Merge branch 'release/v0.3.3'

Author: EtienneCmb

.travis.yml

@@ -1,47 +1,14 @@
 language: python
+dist: trusty
 python:
   - "3.6"
-before_install:
-  # PyQt installation : https://github.com/harvimt/quamash/blob/master/.travis.yml
-  - export DISPLAY=:99.0
-  - sh -e /etc/init.d/xvfb start
-  # Cached Downloads
-  - sudo mkdir -p /downloads
-  - sudo chmod a+rw /downloads
-  - if [ ! -f /downloads/sip.tar.gz ];   then curl -L -o /downloads/sip.tar.gz http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz; fi
-  - if [ ! -f /downloads/pyqt5.tar.gz ]; then curl -L -o /downloads/pyqt5.tar.gz http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-5.4/PyQt-gpl-5.4.tar.gz; fi
-  - echo '6d01ea966a53e4c7ae5c5e48c40e49e5  /downloads/sip.tar.gz' | md5sum -c -
-  - echo '7f2eb79eaf3d7e5e7df5a4e9c8c9340e  /downloads/pyqt5.tar.gz' | md5sum -c -
-  # Builds
-  - sudo mkdir -p /builds
-  - sudo chmod a+rw /builds
+before_script:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
 install:
-  # Qt5
-  - sudo add-apt-repository -y ppa:beineri/opt-qt542
-  - sudo apt-get update
-  - sudo apt-get install -y qt54base
-  # Builds
-  - pushd /builds
-  # SIP
-  - tar xzf /downloads/sip.tar.gz --keep-newer-files
-  - pushd sip-4.16.5
-  - python configure.py
-  - make
-  - sudo make install
-  - popd
-  # Builds Complete
-  - popd
-  - cd ../
-  - mkdir tmp/
-  - cd /tmp
-  - wget http://launchpadlibrarian.net/137699828/libc6_2.17-0ubuntu5_amd64.deb
-  - wget http://launchpadlibrarian.net/137699829/libc6-dev_2.17-0ubuntu5_amd64.deb
-  - mkdir libc6_2.17
-  - cd libc6_2.17
-  - ar p ../libc6_2.17-0ubuntu5_amd64.deb data.tar.gz | tar zx
-  - ar p ../libc6-dev_2.17-0ubuntu5_amd64.deb data.tar.gz | tar zx
-  - cd -
-  # - sudo apt-get update
+  - pushd $PWD
+  # ------------------- PYTHON ENVIRONNEMENT -------------------
   # Deactivate travis environnement :
   - deactivate
   # We do this conditionally because it saves us some downloading if the
@@ -62,29 +29,20 @@ install:
   # Replace dep1 dep2 ... with your dependencies
   - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pip
   - source activate testenv
-  # - pip install pyqt5
+  - pip install mne
   - pip install setuptools
   - pip install nose
+  - pip install PyOpenGL PyOpenGL_accelerate
   - pip install codecov
   - pip install pytest pytest-cov
-  # - pwd
-  # - cd ../
-  - pwd
+  # ------------------- VISPY -------------------
+  - cd ../
   - pip install -e git+https://github.com/vispy/vispy#egg=vispy-dev
   - cd visbrain/
-  - pip install .
-  - LD_LIBRARY_PATH=/tmp/libc6_2.17/lib/x86_64-linux-gnu/ /tmp/libc6_2.17/lib/x86_64-linux-gnu/ld-2.17.so bin/python
-  # - pip install -r requirements.txt
-
-# script:
-#   - py.test -v --cov=./
-
-# # after_success:
-# #   - ./tools/travis-upload-wheel.sh
+  # ------------------- VISBRAIN -------------------
+  - pip install -e .
 script: bash build_install.sh
 cache:
-  directories:
-    - /downloads
   apt: true
 notifications:
     email: false

MANIFEST.in

@@ -1,7 +1,15 @@
+# Add README, LICENSE and requirements :
 include README.rst
 include LICENSE
 include requirements.txt
+
+# Add brain templates and eeg reference file :
 recursive-include visbrain/brain/base/templates *.npz
-recursive-include visbrain/utils/topo *.npz
-recursive-include visbrain/brain/ico *.svg
-recursive-include visbrain/sleep/ico *.svg
+include visbrain/visuals/eegref.npz
+
+# Add visbrain icons :
+include visbrain/brain/brain_icon.svg
+include visbrain/sleep/sleep_icon.svg
+include visbrain/topo/topo_icon.svg
+include visbrain/colorbar/colorbar_icon.svg
+include visbrain/figure/figure_icon.svg

README.rst

@@ -16,7 +16,7 @@ Visbrain
    :align:   center
 
 
-**Visbrain** is an open-source python package and provides hardware accelerated visualizations mainly for neuroscientific data. It is based on top of `VisPy <http://vispy.org/>`_ and PyQt and is distributed under the 3-Clause BSD license. We also provide an on line `documentation <http://visbrain.org>`_, `examples and datasets <http://visbrain.org/auto_examples/>`_ and can also be downloaded from `PyPi <https://pypi.python.org/pypi/visbrain/>`_.
+**Visbrain** is an open-source python 3 package and provides hardware accelerated visualizations mainly for neuroscientific data. It is based on top of `VisPy <http://vispy.org/>`_ and PyQt and is distributed under the 3-Clause BSD license. We also provide an on line `documentation <http://visbrain.org>`_, `examples and datasets <http://visbrain.org/auto_examples/>`_ and can also be downloaded from `PyPi <https://pypi.python.org/pypi/visbrain/>`_.
 
