Commit 6206b3b7 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.17+dfsg

parent 4efa94e1

.circleci/config.yml

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# 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

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# 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

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---

name: Blank issue

about: Create an issue without a template.



---

.github/ISSUE_TEMPLATE/bug_report.md

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---

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

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---

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.