Merge branch 'release/v0.3.6'

Author: EtienneCmb

.gitignore

@@ -78,9 +78,9 @@ atlas_B2.npz
 atlas_B3.npz
 AAL_label_bck.npz
 # *.todo
-Inflated.npz
-WhiteMatter.npz
-Sphere.npz
+inflated.npz
+white.npz
+sphere.npz
 
 docs/generated/
 docs/auto_examples/

.travis.yml

@@ -22,12 +22,11 @@ install:
   # Install dependencies :
   - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pip
   - source activate testenv
-  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate codecov pytest pytest-cov
-  # ------------------- VISPY -------------------
-  - cd ../
-  # Install the developper version of VisPy :
-  - pip install -e git+https://github.com/vispy/vispy#egg=vispy-dev
-  - cd visbrain/
+  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pandas
+
+  # Install testing librairies :
+  - pip install codecov pytest pytest-cov pytest-html
+
   # ------------------- VISBRAIN -------------------
   - pip install -e .
 before_script:
@@ -46,4 +45,5 @@ after_success:
 # does't fix it.
 # before_install:
 #   - sudo apt-get -qq install libfreetype6-dev libjpeg-turbo-progs
-# sudo: required
+# sudo: required
+# py.test --cov --verbose --cov-report=html --html=report.html

MANIFEST.in

@@ -3,16 +3,21 @@ include README.rst
 include LICENSE
 include requirements.txt
 
-# Add brain templates and eeg reference file :
-recursive-include visbrain/brain/base/templates *.npz
-include visbrain/visuals/eegref.npz
+# Brain templates (Don't use recursive-include visbrain/data *.npz) :
+include visbrain/data/templates/B1.npz
+include visbrain/data/templates/B2.npz
+include visbrain/data/templates/B3.npz
+
+# ROI :
+include visbrain/data/roi/brodmann.npz
+include visbrain/data/roi/aal.npz
+include visbrain/data/roi/talairach.npz
+
+# Eegref :
+include visbrain/data/topo/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
+recursive-include visbrain/data/icons *.svg
 
 # Add url path :
-include visbrain/data_url.txt
+include visbrain/data/data_url.txt

README.rst

@@ -37,33 +37,27 @@ Dependencies
 
 Visbrain requires :
 
-* NumPy
+* NumPy >= 1.13
 * SciPy
-* VisPy (*development version*)
+* VisPy >= 0.5.0
 * Matplotlib >= 1.5.5
 * PyQt5
 * Pillow
 
 User installation
 -----------------
 
-Install the latest VisPy version from Github :
-
-.. code-block:: shell
-
-    pip install -e git+https://github.com/vispy/vispy#egg=vispy-dev
-
-Then, install Visbrain :
+Install Visbrain :
 
 .. code-block:: shell
 
     pip install visbrain
 
-We also strongly recommend to install *pyopengl* :
+We also strongly recommend to install *pandas* and *pyopengl* :
 
 .. code-block:: shell
 
-    pip install PyOpenGL PyOpenGL_accelerate
+    pip install pandas PyOpenGL PyOpenGL_accelerate
 
 Modules
 =======

appveyor.yml

@@ -20,12 +20,7 @@ install:
   # Activate testing environnement :
   - activate testenv
   # Install dependencies :
-  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pytest-cov
-  # ------------------- VISPY -------------------
-  - cd ../
-  - pip install -e git+https://github.com/vispy/vispy#egg=vispy-dev
-  - ls
-  - cd visbrain/
+  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pytest-cov pandas
   # ------------------- VISBRAIN -------------------
   - pip install -e .
 

docs/brainAPI.rst

@@ -12,38 +12,39 @@ Main *Brain* class inputs
 
     .. autosummary::
         ~Brain.show
-        ~visbrain.brain.user.BrainUserMethods.quit
         ~visbrain.brain.user.BrainUserMethods.rotate
         ~visbrain.brain.user.BrainUserMethods.background_color
         ~visbrain.brain.user.BrainUserMethods.screenshot
         ~visbrain.brain.user.BrainUserMethods.load_config
         ~visbrain.brain.user.BrainUserMethods.save_config
+
         ~visbrain.brain.user.BrainUserMethods.brain_control
         ~visbrain.brain.user.BrainUserMethods.brain_list
         ~visbrain.brain.user.BrainUserMethods.add_mesh
+
         ~visbrain.brain.user.BrainUserMethods.volume_control
         ~visbrain.brain.user.BrainUserMethods.add_volume
         ~visbrain.brain.user.BrainUserMethods.volume_list
+
         ~visbrain.brain.user.BrainUserMethods.cross_sections_control
+
         ~visbrain.brain.user.BrainUserMethods.sources_control
-        ~visbrain.brain.user.BrainUserMethods.sources_opacity
         ~visbrain.brain.user.BrainUserMethods.sources_display
-        ~visbrain.brain.user.BrainUserMethods.add_sources
-        ~visbrain.brain.user.BrainUserMethods.sources_fit
+        ~visbrain.brain.user.BrainUserMethods.sources_fit_to_vertices
         ~visbrain.brain.user.BrainUserMethods.sources_to_convex_hull
+
         ~visbrain.brain.user.BrainUserMethods.cortical_projection
         ~visbrain.brain.user.BrainUserMethods.cortical_repartition
-        ~visbrain.brain.user.BrainUserMethods.sources_colormap
+
         ~visbrain.brain.user.BrainUserMethods.time_series_control
-        ~visbrain.brain.user.BrainUserMethods.add_time_series
+
         ~visbrain.brain.user.BrainUserMethods.pictures_control
-        ~visbrain.brain.user.BrainUserMethods.add_pictures
+
         ~visbrain.brain.user.BrainUserMethods.connect_control
-        ~visbrain.brain.user.BrainUserMethods.add_connect
+
         ~visbrain.brain.user.BrainUserMethods.roi_control
         ~visbrain.brain.user.BrainUserMethods.roi_list
-        ~visbrain.brain.user.BrainUserMethods.roi_opacity
-        ~visbrain.brain.user.BrainUserMethods.roi_light_reflection
+
         ~visbrain.brain.user.BrainUserMethods.cbar_control
         ~visbrain.brain.user.BrainUserMethods.cbar_select
         ~visbrain.brain.user.BrainUserMethods.cbar_list
@@ -62,11 +63,7 @@ Set of functions for an interactive control of the graphical user interface elem
 
