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Merge pull request #97 from MetaCell/development
Release 0.5
2 parents a068be9 + 294c496 commit bf290b1

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‎.gitmodules‎

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[submodule "netpyne_ui/geppetto"]
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path = netpyne_ui/geppetto
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url = https://github.com/openworm/org.geppetto.frontend.git

‎.travis.yml‎

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env:
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global:
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secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
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before_install:
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- sudo apt-get install -y xserver-xorg-dev libxext-dev libxi-dev
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install:
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- git clone --quiet https://github.com/MetaCell/geppetto-netpyne.git
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- cd geppetto-netpyne
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- 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
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- cd ..
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- npm install --silent -g phantomjs
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- npm install --silent -g casperjs
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- npm install --silent -g phantomjs
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- npm install --silent -g casperjs
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- npm install --silent -g slimerjs
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- npm install --silent -g gl
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python:
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- libgl1-mesa-dri
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- libglapi-mesa
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- libosmesa6
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before_script:
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- "export DISPLAY=:99.0"
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- "sh -e /etc/init.d/xvfb start"
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- "curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'}"
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- firefox --version
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- travis_retry xvfb-run -a --server-args="-screen 0 1024x768x24" casperjs test netpyne-tests.js --host=http://localhost:8888/ --engine=slimerjs
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- sudo docker logs -t netpyne-ui_container
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- python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
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- docker logs -t netpyne-ui_container
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- docker stop $(docker ps -a -q)
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- docker rm $(docker ps -a -q)

‎Dockerfile‎

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FROM jupyter/base-notebook:eb70bcf1a292
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USER root
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RUN apt-get -qq update
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RUN apt-get install -y \
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locales \
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wget \
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gcc \
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g++ \
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build-essential \
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libncurses-dev \
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python2.7 \
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libpython-dev \
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cython \
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libx11-dev \
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git \
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bison \
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flex \
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automake \
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libtool \
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libxext-dev \
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libncurses-dev \
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python2.7-dev \
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xfonts-100dpi \
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libopenmpi-dev \
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python2.7-scipy \
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make \
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zlib1g-dev \
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unzip \
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vim \
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libpng-dev
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# Install latest NEURON
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RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git
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WORKDIR nrn
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RUN ./build.sh
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RUN ./configure --without-x --with-nrnpython=python2 --without-paranrn --prefix="/home/jovyan/work/nrn/" --without-iv
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RUN make --silent -j4
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RUN make --silent install -j4
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# Switch to non sudo, create a Python 2 virtual environment
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FROM metacell/jupyter-neuron:latest
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USER $NB_USER
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# Commenting out the conda update things broke!
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# RUN conda update conda
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RUN conda create --name snakes python=2
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# Install NEURON python
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WORKDIR src/nrnpython
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ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
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RUN /bin/bash -c "source activate snakes && python setup.py install"
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# Install Bokeh
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RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
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ARG netpyneuiBranch=development
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ENV netpyneuiBranch=${netpyneuiBranch}
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RUN echo "$netpyneuiBranch";
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ARG INCUBATOR_VER=unknown
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RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install netpyne_ui"
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WORKDIR /home/jovyan
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RUN git clone --branch CNS18 https://github.com/Neurosim-lab/netpyne_workspace
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WORKDIR /home/jovyan/netpyne_workspace
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CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"
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# Uncomment to run travis using this Dockerfile
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# Clone the source code and creates a symlink to the test folder
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WORKDIR /home/jovyan/work
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RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
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RUN unzip $netpyneuiBranch.zip
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WORKDIR /home/jovyan/netpyne_workspace
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RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/netpyne_ui/tests tests
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CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

‎Dockerfile_dev‎

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FROM jupyter/base-notebook:eb70bcf1a292
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USER root
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FROM metacell/jupyter-neuron:latest
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USER $NB_USER
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ARG netpyneuiBranch=development
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ENV netpyneuiBranch=${netpyneuiBranch}
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RUN echo "$netpyneuiBranch";
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RUN apt-get -qq update
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RUN apt-get install -y \
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locales \
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wget \
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gcc \
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g++ \
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build-essential \
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libncurses-dev \
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python2.7 \
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libpython-dev \
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cython \
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libx11-dev \
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git \
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bison \
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flex \
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automake \
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libtool \
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libxext-dev \
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libncurses-dev \
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python2.7-dev \
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xfonts-100dpi \
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libopenmpi-dev \
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python2.7-scipy \
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make \
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zlib1g-dev \
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unzip \
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vim \
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libpng-dev
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# Install latest iv and NEURON
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RUN git clone --branch 7.6.1crxd https://github.com/adamjhn/nrn.git
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WORKDIR nrn
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RUN ./build.sh
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RUN ./configure --without-x --with-nrnpython=python2 --without-paranrn --prefix="/home/jovyan/work/nrn/" --without-iv
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RUN make --silent -j4
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RUN make --silent install -j4
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# Switch to non sudo, create a Python 2 virtual environment
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USER $NB_USER
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# Commenting out the conda update things broke!
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# RUN conda update conda
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RUN conda create --name snakes python=2
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# Install NEURON python
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WORKDIR src/nrnpython
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ENV PATH="/home/jovyan/work/nrn/x86_64/bin:${PATH}"
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RUN /bin/bash -c "source activate snakes && python setup.py install"
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# Install Bokeh
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RUN /bin/bash -c "source activate snakes && conda install bokeh=0.12.7"
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# Clone NetPyNE-UI and install the development version
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WORKDIR ../../../
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RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
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RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
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RUN unzip $netpyneuiBranch.zip
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WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
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WORKDIR /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/utilities
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RUN /bin/bash -c "source activate snakes && python --version"
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RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch"
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WORKDIR /home/jovyan
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RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
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WORKDIR /home/jovyan/netpyne_workspace
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CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"
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RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/netpyne_ui/tests tests
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CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

‎MANIFEST.in‎

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# Include everything inside this folder
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graft netpyne_ui/geppetto/src/main/webapp/build
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# Include any of these resources at any level
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recursive-include netpyne_ui/geppetto *.png *.css *.woff *.woff2
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# Include any of these resources at any level
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recursive-include netpyne_ui/tests *.hoc
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# Include also root files (basically the extension)
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include netpyne_ui/*

‎NetPyNE-UI‎

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#!/bin/sh
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exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token=''
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exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui

‎netpyne_ui/geppetto‎

Submodule geppetto added at 0077835

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