: |
+              if grep -q html_dev-pattern build.txt || grep -q html_dev-noplot build.txt; then
+                tar czf doc/_build/html/_downloads.tgz doc/_build/html/_downloads
+                rm -Rf doc/_build/html/_downloads
+              fi
+
         # Save the JUnit file
         - store_test_results:
             path: doc/_build/test-results
@@ -286,6 +306,7 @@ jobs:
             key: data-cache-8
             paths:
               - ~/mne_data/MNE-visual_92_categories-data
+              - ~/mne_data/MNE-limo-data
 
 
     linkcheck:
@@ -341,7 +362,7 @@ jobs:
             name: Deploy docs
             command: |
               set -e;
-              if [ "${CIRCLE_BRANCH}" == "master" ] || [ "${CIRCLE_BRANCH}" == "maint/0.18" ]; then
+              if [ "${CIRCLE_BRANCH}" == "master" ] || [ "${CIRCLE_BRANCH}" == "maint/0.19" ]; then
                 git config --global user.email "circle@mne.com";
                 git config --global user.name "Circle CI";
                 cd ~/mne-tools.github.io;
@@ -385,7 +406,7 @@ workflows:
             branches:
               only:
                 - master
-                - maint/0.18
+                - maint/0.19
 
   weekly:
     jobs:

.coveragerc

@@ -7,3 +7,9 @@ omit =
     */bin/*
     */setup.py
     */mne/fixes*
+    */mne/utils/linalg.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if __name__ == .__main__.:

.github/CONTRIBUTING.md

@@ -10,4 +10,4 @@ This project and everyone participating in it is governed by the [MNE-Python's C
 
 ## How to contribute
 
-Before contributing make sure you are familiar with [our contributing guide](https://martinos.org/mne/contributing.html).
+Before contributing make sure you are familiar with [our contributing guide](https://mne.tools/dev/install/contributing.html).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,7 +4,7 @@ about: Create a report to help us improve.
 
 ---
 
-Detailed instructions on how to file a bug can be found in our [FAQ](https://martinos.org/mne/stable/faq.html#i-think-i-found-a-bug-what-do-i-do).
+Detailed instructions on how to file a bug can be found in our [FAQ](https://mne.tools/dev/overview/faq.html#i-think-i-found-a-bug-what-do-i-do).
 
 If your issue is a usage question, please consider asking on our [Gitter channel](https://gitter.im/mne-tools/mne-python) or on our [mailing list](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) instead of opening an issue.
 

.github/ISSUE_TEMPLATE/glossary.md

+---
+name: Missing glossary entry
+about: Suggest a term to be added to our glossary
+
+---
+
+
+#### Suggested term
+(insert here)
+
+
+#### Suggested definition
+(insert here)

.github/PULL_REQUEST_TEMPLATE.md

 Thanks for contributing a pull request! Please make sure you have read the
-[contribution guidelines](https://martinos.org/mne/stable/contributing.html)
+[contribution guidelines](https://mne.tools/dev/install/contributing.html)
 before submitting.
 
 Please be aware that we are a loose team of volunteers so patience is

.gitignore

@@ -44,6 +44,7 @@ build
 coverage
 .cache/
 .pytest_cache/
+__pycache__/
 prof/
 
 dist/
@@ -54,12 +55,12 @@ doc/auto_tutorials/
 doc/modules/generated/
 doc/sphinxext/cachedir
 pip-log.txt
-.coverage
+.coverage*
 tags
 doc/coverages
 doc/samples
 cover
-examples/visualization/foobar.html
+*.html
 
