.circleci/config.yml

+# Tagging a commit with [circle front] will build the front page and perform test-doc.
+# Tagging a commit with [circle full] will build everything.
+version: 2
+jobs:
+    build:
+      docker:
+        # 3.6-jessie is too new for conda
+        - image: circleci/python:3.6-jessie
+      steps:
+        # Get our data and merge with upstream
+        - checkout
+        - run: echo $(git log -1 --pretty=%B) | tee gitlog.txt
+        - run: echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+        - run:
+           command: |
+             if [[ $(cat merge.txt) != "" ]]; then
+               echo "Merging $(cat merge.txt)";
+               git remote add upstream git://github.com/mne-tools/mne-python.git
+               git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+             fi
+
+        # Load our data
+        - restore_cache:
+            keys:
+              - data-cache-0
+              - data-cache-1
+              - data-cache-2
+              - data-cache-3
+              - data-cache-4
+              - data-cache-5
+              - data-cache-6
+              - data-cache-7
+              - data-cache-8
+              - pip-cache
+
+        # Spin up Xvfb
+        - run: /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;
+        - run: echo "export DISPLAY=:99" >> $BASH_ENV;
+        - run: echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV;
+        # Fix libgcc_s.so.1 pthread_cancel bug:
+        # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
+        # https://github.com/golemfactory/golem/issues/1019
+        - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default
+        # Get latest Anaconda running
+        - run:
+            command: |
+              wget -q http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O ~/miniconda.sh;
+              chmod +x ~/miniconda.sh;
+              ~/miniconda.sh -b -p ~/miniconda;
+              echo "export PATH=~/miniconda/bin:$PATH" >> $BASH_ENV;
+        - run:
+            command: |
+              conda update --yes --quiet conda;
+              conda env create --quiet -f environment.yml;
+              source activate mne;
+              conda install sphinx;
+              pip install sphinx_fontawesome sphinx_bootstrap_theme "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
+              pip uninstall --yes mne;
+              echo "source activate mne" >> $BASH_ENV;
+        - save_cache:
+            key: pip-cache
+            paths:
+              - ~/.cache/pip
+        # The conda-provided PyQt5 does not work on CircleCI for some reason,
+        # possibly because the libGL expects a sufficiently modern libgcc
+        # and conda rolls their own (libgcc-ng package).
+        - run: conda remove --yes qt pyqt matplotlib sip libxcb icu vtk
+        - run: pip uninstall --yes mayavi vtk
+        - run: pip install vtk mayavi PyQt5 PyQt5-sip sip matplotlib
+        - run: echo "export LD_PRELOAD=~/miniconda/envs/mne/lib/libgobject-2.0.so.0" >> $BASH_ENV
+        - run: pip install --upgrade "https://api.github.com/repos/nipy/PySurfer/zipball/master"
+        # Look at what we have and fail early if there is some library conflict
+        - run: which python
+        - run: python -c "import mne; mne.sys_info()"
+        - run: LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
+        - run: python -c "import mne; mne.set_config('MNE_LOGGING_LEVEL', 'info')"
+        - run: python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"
+
+        # Figure out if we should run a full, pattern, or noplot version
+        - run: python setup.py develop
+        - run: if ! git remote -v | grep upstream ; then git remote add upstream git://github.com/mne-tools/mne-python.git; fi
+        - run: git fetch upstream
+        - run: git branch -a
+        - run: mkdir -p ~/mne_data
+        - run:
+            command: |
+              touch pattern.txt;
+              if [ "$CIRCLE_BRANCH" == "master" ] || [[ $(cat gitlog.txt) == *"[circle full]"* ]]; then
+                echo html_dev > build.txt;
+              elif [ "$CIRCLE_BRANCH" == "maint/0.17" ]; then
+                echo html_stable > build.txt;
+              else
+                FNAMES=$(git diff --name-only $CIRCLE_BRANCH $(git merge-base $CIRCLE_BRANCH upstream/master));
+                if [[ $(cat gitlog.txt) == *"[circle front]"* ]]; then
+                  FNAMES="tutorials/plot_mne_dspm_source_localization.py tutorials/plot_receptive_field.py examples/connectivity/plot_mne_inverse_label_connectivity.py tutorials/plot_sensors_decoding.py tutorials/plot_stats_cluster_spatio_temporal.py tutorials/plot_visualize_evoked.py "${FNAMES};
+                  python -c "import mne; print(mne.datasets.testing.data_path(update_path=True))";
+                fi;
+                echo FNAMES="$FNAMES";
+                for FNAME in $FNAMES; do
+                  if [[ `expr match $FNAME "\(tutorials\|examples\)/.*plot_.*\.py"` ]] ; then
+                    echo "Checking example $FNAME ...";
+                    PATTERN=`basename $FNAME`"\\|"$PATTERN;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*sample.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.sample.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*spm_face.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.spm_face.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*somato.*" | wc -l) -gt 0 ]]; then
+                      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))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*hf_sef.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.hf_sef.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_auditory.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_auditory.data_path(update_path=True))" --accept-brainstorm-license;
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_raw.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_raw.data_path(update_path=True))" --accept-brainstorm-license;
