Merge pull request #46 from MetaCell/development

Release 0.4

Author: tarelli

.travis.yml

@@ -9,7 +9,10 @@ env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
 install:
-- git clone --quiet -b $TRAVIS_BRANCH https://github.com/MetaCell/geppetto-netpyne.git
+- git clone --quiet  https://github.com/MetaCell/geppetto-netpyne.git
+- cd geppetto-netpyne
+- if [ `git branch -a | egrep "remotes/origin/${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 slimerjs
@@ -38,7 +41,7 @@ before_script:
   - export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
 
 script:
-  - travis_retry docker build -t="netpyne-ui" --build-arg netpyneuiBranch=$TRAVIS_BRANCH .
+  - travis_retry docker build -t="netpyne-ui" --build-arg netpyneuiBranch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
   - travis_retry docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
   - cd $TRAVIS_BUILD_DIR/ && ls
   - cd geppetto-netpyne && ls

Dockerfile

@@ -1,10 +1,6 @@
 FROM jupyter/base-notebook:eb70bcf1a292
 USER root
 
-ARG netpyneuiBranch=0.2M3
-ENV netpyneuiBranch=${netpyneuiBranch}
-RUN echo "$netpyneuiBranch";
-
 RUN apt-get -qq update
 RUN apt-get install -y \
         locales \
@@ -13,7 +9,7 @@ RUN apt-get install -y \
         g++ \
         build-essential \
         libncurses-dev \
-        python \
+        python2.7 \
         libpython-dev \
         cython \
         libx11-dev \
@@ -24,47 +20,44 @@ RUN apt-get install -y \
         libtool \ 
         libxext-dev \
         libncurses-dev \
-        python3-dev \
+        python2.7-dev \
         xfonts-100dpi \ 
-        cython3 \ 
         libopenmpi-dev \
-        python3-scipy \
+        python2.7-scipy \
         make \
         zlib1g-dev \
         unzip \
         vim \
         libpng-dev
 
-# Install latest iv and NEURON
-RUN git clone http://github.com/neuronsimulator/iv
-RUN git clone http://github.com/neuronsimulator/nrn
-WORKDIR iv
-RUN ./build.sh
-RUN ./configure
-RUN make --silent -j4
-RUN make --silent install -j4
-WORKDIR ../nrn
+# Install latest NEURON
+RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git
+WORKDIR nrn
 RUN ./build.sh
-RUN ./configure --with-nrnpython=python2 --with-paranrn
+RUN ./configure --without-x --with-nrnpython=python2 --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
-RUN conda update conda
+# 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 --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple netpyne_ui"
 RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py jupyter_geppetto"
 RUN /bin/bash -c "source activate snakes &&  jupyter serverextension enable --py jupyter_geppetto"
 RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py widgetsnbextension"
 
-RUN mkdir /home/jovyan/netpyne_workspace
+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=''"

Dockerfile_dev

@@ -1,8 +1,8 @@
 FROM jupyter/base-notebook:eb70bcf1a292
 USER root
 
-ARG netpyneuiBranch=0.2M3
-ENV netpyneuiBranch=${netpyneuiBranch}
+ARG netpyneuiBranch=development 
+ENV netpyneuiBranch=${netpyneuiBranch}  
 RUN echo "$netpyneuiBranch";
 
 RUN apt-get -qq update
@@ -13,7 +13,7 @@ RUN apt-get install -y \
         g++ \
         build-essential \
         libncurses-dev \
-        python \
+        python2.7 \
         libpython-dev \
         cython \
         libx11-dev \
@@ -24,48 +24,45 @@ RUN apt-get install -y \
         libtool \ 
         libxext-dev \
         libncurses-dev \
-        python3-dev \
+        python2.7-dev \
         xfonts-100dpi \ 
-        cython3 \ 
         libopenmpi-dev \
-        python3-scipy \
+        python2.7-scipy \
         make \
         zlib1g-dev \
         unzip \
         vim \
         libpng-dev
 
 # Install latest iv and NEURON
-RUN git clone http://github.com/neuronsimulator/iv
-RUN git clone http://github.com/neuronsimulator/nrn
-WORKDIR iv
+RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git
+WORKDIR nrn
 RUN ./build.sh
-RUN ./configure
-RUN make --silent -j4
-RUN make --silent install -j4
-WORKDIR ../nrn
-RUN ./build.sh
-RUN ./configure --with-nrnpython=python2 --with-paranrn
+RUN ./configure --without-x --with-nrnpython=python2 --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
-RUN conda update conda
+# 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 ../../../
 RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
 RUN unzip $netpyneuiBranch.zip
 WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
 RUN /bin/bash -c "source activate snakes && python --version"
-RUN /bin/bash -c "source activate snakes && exec python install.py"
-RUN mkdir /home/jovyan/netpyne_workspace
+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=''"
+CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"