 *.orig
 

.mailmap

@@ -25,7 +25,6 @@ Denis A. Engemann <denis.engemann@gmail.com> Denis Engemann <dengemann@pool-186-
 Denis A. Engemann <denis.engemann@gmail.com> Denis A. Engemann <denisaengemann@Denis-A-Engemanns-MacBook-Air.local>
 Daniel Strohmeier <daniel.strohmeier@googlemail.com> joewalter <daniel.strohmeier@googlemail.com>
 Daniel Strohmeier <daniel.strohmeier@googlemail.com> Daniel Strohmeier <daniel.strohmeier@googlemail.com>
-Dan G. Wakeman <dgwakeman@gmail.com>
 Dan G. Wakeman <dgwakeman@gmail.com> dgwakeman <dgwakeman@users.noreply.github.com>
 Teon Brooks <teon.brooks@gmail.com>
 Teon Brooks <teon.brooks@gmail.com> Teon <teon@nyu.edu>
@@ -127,3 +126,6 @@ Thomas Donoghue <tdonoghue.research@gmail.com> Tom <tdonoghue.research@gmail.com
 Steve Matindi <stevematindi@gmail.com> stevemats <stevematindi@gmail.com>
 Legrand Nicolas <legrand@cyceron.fr> LegrandNico <legrand@cyceron.fr>
 Johannes Kasper <jeythekey@tutanota.com> jeythekey <44215387+jeythekey@users.noreply.github.com>
+Thomas Radman <radman.thomas@gmail.com>
+Joshua J Bear <joshbear@users.noreply.github.com>
+Paul Roujansky <paul@roujansky.eu>

.travis.yml

 language: c
 dist: xenial
-sudo: false
 cache:
   apt: true
   pip: true
@@ -8,9 +7,8 @@ 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=3.6 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning TEST_LOCATION=src
-            PIP_DEPENDENCIES="codecov nitime"
-            TRAVIS_PYTHON_VERSION=3.6 CONDA_VERSION=">=4.3.27"
+    global: PYTHON_VERSION=3.7 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning TEST_LOCATION=src
+            TRAVIS_PYTHON_VERSION=3.7 CONDA_VERSION=">=4.3.27"
             OPENBLAS_NUM_THREADS=1
 
 matrix:
@@ -18,21 +16,22 @@ matrix:
         # No data + style testing
         - os: linux
           env: DEPS=nodata MNE_DONTWRITE_HOME=true MNE_FORCE_SERIAL=true MNE_SKIP_NETWORK_TEST=1
-               CONDA_DEPENDENCIES="numpy scipy matplotlib sphinx pytest pytest-timeout pytest-cov pytest-mock"
-               PIP_DEPENDENCIES="flake8 numpydoc codespell pydocstyle codecov check-manifest pytest-sugar pytest-faulthandler"
+               CONDA_DEPENDENCIES="numpy scipy matplotlib sphinx"
+               PIP_DEPENDENCIES="codecov flake8 numpydoc codespell pydocstyle codecov check-manifest twine"
 
         # Linux
+        # As of 2019/09/19 there is a mysterious joblib bug, so temporarily work around it with MNE_FORCE_SERIAL
         - os: linux
-          env: CONDA_ENVIRONMENT="environment.yml"
+          env: CONDA_ENV="environment.yml"
+               MNE_FORCE_SERIAL=true
 
         # OSX conda
         - os: osx
-          env: CONDA_ENVIRONMENT="environment.yml"
+          env: CONDA_ENV="environment.yml"
 
         # PIP + non-default stim channel
         - os: linux
           env: MNE_STIM_CHANNEL=STI101
-               PYTHON_VERSION=3.7
           language: python
           python: "3.7"
           addons:
@@ -42,36 +41,42 @@ matrix:
         # Old dependencies
         - os: linux
           env: PYTHON_VERSION=3.5
-               CONDA_DEPENDENCIES="numpy=1.11 scipy=0.17 matplotlib=1.5 pandas=0.18 scikit-learn=0.18 pytest pytest-cov pytest-mock pytest-timeout"
+               CONDA_DEPENDENCIES="numpy=1.12 scipy=0.18 matplotlib=2.0 pandas=0.19 scikit-learn=0.18"
+               PIP_DEPENDENCIES="codecov nitime"
+               CONDA_CHANNELS="conda-forge"
 
         # Minimal
         - os: linux
           env: DEPS=minimial
-               CONDA_DEPENDENCIES="numpy scipy matplotlib pytest pytest-cov pytest-mock pytest-timeout"
-               PIP_DEPENDENCIES="pytest-faulthandler pytest-sugar"
+               CONDA_DEPENDENCIES="numpy scipy matplotlib"
+               PIP_DEPENDENCIES="codecov"
 