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_ctf.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_ctf.data_path(update_path=True))" --accept-brainstorm-license;
+                    fi;
+                    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))";
+                      SUBJECTS_DIR=~/mne_data/MNE-sample-data/subjects python -c "import mne; print(mne.datasets.fetch_hcp_mmp_parcellation())" --accept-hcpmmp-license;
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*misc.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.misc.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*testing.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.testing.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*kiloword.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.kiloword.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*mtrf.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.mtrf.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*fieldtrip_cmc.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.fieldtrip_cmc.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*multimodal.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.multimodal.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*opm.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.opm.data_path(update_path=True))";
+                    fi;
+                    if [[ $(cat $FNAME | grep -x ".*datasets.*phantom_4dbti.*" | wc -l) -gt 0 ]]; then
+                      python -c "import mne; print(mne.datasets.phantom_4dbti.data_path(update_path=True))";
+                    fi;
+                  fi;
+                done;
+                echo PATTERN="$PATTERN";
+                if [[ $PATTERN ]]; then
+                  PATTERN="\(${PATTERN::-2}\)";
+                  echo html_dev-pattern > build.txt;
+                else
+                  echo html_dev-noplot > build.txt;
+                fi;
+              fi;
+              echo "$PATTERN" > pattern.txt;
+        - run: echo "PATTERN=$(cat pattern.txt)"
+        - run: echo "BUILD=$(cat build.txt)"
+        - run: ls -al ~/mne_data;
+        - run:
+            command: |
+              if [[ $(cat build.txt) == "html_dev" ]] || [[ $(cat build.txt) == "html_stable" ]]; then
+                SUBJECTS_DIR=~/mne_data/MNE-sample-data/subjects python -c "import mne; mne.datasets._download_all_example_data()";
+              fi;
+        - run: if [ ! -d ~/mne-tools.github.io ]; then git clone https://github.com/mne-tools/mne-tools.github.io.git ~/mne-tools.github.io --depth=1; fi;
+        # Run doctest (if it's full or front) before building the docs
+        - run:
+            command: |
+              if [[ $(cat gitlog.txt) == *"[circle front]"* ]] || [[ $(cat build.txt) == "html_dev" ]] || [[ $(cat build.txt) == "html_stable" ]]; then
+                make test-doc;
+              fi;
+        # Build docs
+        - run:
+            command: |
+              cd doc;
+              PATTERN=$(cat ../pattern.txt) make $(cat ../build.txt);
+        - run: python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"
+
+        - store_artifacts:
+            path: doc/_build/html/
+            destination: html
+
+        # Keep these separate, maybe better in terms of size limitations (?)
+        - save_cache:
+            key: data-cache-0
+            paths:
+              - ~/.mne
+              - ~/mne-tools.github.io
+              - ~/mne_data/mTRF_1.5
+        - save_cache:
+            key: data-cache-1
+            paths:
+              - ~/mne_data/HF_SEF
+              - ~/mne_data/MEGSIM
+        - save_cache:
+            key: data-cache-2
+            paths:
+              - ~/mne_data/MNE-brainstorm-data
+              - ~/mne_data/MNE-eegbci-data
+        - save_cache:
+            key: data-cache-3
+            paths:
+              - ~/mne_data/MNE-fieldtrip_cmc-data
+              - ~/mne_data/MNE-kiloword-data
+        - save_cache:
+            key: data-cache-4
+            paths:
+              - ~/mne_data/MNE-misc-data
+              - ~/mne_data/MNE-multimodal-data
+        - save_cache:
+            key: data-cache-5
+            paths:
+              - ~/mne_data/MNE-OPM-data
+              - ~/mne_data/MNE-phantom-4DBTi
+        - save_cache:
+            key: data-cache-6
+            paths:
+              - ~/mne_data/MNE-sample-data
+              - ~/mne_data/MNE-somato-data
+        - save_cache:
+            key: data-cache-7
+            paths:
+              - ~/mne_data/MNE-spm-face
+              - ~/mne_data/MNE-testing-ata
+        - save_cache:
+            key: data-cache-8
+            paths:
+              - ~/mne_data/MNE-visual_92_categories-data
+
+        - deploy:
+            name: Triage deployment
+            command: |
+              if [ "${CIRCLE_BRANCH}" == "master" ]; then
+                echo "Deploying dev docs.";
+                git config --global user.email "circle@mne.com";
+                git config --global user.name "Circle Ci";
+                pushd ~/mne-tools.github.io && git checkout master && git pull origin master && popd;
+                pushd doc/_build && rm -Rf ~/mne-tools.github.io/dev && cp -a html ~/mne-tools.github.io/dev && popd;
+                pushd ~/mne-tools.github.io && git add -A && git commit -m "CircleCI update of dev docs (${CIRCLE_BUILD_NUM})." && git push origin master && popd;
+              elif [ "${CIRCLE_BRANCH}" == "maint/0.17" ]; then
+                echo "Deploying stable docs.";
+                git config --global user.email "circle@mne.com";
+                git config --global user.name "Circle Ci";
+                pushd ~/mne-tools.github.io && git checkout master && git pull origin master && popd;
+                pushd doc/_build && rm -Rf ~/mne-tools.github.io/stable cp -a html_stable ~/mne-tools.github.io/stable && popd;
+                pushd ~/mne-tools.github.io && git add -A && git commit -m "CircleCI update of stable docs (${CIRCLE_BUILD_NUM})." && git push origin master && popd;
+              else
+                echo "No deployment (build: ${CIRCLE_BRANCH}).";
+              fi

