Merge branch 'development' into plotinclude

Author: Facu

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "netpyne_ui/geppetto"]
+	path = netpyne_ui/geppetto
+	url = https://github.com/openworm/org.geppetto.frontend.git

.travis.yml

@@ -8,13 +8,15 @@ node_js:
 env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
+before_install:
+- sudo apt-get install -y xserver-xorg-dev libxext-dev libxi-dev
 install:
 - git clone --quiet  https://github.com/MetaCell/geppetto-netpyne.git
 - cd geppetto-netpyne
 - if [ `git branch -a | egrep "remotes/origin/${TRAVIS_BRANCH}"` ]; then git checkout $TRAVIS_BRANCH ; else echo "Branch $TRAVIS_BRANCH does not exist for the dependent bundle, checking out development ..." && git checkout development; fi
 - cd ..
-- npm install --silent -g phantomjs 
-- npm install --silent -g casperjs 
+- npm install --silent -g phantomjs
+- npm install --silent -g casperjs
 - npm install --silent -g slimerjs
 - npm install --silent -g gl
 python:
@@ -34,6 +36,7 @@ addons:
     - libgl1-mesa-dri
     - libglapi-mesa
     - libosmesa6
+
 before_script:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"

Dockerfile

@@ -1,49 +1,6 @@
-FROM jupyter/base-notebook:eb70bcf1a292
-USER root
-
-RUN apt-get -qq update
-RUN apt-get install -y \
-        locales \
-        wget \
-        gcc \
-        g++ \
-        build-essential \
-        libncurses-dev \
-        libpython-dev \
-        cython \
-        libx11-dev \
-        git \
-        bison \
-        flex \
-        automake \ 
-        libtool \ 
-        libxext-dev \
-        libncurses-dev \
-        xfonts-100dpi \ 
-        libopenmpi-dev \
-        make \
-        zlib1g-dev \
-        unzip \
-        vim \
-        libpng-dev
-
+FROM metacell/jupyter-neuron:latest
 # Switch to non sudo, create a Python 3 virtual environment 
 USER $NB_USER
-RUN conda create --name snakes python=3.7
-
-# Install latest iv and NEURON
-RUN git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn
-WORKDIR nrn
-RUN ./build.sh
-# Activate conda to configure nrn with the right python version
-RUN /bin/bash -c "source activate snakes && ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix='/home/jovyan/work/nrn/' --without-iv"
-RUN make --silent -j4
-RUN make --silent install -j4
-
-# Install NEURON python
-WORKDIR src/nrnpython
-ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
-RUN /bin/bash -c "source activate snakes && python setup.py install"
 
 ARG INCUBATOR_VER=unknown
 RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install netpyne_ui"

Dockerfile_dev

@@ -1,63 +1,18 @@
-FROM jupyter/base-notebook:eb70bcf1a292
-USER root
+FROM metacell/jupyter-neuron:latest
+USER $NB_USER
 
 ARG netpyneuiBranch=development 
 ENV netpyneuiBranch=${netpyneuiBranch}  
 RUN echo "$netpyneuiBranch";
 
-RUN apt-get -qq update
-RUN apt-get install -y \
-        locales \
-        wget \
-        gcc \
-        g++ \
-        build-essential \
-        libncurses-dev \
-        libpython-dev \
-        cython \
-        libx11-dev \
-        git \
-        bison \
-        flex \
-        automake \ 
-        libtool \ 
-        libxext-dev \
-        libncurses-dev \
-        xfonts-100dpi \ 
-        libopenmpi-dev \
-        make \
-        zlib1g-dev \
-        unzip \
-        vim \
-        libpng-dev
-
-# Switch to non sudo, create a Python 3 virtual environment 
-USER $NB_USER
-RUN conda create --name snakes python=3.7
-
-# Install latest iv and NEURON
-RUN git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn
-WORKDIR nrn
-RUN ./build.sh
-# Activate conda to configure nrn with the right python version
-RUN /bin/bash -c "source activate snakes && ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix='/home/jovyan/work/nrn/' --without-iv"
-RUN make --silent -j4
-RUN make --silent install -j4
-
-
-# Install NEURON python
-WORKDIR src/nrnpython
-ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
-RUN /bin/bash -c "source activate snakes && python setup.py install"
-
 # Clone NetPyNE-UI and install the development version
-WORKDIR ../../../
-RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
+RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
 RUN unzip $netpyneuiBranch.zip
-WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
+WORKDIR /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/utilities
 RUN /bin/bash -c "source activate snakes && python --version"
 RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch"
 WORKDIR /home/jovyan
 RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
-CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"
+RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/netpyne_ui/tests tests
+CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

NetPyNE-UI

@@ -1,2 +1,2 @@
 #!/bin/sh
-exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token=''
+exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui