Merge branch 'development' into plotinclude

Author: Facu

.travis.yml

@@ -67,6 +67,7 @@ script:
   - "curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'}"
   - firefox --version
   - travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24"  casperjs test netpyne-tests.js --host=http://localhost:8888/ --engine=slimerjs
-  - sudo docker logs -t netpyne-ui_container
+  - python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
+  - docker logs -t netpyne-ui_container
   - docker stop $(docker ps -a -q)
   - docker rm $(docker ps -a -q)

Dockerfile

@@ -9,7 +9,6 @@ RUN apt-get install -y \
         g++ \
         build-essential \
         libncurses-dev \
-        python2.7 \
         libpython-dev \
         cython \
         libx11-dev \
@@ -20,36 +19,31 @@ RUN apt-get install -y \
         libtool \ 
         libxext-dev \
         libncurses-dev \
-        python2.7-dev \
         xfonts-100dpi \ 
         libopenmpi-dev \
-        python2.7-scipy \
         make \
         zlib1g-dev \
         unzip \
         vim \
         libpng-dev
 
-# Install latest NEURON
-RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git
+# 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
-RUN ./configure --without-x --with-nrnpython=python2 --without-paranrn --prefix="/home/jovyan/work/nrn/" --without-iv
+# 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
 
-# Switch to non sudo, create a Python 2 virtual environment 
-USER $NB_USER
-# Commenting out the conda update things broke!
-# RUN conda update conda
-RUN conda create --name snakes python=2
-
 # Install NEURON python
 WORKDIR src/nrnpython
 ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
 RUN /bin/bash -c "source activate snakes && python setup.py install"
-# Install Bokeh
-RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
 
 ARG INCUBATOR_VER=unknown
 RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install netpyne_ui"

Dockerfile_dev

@@ -13,7 +13,6 @@ RUN apt-get install -y \
         g++ \
         build-essential \
         libncurses-dev \
-        python2.7 \
         libpython-dev \
         cython \
         libx11-dev \
@@ -24,36 +23,32 @@ RUN apt-get install -y \
         libtool \ 
         libxext-dev \
         libncurses-dev \
-        python2.7-dev \
         xfonts-100dpi \ 
         libopenmpi-dev \
-        python2.7-scipy \
         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 7.6.1crxd https://github.com/adamjhn/nrn.git
+RUN git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn
 WORKDIR nrn
 RUN ./build.sh
-RUN ./configure --without-x --with-nrnpython=python2 --without-paranrn --prefix="/home/jovyan/work/nrn/" --without-iv
+# 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
 
-# Switch to non sudo, create a Python 2 virtual environment 
-USER $NB_USER
-# Commenting out the conda update things broke!
-# RUN conda update conda
-RUN conda create --name snakes python=2
 
 # 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"
-# Install Bokeh
-RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
 
 # Clone NetPyNE-UI and install the development version
 WORKDIR ../../../