.github/CONTRIBUTING.md

+# Contributing to MNE-Python
+
+First off, thanks for taking the time to contribute!
+
+The following is a quick summary to a set of guidelines for contributing to [MNE-Python](https://github.com/mne-python/mne-python) on GitHub. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+
+## Code of Conduct
+
+This project and everyone participating in it is governed by the [MNE-Python's Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [mne-conduct@googlegroups.com](mailto:mne-conduct@googlegroups.com).
+
+## How to contribute
+
+Before contributing make sure you are familiar with [our contributing guide](https://martinos.org/mne/contributing.html).

.github/ISSUE_TEMPLATE/blank.md

+---
+name: Blank issue
+about: Create an issue without a template.
+
+---

.github/ISSUE_TEMPLATE/bug_report.md

+---
+name: Bug report
+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).
+
+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.
+
+
+#### Describe the bug
+Please provide a clear and concise description of the bug.
+
+
+#### Steps and/or code to reproduce
+Please provide a code snippet or [minimal working example (MWE)](https://en.wikipedia.org/wiki/Minimal_Working_Example)
+to replicate your problem.
+
+This MWE should be self-contained, which means that other MNE-Python contributors
+should be able to copy and paste the provided snippet and replicate the bug.
+If possible, use MNE-Python testing examples to reproduce the error. Otherwise,
+provide a small and anonymized portion of your data required to reproduce the bug.
+
+If the code is too long, feel free to put it in a [public gist](https://gist.github.com) and link
+it in the issue.
+
+Example:
+
+```Python
+import mne
+
+fname = mne.datasets.sample.data_path() + '/MEG/sample/sample_audvis_raw.fif'
+raw = mne.io.read_raw_fif(fname)
+raw = mne.concatenate_raws([raw])
+raw.save('test_raw.fif', overwrite=True)
+raw_read = mne.io.read_raw_fif('test_raw.fif')  # this breaks
+```
+
+
+#### Expected results
+Provide a clear and concise description of what you expected to happen.
+
+
+#### Actual results
+Please paste or specifically describe the actual output or traceback.
+
+
+#### Additional information
+Paste the output of `mne.sys_info()` here.

.github/ISSUE_TEMPLATE/feature_request.md

+---
+name: Feature request
+about: Suggest an idea for this project.
+
+---
+
+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.
+
+#### Describe the problem
+Please provide a clear and concise description of the problem.
+
+
+#### Describe your solution
+A clear and concise description of what you want to happen.
+
+
+#### Describe possible alternatives
+A clear and concise description of any alternative solutions or features you have considered.
+
+
+#### Additional context
+Add any other context or screenshots about the feature request 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)
+before submitting.
+
+Please be aware that we are a loose team of volunteers so patience is
+necessary. Assistance handling other issues is very welcome. We value
+all user contributions, no matter how minor they are. If we are slow to
+review, either the pull request needs some benchmarking, tinkering,
+convincing, etc. or more likely the reviewers are simply busy. In either
+case, we ask for your understanding during the review process.
+
+Again, thanks for contributing!
+
+#### Reference issue
+Example: Fixes #1234.
+
+
+#### What does this implement/fix?
+Explain your changes.
+
+
+#### Additional information
+Any additional information you think is important.

.gitignore

@@ -41,6 +41,7 @@ MEGSIM*
 build
 coverage
 .cache/
+.pytest_cache/
 
 dist/
 doc/_build/
@@ -64,3 +65,11 @@ examples/visualization/foobar.html
 
 # sublime
 *-e
+
+# Visual Studio Code
+.vscode
+
+# Emacs
+*.py#
+*.rst#
+

.mailmap

-Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort@inria.fr>
-Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort@gmail.com>
-Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort@m4x.org>
-Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr> Alexandre Gramfort <gramfort@localhost.(none)>
+Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
+Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@inria.fr>
+Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@gmail.com>
+Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <alexandre.gramfort@m4x.org>
+Alexandre Gramfort <alexandre.gramfort@inria.fr> Alexandre Gramfort <gramfort@localhost.(none)>
 Martin Luessi <mluessi@nmr.mgh.harvard.edu> mluessi@nmr.mgh.harvard.edu <mluessi@nmr.mgh.harvard.edu>
 Martin Luessi <mluessi@nmr.mgh.harvard.edu> martin <martin@think.hsd1.ma.comcast.net>
 Martin Luessi <mluessi@nmr.mgh.harvard.edu> martin <martin@think.(none)>
@@ -76,7 +77,9 @@ Jaakko Leppakangas <jaeilepp@gmail.com> jaeilepp <jaeilepp@gmail.com>
 Jair Montoya <montoya.jair.m@gmail.com> jmontoyam <montoya.jair.m@gmail.com>
 Natalie Klein <neklein@andrew.cmu.edu> natalieklein <neklein@andrew.cmu.edu>
 Daniel McCloy <dan.mccloy@gmail.com> drammock <dan.mccloy@gmail.com>
-Fede Raimondo <slashack@gmail.com> Fede <slashack@gmail.com>
+Fede Raimondo <federaimondo@gmail.com> Fede <slashack@gmail.com>
+Fede Raimondo <federaimondo@gmail.com> Fede Raimondo <fraimondo@dc.uba.ar>
+Fede Raimondo <federaimondo@gmail.com> Fede Raimondo <federaimondo@gmail.com>
 Emily Stephen <emilyps14@gmail.com> emilyps14 <emilyps14@gmail.com>
 Marian Dovgialo <mdovgialo@fabrizzio.zfb.fuw.edu.pl>
 Guillaume Dumas <deep@introspection.eu> deep-introspection <deep@introspection.eu>
@@ -100,3 +103,18 @@ Mathurin Massias <mathurin.massias@gmail.com> mathurinm <mathurinm@users.noreply
 Simon Kern <simon.kern@online.de> skjerns <simon.kern@online.de>
 S. M. Gutstein <s.m.gutstein@gmail.com> smgutstein <s.m.gutstein@gmail.com>
 Robin Tibor Schirrmeister <robintibor@gmail.com> robintibor <robintibor@gmail.com>
+Anne-Sophie Dubarry <as_dub@hotmail.com> annesodub <as_dub@hotmail.com>
+Claire Braboszcz <claire@guakamole.org> claire-braboszcz <claire@guakamole.org>
+Larry Eisenman <leisenman@wustl.edu> lneisenman <lneisenman@hotmail.com>
+Mathurin Massias <mathurin.massias@gmail.com> mathurinm <mathurin.massias@gmail.com>
+Pierre Ablin <pierreablin@gmail.com> pierreablin <pierreablin@gmail.com>
+Erik Hornberger <erik.hornberger@shi-g.com> er06645810 <erik.hornberger@shi-g.com>
+Kostiantyn Maksymenko <makkostya@ukr.net> Maksymenko Kostiantyn <makkostya@ukr.net>
+Nathalie Gayraud <nathalie.gayraud@inria.fr> Nathalie <nathalie.gayraud@inria.fr>
+Dominik Krzemiński <raymon92@gmail.com> dokato <raymon92@gmail.com>
+Ezequiel Mikulan <39155887+ezemikulan@users.noreply.github.com> ezemikulan <39155887+ezemikulan@users.noreply.github.com>
+Hubert Banville <hubert.jbanville@gmail.com> hubertjb <hubert.jbanville@gmail.com>
+Sara Sommariva <sommariva@dima.unige.it> sarasommariva <sommariva@dima.unige.it>
+Manu Sutela <manu.sutela@gmail.com> MJAS1 <manu.sutela@gmail.com>
+Joan Massich <mailsik@gmail.com> Joan Massich <sik@visor.udg.edu>
+David Sabbagh <dav.sabbagh@gmail.com> DavidSabbagh <33925146+DavidSabbagh@users.noreply.github.com>
\ No newline at end of file