 # Setup anaconda
 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_ENVIRONMENT" ] && [ -z "$CONDA_DEPENDENCIES" ]; then
-        pip uninstall -y numpy;
+    - if [ -z "$CONDA_ENV" ] && [ -z "$CONDA_DEPENDENCIES" ]; then
+        pip uninstall -yq numpy;
         pip install -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" --pre numpy scipy;
         pip install vtk;
+        pip install $PIP_DEPENDENCIES;
         pip install --upgrade -r requirements.txt;
       else
         git clone https://github.com/astropy/ci-helpers.git;
         source ci-helpers/travis/setup_conda.sh;
-        if [ ! -z "$CONDA_ENVIRONMENT" ]; then
-          pip uninstall --yes mne;
-        fi;
+        if [ ! -z "$CONDA_ENV" ]; then
+          conda activate base;
+          conda env update --file $CONDA_ENV;
+          pip uninstall -yq mne;
+          pip install codecov nitime;
           if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
-          pip install --upgrade pyqt5>=5.10 pylsl;
-        else
-          conda install -c tstenner pylsl;
+            pip install "pyqt5>=5.10";
+          fi;
         fi;
       fi
+    # Always install these via pip so we get the latest possible versions (testing bugfixes)
+    - pip install --upgrade pytest pytest-sugar pytest-cov pytest-mock pytest-timeout
     # Don't source mne_setup_sh here because changing PATH etc. can't be done in a script
     - if [ "${DEPS}" == "" ]; then
         export MNE_ROOT="${PWD}/minimal_cmds";
@@ -104,17 +109,13 @@ install:
     # files to act as a FREESURFER_HOME for the coreg tests
     - if [ "${DEPS}" != "nodata" ]; then
         python -c 'import mne; mne.datasets.testing.data_path(verbose=True)';
-        ls -al $HOME/mne_data/;
-        ls -al $HOME/mne_data/MNE-testing-data/;
-        ls -al $HOME/mne_data/MNE-testing-data/MEG/;
-        ls -al $HOME/mne_data/MNE-testing-data/MEG/sample/;
-        if [ "${DEPS}" == "" ] && [ "${TRAVIS_OS_NAME}" == "linux" ]; then
-          export FREESURFER_HOME=$(python -c 'import mne; print(mne.datasets.testing.data_path())');
-          export MNE_SKIP_FS_FLASH_CALL=1;
-        fi;
       else
         export MNE_SKIP_TESTING_DATASET_TESTS=true;
       fi;
+    - if [ "${DEPS}" == "" ] && [ "${TRAVIS_OS_NAME}" == "linux" ]; then
+        export FREESURFER_HOME=$(python -c 'import mne; print(mne.datasets.testing.data_path())');
+        export MNE_SKIP_FS_FLASH_CALL=1;
+      fi;
     - MNE_DIR=$(python -c 'import mne;print(mne.__path__[0])')
     # We run two versions: one out of the source directory (that makes
     # coveralls coverage work), and one out of the install directory (that
@@ -131,10 +132,8 @@ install:
         ln -s ${SRC_DIR}/setup.cfg ${MNE_DIR}/../setup.cfg;
         ln -s ${SRC_DIR}/.coveragerc ${MNE_DIR}/../.coveragerc;
         cd ${MNE_DIR}/../;
-        COVERAGE=;
       else
         cd ${SRC_DIR};
-        COVERAGE=--with-coverage;
       fi;
 
 
@@ -178,8 +177,8 @@ script:
         pip install -e .;
         python mne/tests/test_evoked.py;
       fi;
-    - echo pytest -m "${CONDITION}" ${USE_DIRS} --cov=mne;
-    - pytest -m "${CONDITION}" ${USE_DIRS} --cov=mne;
+    - echo pytest -m "${CONDITION}" --cov=mne ${USE_DIRS}
+    - pytest -m "${CONDITION}" --cov=mne ${USE_DIRS}
     - if [ "${DEPS}" == "nodata" ]; then
         make pep;
       fi;

CONTRIBUTING.rst

@@ -31,4 +31,4 @@ conduct`_.
 .. _`pull request`: https://help.github.com/en/articles/creating-a-pull-request-from-a-fork
 
 .. _`code of conduct`: https://github.com/mne-tools/mne-python/blob/master/CODE_OF_CONDUCT.md
-.. _`contributing guide`: https://mne-tools.github.io/dev/contributing.html
+.. _`contributing guide`: https://mne-tools.github.io/dev/install/contributing.html

LICENSE.txt

@@ -8,7 +8,7 @@ modification, are permitted provided that the following conditions are met:
     * Redistributions in binary form must reproduce the above copyright
       notice, this list of conditions and the following disclaimer in the
       documentation and/or other materials provided with the distribution.
-    * Neither the names of MNE-Python authors nor the names of any
+    * Neither the name of the copyright holder nor the names of its
       contributors may be used to endorse or promote products derived from
       this software without specific prior written permission.
 

