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Merge v0.4.3
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‎.gitignore

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@@ -89,3 +89,4 @@ docs/auto_examples/
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docs/modules/
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report.html
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notebooks/
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.pytest_cache/

‎.travis.yml

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@@ -1,5 +1,10 @@
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language: python
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cache:
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pip: true
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apt: true
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directories:
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- ~/visbrain_data
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sudo: false
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dist: trusty
@@ -11,13 +16,15 @@ matrix:
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include:
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- env: TEST=standard
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os: linux
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# - env: TEST=standard
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# os: linux
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# python: '3.7'
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- env: TEST=flake
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os: linux
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# - env: TEST=examples
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# os: linux
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# - env: TEST=standard
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# os: osx
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# language: generic
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- env: TEST=examples
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os: linux
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allow_failures:
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- env: TEST=flake
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@@ -42,18 +49,20 @@ before_install:
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install:
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# Create the py3 environnement ;
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- conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy pip
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- conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy pip cython
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- source activate testenv
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# Install dependencies :
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- if [ "${TEST}" == "standard" ]; then
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- if [ "${TEST}" == "standard" ] || [ "${TEST}" == "examples" ]; then
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pip install codecov pytest pytest-cov pytest-sugar pytest-travis-fold openpyxl xlrd;
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pip install mne nibabel pandas tensorpac;
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pip install mne nibabel pandas tensorpac scikit-image;
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pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
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fi;
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- if [ "${TEST}" == "flake" ]; then
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pip install flake8 pep8-naming;
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fi;
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# - pip install PyOpenGL PyOpenGL_accelerate
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# Install latest version vispy :
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- pip install git+https://github.com/vispy/vispy.git
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- pip install PyOpenGL PyOpenGL_accelerate
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# - pip install -q freetype-py husl pypng cassowary imageio
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# ------------------- VISBRAIN -------------------
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- cd ${SRC_DIR}

‎MANIFEST.in

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@@ -3,21 +3,5 @@ include README.rst
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include LICENSE
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include requirements.txt
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# Brain templates (Don't use recursive-include visbrain/data *.npz) :
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include visbrain/data/templates/B1.npz
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include visbrain/data/templates/B2.npz
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include visbrain/data/templates/B3.npz
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# ROI :
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include visbrain/data/roi/brodmann.npz
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include visbrain/data/roi/aal.npz
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include visbrain/data/roi/talairach.npz
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# Eegref :
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include visbrain/data/topo/eegref.npz
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# Add visbrain icons :
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recursive-include visbrain/data/icons *.svg
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# Add url path :
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include visbrain/data/data_url.txt
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include visbrain/data_url.json

‎Makefile

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@@ -1,5 +1,4 @@
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# simple makefile to simplify repetetive build env management tasks under posix
2-
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CTAGS ?= ctags
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all: clean inplace test
@@ -37,8 +36,22 @@ flake: clean-test
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@flake8
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examples: clean
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@echo "NOT CONFIGURED YET"
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@for i in examples/brain/*.py examples/objects/*.py;do \
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echo "-----------------------------------------------"; \
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echo $$i; \
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echo "-----------------------------------------------"; \
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python $$i --visbrain-show=False; \
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echo "\n"; \
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done
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examples-full: clean
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@for i in @for i in examples/*/*.py;do \
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echo "-----------------------------------------------"; \
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echo $$i; \
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echo "-----------------------------------------------"; \
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python $$i --visbrain-show=False; \
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echo "\n"; \
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done
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pypi:
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@python setup.py register -r pypi

‎README.rst

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@@ -46,6 +46,7 @@ Visbrain requires :
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* Matplotlib >= 1.5.5
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* PyQt5
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* Pillow
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* PyOpenGL
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User installation
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-----------------
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.. code-block:: shell
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pip install visbrain
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pip install -U visbrain
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We also strongly recommend to install *pandas* and *pyopengl* :
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.. code-block:: shell
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pip install pandas PyOpenGL PyOpenGL_accelerate
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Modules
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=======
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.. figure:: https://github.com/EtienneCmb/visbrain/blob/master/docs/picture/visbrain_readme.png
69-
:align: center
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* `Brain <http://visbrain.org/brain.html>`_ : visualize EEG/MEG/Intracranial data, connectivity in a standard MNI 3D brain (see `Brain examples <http://visbrain.org/auto_examples/index.html#brain-examples>`_).
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* `Sleep <http://visbrain.org/sleep.html>`_ : visualize and analyze polysomnographic sleep data (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
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* `Signal <http://visbrain.org/signal.html>`_ : data-mining module for time-series inspection (see `Signal examples <http://visbrain.org/auto_examples/index.html#signal-examples>`_).
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* `Topo <http://visbrain.org/topo.html>`_ : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
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* `Figure <http://visbrain.org/figure.html>`_ : figure-layout for high-quality publication-like figures (see `Figure examples <http://visbrain.org/auto_examples/index.html#figure-examples>`_).
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* `Colorbar <http://visbrain.org/colorbar.html>`_ : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
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Contribution
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============
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Main developers
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---------------
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* `Etienne Combrisson <http://etiennecmb.github.io>`_
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* `Raphael Vallat <https://raphaelvallat.github.io>`_
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With the help of
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----------------
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*Karim Jerbi, Christian O'Reilly, David Meunier, Dmitri Altukchov, Tarek Lajnef, Perrine Ruby, JB Einchenlaub, kevroy314, Annalisa Pascarella, Thomas Thiery, Yann Harel, Anne-Lise Saive, Golnush Alamian*