.travis.yml

@@ -3,75 +3,68 @@ dist: trusty
 sudo: false
 cache:
   apt: true
+  pip: true
 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 pytest-faulthandler pytest-sugar" OPTION=""
-            TRAVIS_PYTHON_VERSION=3.6
+            PIP_DEPENDENCIES="codecov pytest-faulthandler" OPTION=""
+            TRAVIS_PYTHON_VERSION=3.6 CONDA_VERSION=">=4.3.27"
+            OPENBLAS_NUM_THREADS=1
 
 matrix:
     include:
         # 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 nose pytest pytest-cov"
-               PIP_DEPENDENCIES="flake8 numpydoc codespell git+git://github.com/PyCQA/pydocstyle.git codecov check-manifest pytest-sugar"
+               CONDA_DEPENDENCIES="numpy scipy matplotlib sphinx pytest pytest-cov"
+               PIP_DEPENDENCIES="flake8 numpydoc codespell git+git://github.com/PyCQA/pydocstyle.git codecov check-manifest"
                OPTION="--doctest-ignore-import-errors"
 
         # Linux
         - os: linux
           env: CONDA_ENVIRONMENT="environment.yml"
-               SPLIT=0
-        - os: linux
-          env: CONDA_ENVIRONMENT="environment.yml"
-               SPLIT=1
 
-        # OSX
+        # OSX conda
         - os: osx
           env: CONDA_ENVIRONMENT="environment.yml"
-               SPLIT=0
-        - os: osx
-          env: CONDA_ENVIRONMENT="environment.yml"
-               SPLIT=1
 
-        # 2.7 + non-default stim channel
-        - os: linux
-          env: CONDA_ENVIRONMENT="environment2.yml" MNE_STIM_CHANNEL=STI101
-               SPLIT=0
+        # PIP + non-default stim channel
         - os: linux
-          env: CONDA_ENVIRONMENT="environment2.yml" MNE_STIM_CHANNEL=STI101
-               SPLIT=1
+          env: MNE_STIM_CHANNEL=STI101
+          language: python
+          python: "3.6"
 
         # 2.7 Old dependencies
         - os: linux
           env: PYTHON_VERSION=2.7
-               CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
-               SPLIT=0
-        - os: linux
-          env: PYTHON_VERSION=2.7
-               CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
-               SPLIT=1
+               CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.13 scikit-learn=0.15 pytest pytest-cov"
 
         # Minimal
         - os: linux
           env: DEPS=minimial
-               CONDA_DEPENDENCIES="numpy scipy matplotlib nose pytest pytest-cov"
-               SPLIT=0
-        - os: linux
-          env: DEPS=minimial
-               CONDA_DEPENDENCIES="numpy scipy matplotlib nose pytest pytest-cov"
-               SPLIT=1
+               CONDA_DEPENDENCIES="numpy scipy matplotlib pytest pytest-cov"
 
 # 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;
-    - git clone https://github.com/astropy/ci-helpers.git
-    - source ci-helpers/travis/setup_conda.sh
-    - if [ ! -z $CONDA_ENVIRONMENT ]; then
+    - if [ -z "$CONDA_ENVIRONMENT" ] && [ -z "$CONDA_DEPENDENCIES" ]; then
+        pip uninstall -y numpy;
+        pip install numpy scipy vtk;
+        pip install -r requirements.txt;
+      else
+        git clone https://github.com/astropy/ci-helpers.git;
+        source ci-helpers/travis/setup_conda.sh;
+        if [ ! -z "$CONDA_ENVIRONMENT" ]; then
           pip uninstall --yes mne;
         fi;
+        if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
+          pip install --upgrade pyqt5>=5.10;
+        fi;
+      fi
     # Don't source mne_setup_sh here because changing PATH etc. can't be done in a script
     - if [ "${DEPS}" == "" ]; then
         export MNE_ROOT="${PWD}/minimal_cmds";
@@ -88,6 +81,11 @@ before_install:
       fi;
 