Makefile

@@ -5,7 +5,7 @@
 PYTHON ?= python
 PYTESTS ?= py.test
 CTAGS ?= ctags
-CODESPELL_SKIPS ?= "*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt"
+CODESPELL_SKIPS ?= "*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg"
 CODESPELL_DIRS ?= mne/ doc/ tutorials/ examples/
 all: clean inplace test test-doc
 
@@ -17,7 +17,7 @@ clean-so:
 	find . -name "*.pyd" | xargs rm -f
 
 clean-build:
-	rm -rf _build
+	rm -rf build dist
 
 clean-ctags:
 	rm -f tags
@@ -31,6 +31,12 @@ in: inplace # just a shortcut
 inplace:
 	$(PYTHON) setup.py build_ext -i
 
+wheel:
+	$(PYTHON) setup.py sdist bdist_wheel
+
+wheel_quiet:
+	$(PYTHON) setup.py -q sdist bdist_wheel
+
 sample_data:
 	@python -c "import mne; mne.datasets.sample.data_path(verbose=True);"
 
@@ -67,7 +73,7 @@ test-no-sample-with-coverage: in testing_data
 	$(PYTESTS) --cov=mne --cov-report html:coverage
 
 test-doc: sample_data testing_data
-	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/
+	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --fulltrace
 
 test-coverage: testing_data
 	rm -rf coverage .coverage
@@ -115,8 +121,8 @@ docstring:
 check-manifest:
 	check-manifest --ignore .circleci*,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store
 
-check-readme:
-	python setup.py check --restructuredtext --strict
+check-readme: clean wheel_quiet
+	twine check dist/*
 
 nesting:
 	@echo "Running import nesting tests"

README.rst

@@ -20,8 +20,8 @@
 .. |Zenodo| image:: https://zenodo.org/badge/5822/mne-tools/mne-python.svg
 .. _Zenodo: https://zenodo.org/badge/latestdoi/5822/mne-tools/mne-python
 
-.. |MNE| image:: https://martinos.org/mne/stable/_static/mne_logo.png
-.. _MNE: https://martinos.org/mne
+.. |MNE| image:: https://mne.tools/stable/_static/mne_logo.png
+.. _MNE: https://mne.tools/dev/
 
 MNE-Python
 ==========
@@ -48,10 +48,12 @@ To install the latest stable version of MNE-Python, you can use pip_ in a termin
 
     pip install -U mne
 
-**Note** that MNE-Python 0.17 will be the last release to support Python 2. From MNE-Python 0.18, only Python 3 will be supported.
+**Note** that MNE-Python 0.17 was the last release to support Python 2.
+MNE-Python 0.18 only works under Python 3, and MNE-Python 0.19 requires
+Python 3.5 or higher.
 
 For more complete instructions and more advanced installation methods (e.g. for
-the latest development version), see the `getting started page`_.
+the latest development version), see the `installation guide`_.
 
 
 Get the latest code
@@ -79,21 +81,21 @@ Dependencies
 The minimum required dependencies to run MNE-Python are:
 
 - Python >= 3.5
-- NumPy >= 1.11.3
-- SciPy >= 0.17.1
+- NumPy >= 1.12.1
+- SciPy >= 0.18.1
 
 For full functionality, some functions require:
 
-- Matplotlib >= 1.5
+- Matplotlib >= 2.0.2
 - Mayavi >= 4.6
 - PySurfer >= 0.8
-- Scikit-learn >= 0.18
+- Scikit-learn >= 0.18.2
+- Numba >= 0.40
 - NiBabel >= 2.1.0
-- Pandas >= 0.18
+- Pandas >= 0.19.2
 - Picard >= 0.3
 - CuPy >= 4.0 (for NVIDIA CUDA acceleration)
 - DIPY >= 0.10.1
-- PyLSL >= 1.12
 - PyVista >= 0.20.1
 
 Contributing to MNE-Python
@@ -101,7 +103,7 @@ Contributing to MNE-Python
 
 Please see the documentation on the MNE-Python homepage:
 
