Merge v0.4.3

EtienneCmb · Oct 3, 2018 · ffb7859 · ffb7859
2 parents 8247246 + aff10a6
commit ffb7859
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Showing 276 changed files with 5,197 additions and 21,155 deletions.
diff --git a/.gitignore b/.gitignore
@@ -89,3 +89,4 @@ docs/auto_examples/
 docs/modules/
 report.html
 notebooks/
+.pytest_cache/
diff --git a/.travis.yml b/.travis.yml
@@ -1,5 +1,10 @@
 language: python
 
+cache:
+  pip: true
+  apt: true
+  directories:
+    - ~/visbrain_data
 
 sudo: false
 dist: trusty
@@ -11,13 +16,15 @@ matrix:
   include:
     - env: TEST=standard
       os: linux
+    # - env: TEST=standard
+    #   os: linux
+    #   python: '3.7'
     - env: TEST=flake
       os: linux
-    # - env: TEST=examples
-    #   os: linux
     # - env: TEST=standard
     #   os: osx
-    #   language: generic
+    - env: TEST=examples
+      os: linux
   allow_failures:
     - env: TEST=flake
 
@@ -42,18 +49,20 @@ before_install:
 
 install:
     # Create the py3 environnement ;
-    - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy pip
+    - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION numpy scipy pip cython
     - source activate testenv
     # Install dependencies :
-    - if [ "${TEST}" == "standard" ]; then
+    - if [ "${TEST}" == "standard" ] || [ "${TEST}" == "examples" ]; then
         pip install codecov pytest pytest-cov pytest-sugar pytest-travis-fold openpyxl xlrd;
-        pip install mne nibabel pandas tensorpac;
+        pip install mne nibabel pandas tensorpac scikit-image;
         pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
       fi;
     - if [ "${TEST}" == "flake" ]; then
         pip install flake8 pep8-naming;
       fi;
-    # - pip install PyOpenGL PyOpenGL_accelerate
+    # Install latest version vispy :
+    - pip install git+https://github.com/vispy/vispy.git
+    - pip install PyOpenGL PyOpenGL_accelerate
     # - pip install -q freetype-py husl pypng cassowary imageio
     # ------------------- VISBRAIN -------------------
     - cd ${SRC_DIR}

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,21 +3,5 @@ include README.rst
 include LICENSE
 include requirements.txt
 
-# 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 :
-recursive-include visbrain/data/icons *.svg
-
 # Add url path :
-include visbrain/data/data_url.txt
+include visbrain/data_url.json
diff --git a/Makefile b/Makefile
@@ -1,5 +1,4 @@
 # simple makefile to simplify repetetive build env management tasks under posix
-
 CTAGS ?= ctags
 
 all: clean inplace test
@@ -37,8 +36,22 @@ flake: clean-test
 	@flake8
 
 examples: clean
-	@echo "NOT CONFIGURED YET"
-
+	@for i in examples/brain/*.py examples/objects/*.py;do \
+		echo "-----------------------------------------------"; \
+		echo $$i; \
+		echo "-----------------------------------------------"; \
+		python $$i --visbrain-show=False; \
+		echo "\n"; \
+	done
+
+examples-full: clean
+	@for i in @for i in examples/*/*.py;do \
+		echo "-----------------------------------------------"; \
+		echo $$i; \
+		echo "-----------------------------------------------"; \
+		python $$i --visbrain-show=False; \
+		echo "\n"; \
+	done
 
 pypi:
 	@python setup.py register -r pypi

diff --git a/README.rst b/README.rst
@@ -46,6 +46,7 @@ Visbrain requires :
 * Matplotlib >= 1.5.5
 * PyQt5
 * Pillow
+* PyOpenGL
 
 User installation
 -----------------
@@ -54,38 +55,5 @@ Install Visbrain :
 
 .. code-block:: shell
 
-    pip install visbrain
+    pip install -U visbrain
 
-We also strongly recommend to install *pandas* and *pyopengl* :
-
-.. code-block:: shell
-
-    pip install pandas PyOpenGL PyOpenGL_accelerate
-
-Modules
-=======
-
-.. figure::  https://github.com/EtienneCmb/visbrain/blob/master/docs/picture/visbrain_readme.png
-   :align:   center
-
-* `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>`_).
-* `Sleep <http://visbrain.org/sleep.html>`_ : visualize and analyze polysomnographic sleep data (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
-* `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>`_).
-* `Topo <http://visbrain.org/topo.html>`_ : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
-* `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>`_).
-
-
-Contribution
-============
-
-Main developers
----------------
-
-* `Etienne Combrisson <http://etiennecmb.github.io>`_
-* `Raphael Vallat <https://raphaelvallat.github.io>`_
-
-With the help of
-----------------
-
-*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*
diff --git a/appveyor.yml b/appveyor.yml
@@ -23,12 +23,14 @@ install:
   - "conda config --set always_yes yes --set changeps1 no"
   - "conda update -q conda"
   - "conda info -a"
-  - "conda create -q -n testenv python=%PYTHON_VERSION% numpy scipy matplotlib pip"
+  - "conda create -q -n testenv python=%PYTHON_VERSION% numpy scipy matplotlib pip cython"
   # Activate testing environnement :
   - "activate testenv"
   - "python -m pip install --upgrade pip"
+  # Install latest vispy version :
+  - pip install git+https://github.com/vispy/vispy.git
   # Install dependencies :
-  - "pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pandas openpyxl tensorpac xlrd"
+  - "pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pandas openpyxl tensorpac xlrd scikit-image"
   - "pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt"
   - "dir"
   # ------------------- VISBRAIN -------------------