 install:
+    # Rvm overrides cd with a function so that it can hook into it to run
+    # some scripts, see https://github.com/travis-ci/travis-ci/issues/8703
+    - if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
+        unset -f cd;
+      fi;
     # Suppress the parallel outputs for logging cleanliness
     - python setup.py build
     - python setup.py install
@@ -144,28 +142,36 @@ script:
         CONDITION='not ultraslowtest';
       fi;
     - python -c "import mne; print(mne.sys_info())"
-    # Determine directories to test
+    # Determine directories to test (could use SPLIT=0 SPLIT=1 but currently
+    # we are fast enough, so disable it)
     - if [ -z ${SPLIT} ]; then
         USE_DIRS="mne/";
       else
         if [ "${SPLIT}" == "0" ]; then
           MNE_DIRS=". beamformer channels commands connectivity datasets decoding forward gui inverse_sparse io";
-        else
+        elif [ "${SPLIT}" == "1" ]; then
           MNE_DIRS="minimum_norm preprocessing realtime simulation stats time_frequency viz";
+        elif [ "${SPLIT}" == "2" ]; then
+          MNE_DIRS=".";
+        else
+          MNE_DIRS="beamformer channels commands connectivity datasets decoding forward gui inverse_sparse io";
         fi;
         USE_DIRS="";
         for DIR in ${MNE_DIRS}; do
-          USE_DIRS="mne/${DIR}/tests ${USE_DIRS}";
+          if [ "${DIR}" == "." ]; then
+            USE_DIRS="mne/tests mne/*.py ${USE_DIRS}";
+          else
+            USE_DIRS="mne/${DIR}/ ${USE_DIRS}";
+          fi;
         done;
       fi;
     - echo py.test -m "${CONDITION}" ${OPTION} ${USE_DIRS} --cov=mne;
     - py.test -m "${CONDITION}" ${OPTION} ${USE_DIRS} --cov=mne;
     - if [ "${DEPS}" == "nodata" ]; then
         make pep;
-        check-manifest --ignore doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data;
       fi;
 
-after_success:
+after_script:
     # Need to run from source dir to exectue "git" commands
     - cd ${SRC_DIR};
     - codecov;

CODE_OF_CONDUCT.md

+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at mne-conduct@googlegroups.com. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

MANIFEST.in

 include *.rst
 include LICENSE.txt
+include requirements.txt
 include mne/__init__.py
 
 recursive-include examples *.py
@@ -34,13 +35,22 @@ recursive-exclude examples/MNE-somato-data *
 exclude Makefile
 exclude .coveragerc
 exclude *.yml
-exclude dictionary.txt
+exclude ignore_words.txt
 exclude .mailmap
 recursive-exclude mne *.pyc
 
 recursive-exclude doc *
 recursive-exclude logo *
 
+exclude CODE_OF_CONDUCT.md
+exclude .github
+exclude .github/CONTRIBUTING.md
+exclude .github/ISSUE_TEMPLATE
+exclude .github/ISSUE_TEMPLATE/blank.md
+exclude .github/ISSUE_TEMPLATE/bug_report.md
+exclude .github/ISSUE_TEMPLATE/feature_request.md
+exclude .github/PULL_REQUEST_TEMPLATE.md
+
 # Test files
 
 recursive-exclude mne/io/tests/data *

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"
+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"
 CODESPELL_DIRS ?= mne/ doc/ tutorials/ examples/
 all: clean inplace test test-doc
 
@@ -37,6 +37,8 @@ sample_data:
 testing_data:
 	@python -c "import mne; mne.datasets.testing.data_path(verbose=True);"
 
+pytest: test
+
 test: in
 	rm -f .coverage
 	$(PYTESTS) -m 'not ultraslowtest' mne
@@ -97,21 +99,31 @@ flake:
 	@echo "flake8 passed"
 
 codespell:  # running manually
-	@codespell -w -i 3 -q 3 -S $(CODESPELL_SKIPS) -D ./dictionary.txt $(CODESPELL_DIRS)
+	@codespell -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
 
 codespell-error:  # running on travis
-	@codespell -i 0 -q 7 -S $(CODESPELL_SKIPS) -D ./dictionary.txt $(CODESPELL_DIRS)
+	@codespell -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt $(CODESPELL_DIRS)
 
 pydocstyle:
 	@echo "Running pydocstyle"
-	@pydocstyle
+	@pydocstyle mne
 
 docstring:
 	@echo "Running docstring tests"
 	@$(PYTESTS) --doctest-modules mne/tests/test_docstring_parameters.py
 
+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
+
+nesting:
+	@echo "Running import nesting tests"
+	@$(PYTESTS) mne/tests/test_import_nesting.py
+
 pep:
-	@$(MAKE) -k flake pydocstyle docstring codespell-error
+	@$(MAKE) -k flake pydocstyle docstring codespell-error check-manifest nesting check-readme
 
 manpages:
 	@echo "I: generating manpages"
@@ -131,5 +143,4 @@ build-doc-stable:
 	cd doc; make clean
 	cd doc; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html_stable
 
-docstyle:
-	@pydocstyle
+docstyle: pydocstyle

README.rst

@@ -6,9 +6,9 @@
 |MNE|_
 
 .. |Travis| image:: https://api.travis-ci.org/mne-tools/mne-python.png?branch=master
-.. _Travis: https://travis-ci.org/mne-tools/mne-python
+.. _Travis: https://travis-ci.org/mne-tools/mne-python/branches
 
-.. |Appveyor| image:: https://ci.appveyor.com/api/projects/status/7isroetnxsp7hgxv/branch/master?svg=true
+.. |Appveyor| image:: https://ci.appveyor.com/api/projects/status/jg8ncqql9wayo8mg/branch/master?svg=true
 .. _Appveyor: https://ci.appveyor.com/project/mne-tools/mne-python/branch/master
 