 Show graphical interface
 ++++++++++++++++++++++++
-.. automethod:: visbrain.brain.brain.Brain.show
-
-Quit graphical interface
-++++++++++++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.quit
+.. automethod:: visbrain.pyqt_module.PyQtModule.show
 
 Rotation
 ++++++++
@@ -159,21 +156,13 @@ Control sources
 +++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.sources_control
 
-Opacity
-+++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.sources_opacity
-
 Select sources
 ++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.sources_display
 
-Add source object
-+++++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.add_sources
-
 Fit to an object
 ++++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.sources_fit
+.. automethod:: visbrain.brain.user.BrainUserMethods.sources_fit_to_vertices
 
 Convert into convex hull
 ++++++++++++++++++++++++
@@ -192,10 +181,6 @@ Cortical repartition
 ++++++++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.cortical_repartition
 
-Colormap
-++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.sources_colormap
-
 .. ##########################################################################
 ..                               TIME-SERIES
 .. ##########################################################################
@@ -210,11 +195,6 @@ Time-series control
 .. automethod:: visbrain.brain.user.BrainUserMethods.time_series_control
 
 
-Add time-series
-+++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.add_time_series
-
-
 .. ##########################################################################
 ..                                PICTURES
 .. ##########################################################################
@@ -228,10 +208,6 @@ Pictures control
 ++++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.pictures_control
 
-Add pictures
-++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.add_pictures
-
 .. ##########################################################################
 ..                           CONNECTIVITY
 .. ##########################################################################
@@ -247,10 +223,6 @@ Control Connectivity
 ++++++++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.connect_control
 
-Add connectivity object
-+++++++++++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.add_connect
-
 .. ##########################################################################
 ..                                    ROI
 .. ##########################################################################
@@ -270,14 +242,6 @@ List of suported ROI
 ++++++++++++++++++++
 .. automethod:: visbrain.brain.user.BrainUserMethods.roi_list
 
-Opacity
-+++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.roi_opacity
-
-Light reflection
-++++++++++++++++
-.. automethod:: visbrain.brain.user.BrainUserMethods.roi_light_reflection
-
 .. ##########################################################################
 ..                              COLORBAR
 .. ##########################################################################

docs/conf.py

@@ -82,9 +82,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.3.5'
+version = '0.3.6'
 # The full version, including alpha/beta/rc tags.
-release = '0.3.5'
+release = '0.3.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/documentation.rst

@@ -13,5 +13,6 @@ Documentation
     topo
     colorbar
     figure
+    objects
     utils
     io

docs/index.rst

@@ -46,29 +46,25 @@ Dependencies
 
 Here's the list of visbrain's dependencies :
 
-* Numpy
+* Numpy (>= 1.13)
 * Scipy
-* Vispy : fast graphics rendering
-* Matplotlib : mainly for colors and colormaps integration
+* Vispy (>= 0.5.0) : fast graphics rendering
+* Matplotlib (>= 1.5.5): mainly for colors and colormaps integration
 * PyQt5 : Graphical User Interface components
 * Pillow : for screenshots and image file format support.
 
-We also strongly recommend to install *pyopengl* :
+We also strongly recommend to install *pandas* and *pyopengl* :
 
 .. code-block:: shell
 
-    pip install PyOpenGL PyOpenGL_accelerate
+    pip install pandas PyOpenGL PyOpenGL_accelerate
 
-PyQt5 version
-=============
+Installation
+============
 
 For the PyQt5 version, Matplotlib's version should be >= 1.5.5. If PyQt is not installed, run either **pip install pyqt5** or **conda install pyqt**. Then, in a terminal run :
 
-.. code-block:: shell
-
-    pip install -e git+https://github.com/vispy/vispy#egg=vispy-dev
-
-Finally, install Visbrain :
+Install Visbrain :
 
 .. code-block:: shell