-https://martinos.org/mne/contributing.html
+https://mne.tools/dev/install/contributing.html
 
 
 Mailing list
@@ -149,7 +151,7 @@ MNE-Python is **BSD-licenced** (3 clause):
     damage.**
 
 
-.. _MNE-Python software: https://martinos.org/mne
-.. _MNE documentation: http://martinos.org/mne/documentation.html
-.. _getting started page: https://martinos.org/mne/getting_started.html
+.. _MNE-Python software: https://mne.tools/dev/
+.. _MNE documentation: https://mne.tools/dev/overview/index.html
+.. _installation guide: https://mne.tools/dev/install/index.html
 .. _pip: https://pip.pypa.io/en/stable/

azure-pipelines.yml

@@ -13,23 +13,22 @@ jobs:
   variables:
     MNE_LOGGING_LEVEL: 'warning'
     MNE_FORCE_SERIAL: 'true'
-    PIP_DEPENDENCIES: 'codecov'
     OPENBLAS_NUM_THREADS: 1
     AZURE_CI_WINDOWS: 'true'
+    PYTHON_VERSION: '3.7'
+    CONDA_VERSION: '>=4.3.27'
   strategy:
     maxParallel: 4
     matrix:
       # Eventually we should test x86 (32-bit), but it was a nightmare
       # to get it to download 32-bit Anaconda properly, and VTK does not ship
       # 32-bit Windows binaries via pip.
-      Python36-64bit-full-conda:
-        PYTHON_VERSION: '3.6'
+      Python37-64bit-full-conda:
         PLATFORM: 'x86-64'
         TEST_MODE: 'conda'
-        CONDA_ENVIRONMENT: 'environment.yml'
+        CONDA_ENV: 'environment.yml'
         PIP_NO_UPGRADE: 'True'
       Python37-64bit-full-pip:
-        PYTHON_VERSION: '3.7'
         PYTHON_ARCH: 'x64'
         TEST_MODE: 'pip'
   steps:
@@ -52,8 +51,7 @@ jobs:
       $PSDefaultParameterValues['*:ErrorAction']='Stop'
       pip install --upgrade numpy scipy vtk
       pip install --upgrade -r requirements.txt
-      pip install $env:PIP_DEPENDENCIES
-      pip install pylsl
+      pip install codecov
     condition: eq(variables['TEST_MODE'], 'pip')
     displayName: 'Install dependencies with pip'
   - powershell: |
@@ -62,13 +60,13 @@ jobs:
       $PSDefaultParameterValues['*:ErrorAction']='Stop'
       $env:PYTHON = '$(System.DefaultWorkingDirectory)' + '\conda'
       git clone git://github.com/astropy/ci-helpers.git
-      cd ci-helpers
-      git checkout nopip
-      cd ..
       powershell ci-helpers/appveyor/install-miniconda.ps1
-      $env:PATH = $env:PYTHON + "\envs\test;" + $env:PYTHON + "\envs\test\Scripts;" + $env:PYTHON + ";" + $env:PYTHON + "\Scripts;" + $env:PATH
+      $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
       pip uninstall -yq mne
-      pip install pylsl
+      pip install codecov
       Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)
     condition: eq(variables['TEST_MODE'], 'conda')
     displayName: 'Install dependencies with conda'
@@ -78,7 +76,7 @@ jobs:
     displayName: 'Print config'
   - script: python -c "import mne; mne.datasets.testing.data_path(verbose=True)"
     displayName: 'Get test data'
-  - script: pytest -m "not ultraslowtest" mne --cov=mne
+  - script: pytest -m "not ultraslowtest" --cov=mne mne
     displayName: 'Run tests'
   - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
     displayName: 'Codecov'