 .. |Circle| image:: https://circleci.com/gh/mne-tools/mne-python.svg?style=svg
@@ -20,84 +20,94 @@
 .. |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:: http://mne-tools.github.io/dev/_static/mne_logo.png
-.. _MNE: https://mne-tools.github.io
+.. |MNE| image:: https://martinos.org/mne/stable/_static/mne_logo.png
+.. _MNE: https://martinos.org/mne
 
-`MNE-Python <http://mne-tools.github.io/>`_
-=======================================================
+MNE-Python
+==========
 
-This package is designed for sensor- and source-space analysis of [M/E]EG
-data, including frequency-domain and time-frequency analyses, MVPA/decoding
-and non-parametric statistics. This package generally evolves quickly and
-user contributions can easily be incorporated thanks to the open
-development environment .
+`MNE-Python software`_ is an open-source Python package for exploring,
+visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG,
+ECoG, and more. It includes modules for data input/output, preprocessing,
+visualization, source estimation, time-frequency analysis, connectivity analysis,
+machine learning, and statistics.
 
-Get more information
-^^^^^^^^^^^^^^^^^^^^
 
-If you're unfamiliar with MNE, you can visit the
-`MNE homepage <http://mne-tools.github.io/>`_ for full user documentation.
+Documentation
+^^^^^^^^^^^^^
+
+`MNE documentation`_ for MNE-Python is available online.
 
-Get the latest code
-^^^^^^^^^^^^^^^^^^^
 
-To get the latest code using `git <https://git-scm.com/>`_, simply type:
+Installing MNE-Python
+^^^^^^^^^^^^^^^^^^^^^
+
+To install the latest stable version of MNE-Python, you can use pip_ in a terminal:
 
 .. code-block:: bash
 
-    $ git clone git://github.com/mne-tools/mne-python.git
+    pip install -U mne
 
-If you don't have git installed, you can download a
-`zip of the latest code <https://github.com/mne-tools/mne-python/archive/master.zip>`_.
+**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.
 
-Install MNE-python
-^^^^^^^^^^^^^^^^^^
+For more complete instructions and more advanced installation methods (e.g. for
+the latest development version), see the `getting started page`_.
 
-As with most Python packages, to install the latest stable version of
-MNE-Python, you can do:
+
+Get the latest code
+^^^^^^^^^^^^^^^^^^^
+
+To install the latest version of the code using pip_ open a terminal and type:
 
 .. code-block:: bash
 
-    $ pip install mne
+    pip install -U https://api.github.com/repos/mne-tools/mne-python/zipball/master
+
+To get the latest code using `git <https://git-scm.com/>`__, open a terminal and type:
+
+.. code-block:: bash
+
+    git clone git://github.com/mne-tools/mne-python.git
+
+Alternatively, you can also download a
+`zip file of the latest development version <https://github.com/mne-tools/mne-python/archive/master.zip>`__.
 
-For more complete instructions and more advanced install methods (e.g. for
-the latest development version), see the
-`getting started page <http://mne-tools.github.io/stable/getting_started.html>`_
-page.
 
 Dependencies
 ^^^^^^^^^^^^
 
-The minimum required dependencies to run the software are:
+The minimum required dependencies to run MNE-Python are:
 
 - Python >= 2.7
 - NumPy >= 1.8
 - SciPy >= 0.12
-  - matplotlib >= 1.3
 
 For full functionality, some functions require:
 
-  - scikit-learn >= 0.18
-  - nibabel >= 2.1.0
-  - pandas >= 0.12
+- Matplotlib >= 1.3
+- Mayavi >= 4.6
+- PySurfer >= 0.8
+- Scikit-learn >= 0.15 (>= 0.18 recommended)
+- NiBabel >= 2.1.0
+- Pandas >= 0.13
+- Picard >= 0.3
+- CuPy >= 4.0 (for NVIDIA CUDA acceleration)
+- DIPY >= 0.10.1
 
-To use NVIDIA CUDA for resampling and FFT FIR filtering, you will also need
-to install the NVIDIA CUDA SDK, pycuda, and scikits.cuda. See the
-`getting started page <http://mne-tools.github.io/stable/getting_started.html>`_
-for more information.
+Contributing to MNE-Python
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Contribute to MNE-python
-^^^^^^^^^^^^^^^^^^^^^^^^
+Please see the documentation on the MNE-Python homepage:
 
-Please see the documentation on the MNE-python homepage:
+https://martinos.org/mne/contributing.html
 
-http://martinos.org/mne/contributing.html
 
 Mailing list
 ^^^^^^^^^^^^
 
 http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
 
+
 Licensing
 ^^^^^^^^^
 
@@ -106,7 +116,7 @@ MNE-Python is **BSD-licenced** (3 clause):
     This software is OSI Certified Open Source Software.
     OSI Certified is a certification mark of the Open Source Initiative.
 
-    Copyright (c) 2011, authors of MNE-Python
+    Copyright (c) 2011-2017, authors of MNE-Python.
     All rights reserved.
 
     Redistribution and use in source and binary forms, with or without
@@ -135,3 +145,10 @@ MNE-Python is **BSD-licenced** (3 clause):
     (including negligence or otherwise) arising in any way out of the use
     of this software, even if advised of the possibility of such
     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
+.. _pip: https://pip.pypa.io/en/stable/
+

appveyor.yml

@@ -4,7 +4,7 @@ environment:
       CONDA_ENVIRONMENT: "environment.yml"
       PIP_DEPENDENCIES: "codecov pytest-faulthandler"
   matrix:
-      - PYTHON_VERSION: "2.7"
+      - PYTHON_VERSION: "3.6"
         PYTHON_ARCH: "64"
 
 install:

bin/mne

@@ -23,6 +23,7 @@ def print_help():
     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]):