diff --git a/circle.yml b/circle.yml
@@ -1,59 +1,82 @@
-general:
-  branches:
-    ignore:
-      - gh-pages
-
-
-machine:
-  environment:
-    # We need to set this variable to let Anaconda take precedence
-    PATH: "/home/ubuntu/miniconda3/envs/circleenv/bin:/home/ubuntu/miniconda3/bin:$PATH"
-    DISPLAY: ":99.0"
-  python:
-      version: 3.6.0
-
-dependencies:
-  cache_directories:
-    - "~/miniconda3"
-  # 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/miniconda3" ]; then
-        echo "Setting up conda";
-        wget -q http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh;
-        chmod +x ~/miniconda.sh;
-        ~/miniconda.sh -b -p /home/ubuntu/miniconda3;
-        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=3.6 pip;
-      else
-        echo "Conda env already set up.";
-      fi;
-    - conda install -n circleenv --yes numpy scipy pip;
-    - pip install pytest pytest-travis-fold;
-    - pip install mne nibabel pandas openpyxl tensorpac xlrd;
-    - pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
-    - ls -al /home/ubuntu/miniconda3;
-    - ls -al /home/ubuntu/miniconda3/bin;
-    - echo $PATH;
-    - echo $CIRCLE_BRANCH
-    - which python;
-    - which pip;
-
-  override:
-    - cd /home/ubuntu/visbrain && pip install -e .;
-    - /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:
-    - py.test:
-        timeout: 1500
+version: 2
+jobs:
+    build:
+      branches:
+        ignore:
+          - gh-pages
+        only:
+          - master
+          - develop
+      docker:
+        - image: circleci/python:3.6-jessie
+      steps:
+        - checkout
+        - run:
+            name: Clean CircleCI
+            command: |
+              rm -rf ~/.pyenv;
+              rm -rf ~/virtualenvs;
+        - run:
+            name: Spin up Xvfb
+            command: |
+              /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;
+              echo "export DISPLAY=:99" >> $BASH_ENV;
+        - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default;
+        - restore_cache:
+            keys:
+              - data-cache
+              - pip-cache
+              - miniconda-cache
+        - run:
+            name: Install miniconda
+            command: |
+              if [ ! -d "~/miniconda3" ]; then
+                wget -q http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh;
+                chmod +x ~/miniconda.sh;
+                ~/miniconda.sh -b -p ~/miniconda3;
+                echo "export PATH=~/miniconda3/bin:$PATH" >> $BASH_ENV;
+              else
+                echo "Miniconda3 already set up.";
+              fi
+        - save_cache:
+            key: miniconda-cache
+            paths:
+              - ~/.cache/miniconda
+        - run:
+            name: Setup Python environment
+            command: |
+              conda update --yes --quiet conda;
+              conda create -n testenv --yes python=3.6 numpy scipy pip cython qt==5.9.4 matplotlib==2.2.2 pyqt==5.9.2 ;
+              source activate testenv;
+              pip install -U pip;
+              pip install git+https://github.com/vispy/vispy.git;
+              pip install pytest pytest-travis-fold;
+              pip install mne nibabel pandas openpyxl tensorpac xlrd scikit-image;
+              pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
+              echo $PATH;
+              echo $CIRCLE_BRANCH;
+              which python;
+              which pip;
+        - save_cache:
+            key: pip-cache
+            paths:
+              - ~/.cache/pip
+        - run:
+            name: Install visbrain
+            command: |
+              source activate testenv;
+              python setup.py develop;
+        - run:
+            name: run tests
+            command: |
+              mkdir test-reports
+              source activate testenv;
+              pytest --junitxml=test-reports/junit.xml
+        - store_test_results:
+            path: test-reports
+        - store_artifacts:
+            path: test-reports 
+        - save_cache:
+            key: data-cache
+            paths:
+              - ~/.visbrain_data
diff --git a/docs/_static/visbrain_styles.css b/docs/_static/visbrain_styles.css
@@ -76,12 +76,12 @@ th {
 
 /* ############################ ALERT ############################*/
 .alert-info {
-    background-color: #47a7f5;
-    font-weight: bold;
+    color: black;
+    background-color: #c7e4fc;
 }
 .alert-warning {
-    background-color: #FD9500;
-    font-weight: bold;
+    color: black;
+    background-color: #fedfb2;
 }
 .alert-primary {
     background-color: #4b4d39;