bin/mne

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import sys
-import glob
-import subprocess
-import os.path as op
-
 import mne
-
-mne_bin_dir = op.dirname(mne.__file__)
-valid_commands = sorted(glob.glob(op.join(mne_bin_dir,
-                                          'commands', 'mne_*.py')))
-valid_commands = [c.split(op.sep)[-1][4:-3] for c in valid_commands]
-
-
-def print_help():
-    print("Usage : mne command options\n")
-    print("Accepted commands :\n")
-    for c in valid_commands:
-        print("\t- %s" % c)
-    print("\nExample : mne browse_raw --raw sample_audvis_raw.fif")
-    print("\nGetting help example : mne compute_proj_eog -h")
-    sys.exit(0)
-
-
-if len(sys.argv) == 1:
-    print_help()
-elif ("help" in sys.argv[1] or "-h" in sys.argv[1]):
-    print_help()
-elif sys.argv[1] == "--version":
-    print("MNE %s" % mne.__version__)
-elif sys.argv[1] not in valid_commands:
-    print('Invalid command: "%s"\n' % sys.argv[1])
-    print_help()
-    sys.exit(0)
-else:
-    cmd = sys.argv[1]
-    cmd_path = op.join(mne_bin_dir, 'commands', 'mne_%s.py' % cmd)
-    sys.exit(subprocess.call([sys.executable, cmd_path] + sys.argv[2:]))
+mne.commands.utils.main()

debian/changelog

+python-mne (0.19.1+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * Breaks+Replaces: python-mne
+    Closes: #939623
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Replace Build-Depends forcing Python2 to mayavi2 (python-vtk6 | python-vtk)
+    by python3-vtk7
+  * Recommends: s/mayavi2/python3-vtk7/
+    Suggests: mayavi2
+
+ -- Andreas Tille <tille@debian.org>  Tue, 03 Dec 2019 09:52:14 +0100
+
 python-mne (0.18.1+dfsg-0.1) unstable; urgency=medium
 
   * Non-maintainer upload (with team approval).

debian/compat

-12

debian/control

 Source: python-mne
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders:
- Yaroslav Halchenko <debian@onerussian.com>,
- Michael Hanke <michael.hanke@gmail.com>,
+Uploaders: Yaroslav Halchenko <debian@onerussian.com>,
+           Michael Hanke <michael.hanke@gmail.com>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends:
- debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                libgl1-mesa-dri,
                libjs-jquery,
                libjs-jquery-ui,
- mayavi2 (>= 4.4.3~) | python-vtk6 | python-vtk,
+               python3-vtk7,
                python3-all,
                python3-coverage,
                python3-joblib,
@@ -29,16 +27,15 @@ Build-Depends:
                python3-sphinx,
                xauth,
                xvfb,
- yui-compressor,
-Standards-Version: 4.3.0
+               yui-compressor
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-mne
 Vcs-Git: https://salsa.debian.org/med-team/python-mne.git
 Homepage: http://martinos.org/mne
 
 Package: python3-mne
 Architecture: all
-Depends:
- help2man,
+Depends: help2man,
          libgl1-mesa-dri,
          libjs-bootstrap,
          libjs-d3,
@@ -52,18 +49,18 @@ Depends:
          xauth,
          xvfb,
          ${misc:Depends},
- ${python3:Depends},
-Recommends:
- mayavi2,
+         ${python3:Depends}
+Recommends: python3-vtk7,
             python3-nibabel,
             python3-nose,
- python3-pytest,
-Suggests:
+            python3-pytest
+Suggests: mayavi2,
           ipython,
           python3-dap,
- python3-pycuda,
-Provides:
- ${python3:Provides},
+          python3-pycuda
+Breaks: python-mne
+Provides: ${python3:Provides}
+Replaces: python-mne
 Description: Python modules for MEG and EEG data analysis
  This package is designed for sensor- and source-space analysis of MEG
  and EEG data, including frequency-domain and time-frequency analyses

debian/copyright

@@ -2,7 +2,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: MNE-Python
 Upstream-Contact: Alexandre Gramfort <alexandre.gramfort@m4x.org>
 Source: http://github.com/mne-tools/mne-python
-Files-Excluded: mne/html/*.min.js
+Files-Excluded: mne/html/jquery.js
+                mne/html/*.min.js
                 mne/html/*.min.css
 Comment: File AppEULA.rst refers to code that is documented in this package but not shipped with it.
 
@@ -33,18 +34,10 @@ Files: mne/externals/jdcal.py
 Copyright: 2010, Prasanth Nair, <prasanthhn@gmail.com>
 License: BSD-2-Clause
 
-Files: mne/externals/six.py
-Copyright: 2010-2013 Benjamin Peterson
-License: Expat
-
 Files: mne/externals/tempita/*
 Copyright: 2008 Ian Bicking and Contributors
 License: Expat
 
-Files: mne/html/mpld3*
-Copyright: 2013, Jake Vanderplas
-License: BSD-3-Clause
-
 License: BSD-2-Clause
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are