circle.yml

-machine:
-  environment:
-    # We need to set this variable to let Anaconda take precedence
-    PATH: "/home/ubuntu/miniconda/envs/circleenv/bin:/home/ubuntu/miniconda/bin:$PATH"
-    DISPLAY: ":99.0"
-
-# We should really build merged versions like on Travis, not the individual branches
-# Adapted from:
-# https://gist.github.com/amacneil/f14db753919e0af2d7d2f5a8da7fce65
-checkout:
-  post:
-    - echo $(git log -1 --pretty=%B) > gitlog.txt
-    - echo ${CI_PULL_REQUEST//*pull\//} > merge.txt
-    - if [[ $(cat merge.txt) != "" ]]; then
-        echo "Merging $(cat merge.txt)";
-        git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge";
-      fi
-
-dependencies:
-  cache_directories:
-    - "~/miniconda"
-    - "~/.mne"
-    - "~/mne_data/HF_SEF"
-    - "~/mne_data/MNE-sample-data"
-    - "~/mne_data/MNE-testing-data"
-    - "~/mne_data/MNE-misc-data"
-    - "~/mne_data/MNE-spm-face"
-    - "~/mne_data/MNE-somato-data"
-    - "~/mne_data/MNE-brainstorm-data"
-    - "~/mne_data/MEGSIM"
-    - "~/mne_data/MNE-eegbci-data"
-    - "~/mne_data/mTRF_1.5"
-    - "~/mne_data/MNE-fieldtrip_cmc-data"
-    - "~/mne-tools.github.io"
-  # Various dependencies
-  pre:
-    # Get a running Python
-    - cd ~;
-    # Disable pyenv (no cleaner way provided by CircleCI as it prepends pyenv version to PATH)
-    - rm -rf ~/.pyenv;
-    - rm -rf ~/virtualenvs;
-    # Get Anaconda and conda-based requirements
-    - >
-      if [ ! -d "/home/ubuntu/miniconda" ]; then
-        echo "Setting up conda";
-        wget -q http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O ~/miniconda.sh;
-        chmod +x ~/miniconda.sh;
-        ~/miniconda.sh -b -p /home/ubuntu/miniconda;
-        conda update --yes --quiet conda;
-      else
-        echo "Conda already set up.";
-      fi
-    - if ! conda env list | grep circleenv; then
-        conda create -n circleenv --yes pip python=2.7 pip;
-        sed -i "s/ENABLE_USER_SITE = .*/ENABLE_USER_SITE = False/g" /home/ubuntu/miniconda/envs/circleenv/lib/python2.7/site.py;
-      else
-        echo "Conda env already set up.";
-      fi;
-    - conda install -n circleenv --yes numpy scipy scikit-learn matplotlib sphinx pillow six IPython pandas mayavi nose;
-    - ls -al /home/ubuntu/miniconda;
-    - ls -al /home/ubuntu/miniconda/bin;
-    - echo $PATH;
-    - echo $CIRCLE_BRANCH
-    - which python;
-    - which pip;
-    - cat /home/ubuntu/miniconda/envs/circleenv/lib/python2.7/site.py | grep "ENABLE_USER_SITE"
-    - pip install --upgrade pyface;
-    - pip install --upgrade git+https://github.com/enthought/mayavi.git
-    - git clone https://github.com/sphinx-gallery/sphinx-gallery.git;
-    - cd sphinx-gallery && pip install -r requirements.txt && python setup.py develop;
-    - pip install sphinx_bootstrap_theme pysurfer nilearn neo numpydoc;
-
-  override:
-    # Figure out if we should run a full, pattern, or noplot version
-    - cd /home/ubuntu/mne-python && python setup.py develop;
-    - if ! git remote -v | grep upstream ; then git remote add upstream git://github.com/mne-tools/mne-python.git; fi;
-    - git fetch upstream;
-    - git branch -a;
-    - mkdir -p ~/mne_data;
-    - if [[ $(cat gitlog.txt) == *"[circle front]"* ]]; then
-        PATTERN="plot_mne_dspm_source_localization.py\|plot_receptive_field.py\|plot_mne_inverse_label_connectivity.py\|plot_sensors_decoding.py\|plot_stats_cluster_spatio_temporal.py\|plot_visualize_evoked.py\|";
-      else
-        PATTERN="";
-      fi;
-      if [ "$CIRCLE_BRANCH" == "master" ] || [[ $(cat gitlog.txt) == *"[circle full]"* ]]; then
-        echo html_dev > build.txt;
-      elif [ "$CIRCLE_BRANCH" == "maint/0.15" ]; then
-        echo html_stable > build.txt;
-      else
-        FNAMES=$(git diff --name-only $CIRCLE_BRANCH $(git merge-base $CIRCLE_BRANCH upstream/master));
-        echo FNAMES="$FNAMES";
-        for FNAME in $FNAMES; do
-          if [[ `expr match $FNAME "\(tutorials\|examples\)/.*plot_.*\.py"` ]] ; then
-            echo "Checking example $FNAME ...";
-            PATTERN=`basename $FNAME`"\\|"$PATTERN;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*sample.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.sample.data_path(update_path=True))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*spm_face.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.spm_face.data_path(update_path=True))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*somato.*" | wc -l) -gt 0 ]]; then
-              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))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*hf_sef.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.hf_sef.data_path(update_path=True))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_auditory.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.brainstorm.bst_auditory.data_path(update_path=True))" --accept-brainstorm-license;
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_raw.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.brainstorm.bst_raw.data_path(update_path=True))" --accept-brainstorm-license;
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_ctf.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_ctf.data_path(update_path=True))" --accept-brainstorm-license;
-            fi;
-            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))";
-              SUBJECTS_DIR=~/mne_data/MNE-sample-data/subjects python -c "import mne; print(mne.datasets.fetch_hcp_mmp_parcellation())" --accept-hcpmmp-license;
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*misc.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.misc.data_path(update_path=True))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*mtrf.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.mtrf.data_path(update_path=True))";
-            fi;
-            if [[ $(cat $FNAME | grep -x ".*datasets.*fieldtrip_cmc.*" | wc -l) -gt 0 ]]; then
-              python -c "import mne; print(mne.datasets.fieldtrip_cmc.data_path(update_path=True))";
-            fi;
-          fi;
-        done;
-        echo PATTERN="$PATTERN";
-        echo NEED_SAMPLE="$NEED_SAMPLE";
-        if [[ $PATTERN ]]; then
-          PATTERN="\(${PATTERN::-2}\)";
-          echo html_dev-pattern > build.txt;
-        else
-          echo html_dev-noplot > build.txt;
-        fi;
-      fi;
-      echo "$PATTERN" > pattern.txt;
-    - echo BUILD="$(cat build.txt)"
-    - ls -al ~/mne_data;
-    - if [[ $(cat build.txt) == "html_dev" ]] || [[ $(cat build.txt) == "html_stable" ]]; then
-        SUBJECTS_DIR=/home/ubuntu/mne_data/MNE-sample-data/subjects python -c "import mne; mne.datasets._download_all_example_data()";
-      fi;
-    - python -c "import mne; mne.sys_info()";
-    - >
-      if [ ! -d "/home/ubuntu/mne-tools.github.io" ]; then
-        cd .. && git clone https://github.com/mne-tools/mne-tools.github.io.git && cd mne-tools.github.io;
-      fi;
-    - /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;
-
-test:
-  override:
-    # Mayavi can bomb on exit (yay!), turning a successful build into a failure.
-    # We thus tee into a log (which returns 0) and then parse afterward for
-    # what immediately precedes the "Build finished." line.
-    - if [[ $(cat build.txt) == "html_dev-noplot" ]]; then cd doc && make html_dev-noplot | tee $CIRCLE_ARTIFACTS/log.txt; elif [[ $(cat build.txt) == "html_dev-pattern" ]]; then cd doc && PATTERN=$(cat ../pattern.txt) make html_dev-pattern | tee $CIRCLE_ARTIFACTS/log.txt; else make test-doc; cd doc; make $(cat ../build.txt) | tee $CIRCLE_ARTIFACTS/log.txt; fi:
-          timeout: 1500
-    - tail $CIRCLE_ARTIFACTS/log.txt | grep -E "auto_tutorials\s*\[100%\]\s*plot_|Build finished"
-  post:
-    - if [[ $(cat build.txt) == "html_stable" ]]; then
-        cp -a doc/_build/html_stable $CIRCLE_ARTIFACTS/;
-      else
-        cp -a doc/_build/html $CIRCLE_ARTIFACTS/;
-      fi;
-
-deployment:
-  production:
-    branch: master
-    commands:
-      - git config --global user.email "circle@mne.com"
-      - git config --global user.name "Circle Ci"
-      - cd ../mne-tools.github.io && git checkout master && git pull origin master
-      - cd doc/_build && rm -Rf ~/mne-tools.github.io/dev && cp -a html ~/mne-tools.github.io/dev
-      - cd ../mne-tools.github.io && git add -A && git commit -m 'Automated update of dev docs.' && git push origin master
-  stable:
-    branch: maint/0.15
-    commands:
-      - git config --global user.email "circle@mne.com"
-      - git config --global user.name "Circle Ci"
-      - cd ../mne-tools.github.io && git checkout master && git pull origin master
-      - cd doc/_build && rm -Rf ~/mne-tools.github.io/stable && cp -a html_stable ~/mne-tools.github.io/stable
-      - cd ../mne-tools.github.io && git add -A && git commit -m 'Automated update of stable docs.' && git push origin master