‎appveyor.yml

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@@ -23,12 +23,14 @@ install:
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- "conda config --set always_yes yes --set changeps1 no"
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- "conda update -q conda"
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- "conda info -a"
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- "conda create -q -n testenv python=%PYTHON_VERSION% numpy scipy matplotlib pip"
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- "conda create -q -n testenv python=%PYTHON_VERSION% numpy scipy matplotlib pip cython"
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# Activate testing environnement :
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- "activate testenv"
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- "python -m pip install --upgrade pip"
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# Install latest vispy version :
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- pip install git+https://github.com/vispy/vispy.git
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# Install dependencies :
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- "pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pandas openpyxl tensorpac xlrd"
33+
- "pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pandas openpyxl tensorpac xlrd scikit-image"
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- "pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt"
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- "dir"
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# ------------------- VISBRAIN -------------------

‎circle.yml

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general:
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branches:
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ignore:
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- gh-pages
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machine:
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environment:
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# We need to set this variable to let Anaconda take precedence
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PATH: "/home/ubuntu/miniconda3/envs/circleenv/bin:/home/ubuntu/miniconda3/bin:$PATH"
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DISPLAY: ":99.0"
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python:
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version: 3.6.0
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dependencies:
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cache_directories:
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- "~/miniconda3"
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# Various dependencies
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pre:
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# Get a running Python
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- cd ~;
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# Disable pyenv (no cleaner way provided by CircleCI as it prepends pyenv version to PATH)
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- rm -rf ~/.pyenv;
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- rm -rf ~/virtualenvs;
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# Get Anaconda and conda-based requirements
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- >
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if [ ! -d "/home/ubuntu/miniconda3" ]; then
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echo "Setting up conda";
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wget -q http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh;
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chmod +x ~/miniconda.sh;
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~/miniconda.sh -b -p /home/ubuntu/miniconda3;
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conda update --yes --quiet conda;
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else
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echo "Conda already set up.";
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fi
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- if ! conda env list | grep circleenv; then
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conda create -n circleenv --yes pip python=3.6 pip;
38-
else
39-
echo "Conda env already set up.";
40-
fi;
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- conda install -n circleenv --yes numpy scipy pip;
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- pip install pytest pytest-travis-fold;
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- pip install mne nibabel pandas openpyxl tensorpac xlrd;
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- pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
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- ls -al /home/ubuntu/miniconda3;
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- ls -al /home/ubuntu/miniconda3/bin;
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- echo $PATH;
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- echo $CIRCLE_BRANCH
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- which python;
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- which pip;
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override:
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- cd /home/ubuntu/visbrain && pip install -e .;
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- /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;
55-
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test:
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override:
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- py.test:
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timeout: 1500
1+
version: 2
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jobs:
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build:
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branches:
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ignore:
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- gh-pages
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only:
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- master
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- develop
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docker:
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- image: circleci/python:3.6-jessie
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steps:
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- checkout
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- run:
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name: Clean CircleCI
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command: |
17+
rm -rf ~/.pyenv;
18+
rm -rf ~/virtualenvs;
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- run:
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name: Spin up Xvfb
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command: |
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/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;
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echo "export DISPLAY=:99" >> $BASH_ENV;
24+
- run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default;
25+
- restore_cache:
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keys:
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- data-cache
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- pip-cache
29+
- miniconda-cache
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- run:
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name: Install miniconda
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command: |
33+
if [ ! -d "~/miniconda3" ]; then
34+
wget -q http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh;
35+
chmod +x ~/miniconda.sh;
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~/miniconda.sh -b -p ~/miniconda3;
37+
echo "export PATH=~/miniconda3/bin:$PATH" >> $BASH_ENV;
38+
else
39+
echo "Miniconda3 already set up.";
40+
fi
41+
- save_cache:
42+
key: miniconda-cache
43+
paths:
44+
- ~/.cache/miniconda
45+
- run:
46+
name: Setup Python environment
47+
command: |
48+
conda update --yes --quiet conda;
49+
conda create -n testenv --yes python=3.6 numpy scipy pip cython qt==5.9.4 matplotlib==2.2.2 pyqt==5.9.2 ;
50+
source activate testenv;
51+
pip install -U pip;
52+
pip install git+https://github.com/vispy/vispy.git;
53+
pip install pytest pytest-travis-fold;
54+
pip install mne nibabel pandas openpyxl tensorpac xlrd scikit-image;
55+
pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
56+
echo $PATH;
57+
echo $CIRCLE_BRANCH;
58+
which python;
59+
which pip;
60+
- save_cache:
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key: pip-cache
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paths:
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- ~/.cache/pip
64+
- run:
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name: Install visbrain
66+
command: |
67+
source activate testenv;
68+
python setup.py develop;
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- run:
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name: run tests
71+
command: |
72+
mkdir test-reports
73+
source activate testenv;
74+
pytest --junitxml=test-reports/junit.xml
75+
- store_test_results:
76+
path: test-reports
77+
- store_artifacts:
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path: test-reports
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- save_cache:
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key: data-cache
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paths:
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- ~/.visbrain_data

‎docs/_static/visbrain_styles.css

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/* ############################ ALERT ############################*/
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.alert-info {
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background-color: #47a7f5;
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font-weight: bold;
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color: black;
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background-color: #c7e4fc;
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}
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.alert-warning {
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background-color: #FD9500;
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font-weight: bold;
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color: black;
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background-color: #fedfb2;
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}
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.alert-primary {
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background-color: #4b4d39;

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