 Important links
 ===============
@@ -60,7 +60,7 @@ We also strongly recommend to install *pyopengl* :
 
 .. code-block:: shell
 
-    pip install pyopengl
+    pip install PyOpenGL PyOpenGL_accelerate
 
 Modules
 =======
@@ -75,62 +75,6 @@ Modules
 * `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>`_).
 * `Colorbar <http://visbrain.org/colorbar.html>`_ : colorbar editor (see `Colorbar examples <http://visbrain.org/auto_examples/index.html#colorbar-examples>`_).
 
-.. Brain
-.. -----
-
-.. The `Brain <http://etiennecmb.github.io/visbrain/brain.html>`_ module is primarily designed for visualizations within a 3D opaque/transparent brain and can be used for :
-
-.. * Integrate EEG/MEG/Intracranial sources/electrodes and connectivity.
-.. * Display Regions of Interest (ROI) based either on Brodmann or AAL atlases.
-.. * Project source's activity onto the brain/ROI surface.
-.. * An extended control of colors. 
-.. * Export in HD pictures with auto-cropping functionalities.
-.. * GUI or command line control.
-.. * `Brain xxamples and datasets <https://github.com/EtienneCmb/visbrain/tree/master/examples/brain>`_.
-
-.. .. figure::  https://github.com/EtienneCmb/visbrain/blob/master/docs/picture/example.png
-..    :align:   center
-
-.. Sleep
-.. -----
-
-.. `Sleep <http://etiennecmb.github.io/visbrain/sleep.html>`_ is a GUI based module for sleep data visualization and edition under Python. Main functionalities are :
-
-.. * Load BrainVision, Micromed or European Data Format. Other file formats can be loaded using `MNE Python <http://mne-tools.github.io/stable/python_reference.html?highlight=io#module-mne.io>`_ and then pass as raw data.
-.. * Visualize polysomnographic data / spectrogram / topographic maps.
-.. * Load, edit and save hypnogram data or as publication-ready figures.
-.. * Perform automatic event detections (Spindles / REM / Peaks / Slow waves / K-complex / Muscle twitches).
-.. * Signal processing tools (filtering / wavelets / power...) and re-referencing (either to a single channel, common average or bipolarization).
-.. * `Sleep examples and datasets <https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing>`_.
-
-.. .. figure::  https://github.com/EtienneCmb/visbrain/blob/master/docs/picture/Sleep_main.png
-..    :align:   center
-
-.. Ndviz
-.. -----
-
-.. `Ndviz <http://etiennecmb.github.io/visbrain/ndviz.html>`_ was designed to visualize multidimensional data and also includes basic plots :
-
-.. * Visualize large datasets into a grid.
-.. * Basic plotting forms (continuous line / cloud of points / image).
-.. * Compute histogram / spectrogram.
-.. * Swap data dimensions from the GUI.
-.. * `Ndviz examples <https://github.com/EtienneCmb/visbrain/tree/master/examples/ndviz>`_.
-
-.. .. figure::  https://github.com/EtienneCmb/visbrain/blob/master/docs/picture/ndviz_example.png
-..    :align:   center
-
-.. Figure
-.. ------
-
-.. `Figure <http://etiennecmb.github.io/visbrain/figure.html>`_ is the only module which do not rely on a GUI or VisPy. It's a Matplotlib wrapper to simplify scientific figures production and allows :
-
-.. * Load images and grid disposition.
-.. * Add x/y labels and titles.
-.. * Simple colorbar control.
-.. * Export the final figure with dpi control.
-.. * `Figure examples <https://github.com/EtienneCmb/visbrain/tree/master/examples/figure>`_.
-
 
 Contribution
 ============

build_install.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 source activate testenv
-py.test --cov
+py.test --cov --verbose

docs/conf.py

@@ -79,9 +79,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.3.2'
+version = '0.3.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.2'
+release = '0.3.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/figure.rst

@@ -71,7 +71,7 @@ Example
     # Alternatively, you can show the figure :
     f.show()
 
-.. figure::  picture/figure.png
+.. figure::  picture/picfigure/figure_example.png
    :align:   center
 
    Code above : four exported figures from the Brain module are aranged in a (2, 2) grid. Then, some have a colorbar, xlabel, ylabel. Finally, there is two shared colorbars.

docs/index.rst

@@ -19,7 +19,7 @@
 Visbrain documentation
 ######################
 
-Visbrain is a python package dedicated to multi-purpose neuroscience visualization tools. Here is the list of the current modules :
+Visbrain is a python 3 package dedicated to multi-purpose neuroscience visualization tools. Here is the list of the current modules :
 
 .. figure::  /picture/visbrain_readme.png
    :align:   center
@@ -52,7 +52,7 @@ We also strongly recommend to install *pyopengl* :
 
 .. code-block:: shell
 
-    pip install pyopengl
+    pip install PyOpenGL PyOpenGL_accelerate
 
 PyQt5 version
 =============

docs/ndviz.rst

@@ -15,7 +15,7 @@ Description
 The Ndviz module groups a bundle of functionalities for the visualization of mutli-dimentional data. It can be used to represent all of your signals in a single canvas (see this `example <https://github.com/vispy/vispy/blob/master/examples/demo/gloo/realtime_signals.py>`_ by `Cyrille Rossant <https://github.com/rossant>`_ for the original script). Each single signal can then be ploted as a traditional continious line, a cloud of points, a histogram, a spectrogram or as an image.
 
 
-.. figure::  picture/ndviz_example.png
+.. figure::  picture/picndviz/ndviz_example.png
    :align:   center
 
 Use the following command to import Ndviz :