debian/changelog

+python-mne (0.17+dfsg-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Testsuite: autopkgtest-pkg-python
+
+ -- Andreas Tille <tille@debian.org>  Wed, 19 Dec 2018 09:05:00 +0100
+
 python-mne (0.15.2+dfsg-2) unstable; urgency=medium
 
   * up_check_numpy to skip a test for warnings being issued with 

debian/compat

-10
+11

debian/control

@@ -4,8 +4,9 @@ Uploaders: Alexandre Gramfort <alexandre.gramfort@m4x.org>,
            Yaroslav Halchenko <debian@onerussian.com>,
            Michael Hanke <michael.hanke@gmail.com>
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python-all,
                python-nibabel,
                python-numpy,
@@ -27,9 +28,9 @@ Build-Depends: debhelper (>= 10),
                libjs-jquery,
                libjs-jquery-ui,
                yui-compressor
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-mne.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-mne.git
+Standards-Version: 4.2.1
+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
 X-Python-Version: >= 2.7
 

debian/patches/deb_paths

@@ -6,16 +6,7 @@ Reviewed-By: Yaroslav O. Halchenko <debian@onerussian.com>
 
 --- a/mne/report.py
 +++ b/mne/report.py
-@@ -30,7 +30,7 @@ from .parallel import parallel_func, che
- 
- from .externals.tempita import HTMLTemplate, Template
- from .externals.six import BytesIO
--from .externals.six import moves
-+from .externals.six import moves, PY3
- 
- VALID_EXTENSIONS = ['raw.fif', 'raw.fif.gz', 'sss.fif', 'sss.fif.gz',
-                     '-eve.fif', '-eve.fif.gz', '-cov.fif', '-cov.fif.gz',
-@@ -1201,21 +1201,27 @@ class Report(object):
+@@ -1359,21 +1359,27 @@ class Report(object):
      @verbose
      def _init_render(self, verbose=None):
          """Initialize the renderer."""