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Merge pull request #47 from MetaCell/development
June Alpha Release
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‎.gitignore‎

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@@ -6,4 +6,7 @@ pygeppetto/
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org.geppetto.frontend.jupyter/
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*.ipynb
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init.py
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.idea/
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.idea/
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netpyne/
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*.log
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.python-version

‎.gitmodules‎

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[submodule "hnn_ui/geppetto"]
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path = hnn_ui/geppetto
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url = https://github.com/openworm/org.geppetto.frontend.git
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branch = refactor-upgrade-materialui

‎.travis.yml‎

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language: python
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os: linux
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sudo: false
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dist: trusty
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bundler_args: --retry 5
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node_js:
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- "7"
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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-hnn.git
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- cd geppetto-hnn
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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 slimerjs
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- npm install --silent -g gl
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python:
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- "2.7"
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- "3.5"
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edge: true
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notifications:
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slack: metacell:5ALSeoP88DqIhORUJvxE56sq
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services:
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- docker
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addons:
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firefox: "58.0"
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apt:
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packages:
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- mesa-utils
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- xvfb
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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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- export SLIMERJSLAUNCHER=/home/travis/firefox-58.0/firefox/firefox
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- export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
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script:
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- travis_wait travis_retry docker build -t="hnn-ui" --build-arg hnnuiBranch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
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- travis_retry docker run -t -dit --name=hnn-ui_container -h localhost -p 8888:8888 hnn-ui:latest
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- cd $TRAVIS_BUILD_DIR/ && ls
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- cd geppetto-hnn && ls
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- cd tests
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- bash utilities/hnn-server-status.sh
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- sleep 30
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- http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
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- echo "$http_status"
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- while [ "$http_status" == "404" ]; do
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echo "Restart run";
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echo "Printing logs for debugging purposes";
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docker stop $(docker ps -a -q);
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docker rm $(docker ps -a -q);
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docker run -t -dit --name=hnn-ui_container -h localhost -p 8888:8888 hnn-ui:latest
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bash utilities/hnn-server-status.sh
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sleep 30;
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http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
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echo "Done restarting";
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echo "$http_status";
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done;
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- http_status=$(curl -s -I $1 http://localhost:28081 | grep HTTP/1.1 | awk {'print $2'})
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- echo "$http_status";
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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 hnn-tests.js --host=http://localhost:8888/ --engine=slimerjs
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- python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
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- docker logs -t hnn-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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# The purpose of this Dockerfile is to serve as skeleton for a future production version.
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# Therefore currently it is NOT functional
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FROM metacell/jupyter-neuron:latest
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USER $NB_USER
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ARG hnnuiBranch=development
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ENV hnnuiBranch=${hnnuiBranch}
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RUN echo "$hnnuiBranch";
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ARG INCUBATOR_VER=unknown
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RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install netpyne_ui"
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RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py jupyter_geppetto"
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RUN /bin/bash -c "source activate snakes && jupyter serverextension enable --py jupyter_geppetto"
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RUN /bin/bash -c "source activate snakes && jupyter nbextension enable --py widgetsnbextension"
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WORKDIR /home/jovyan/work
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RUN wget https://github.com/MetaCell/HNN-UI/archive/$hnnuiBranch.zip -q
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RUN unzip $hnnuiBranch.zip
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WORKDIR /home/jovyan/work/HNN-UI-$hnnuiBranch/utilities
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CMD /bin/bash -c "exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=hnn_ui"

‎Dockerfile_dev‎

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FROM metacell/jupyter-neuron:development
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ARG hnnuiBranch=development
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RUN echo $hnnuiBranch
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# Clone HNN-UI and install the development version
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RUN git clone -b $hnnuiBranch https://github.com/MetaCell/HNN-UI &&\
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cd HNN-UI/utilities &&\
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python install.py
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WORKDIR $HOME/HNN-UI
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CMD jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=hnn_ui

‎HNN-UI‎

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

‎README.md‎

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# HNN-GUI
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# HNN Web User Interface
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This repository hosts the User Interface for [HNN](https://hnn.brown.edu/). HNN is a user-friendly software tool that gives researchers and clinicians the ability to test and develop hypotheses on the circuit mechanism underlying their EEG/MEG data in an easy-to-use environment.
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This repository hosts the web-based user interface for [HNN](https://hnn.brown.edu/). HNN is a user-friendly software tool that gives researchers and clinicians the ability to test and develop hypotheses on the circuit mechanism underlying their EEG/MEG data in an easy-to-use environment.
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![](https://raw.githubusercontent.com/MetaCell/HNN-UI/development/docs/wiki6.png)
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## [Documentation](https://github.com/MetaCell/HNN-UI/wiki)
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## Install HNN User Interface from sources (for developers)
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Make sure you have [NEURON installed](https://github.com/MetaCell/NetPyNE-UI/wiki/Installing-NEURON-(version-7.6.2-with-crxd)) and then:
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```
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git clone https://github.com/MetaCell/HNN-UI
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cd utilities
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python install.py
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cd ..
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./HNN-UI
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```
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‎README.rst‎

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New user interface
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for `HNN <https://hnn.brown.edu/>`__ based on web
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technologies.
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The UI connects to
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`nrnpython <http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/python.html>`__
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through a `Geppetto <http://git.geppetto.org>`__ extension for `Jupyter
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Notebook <http://jupyter.org/>`__.
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HNN-UI
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======
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User Interface for HNN.
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See the `Repo <https://github.com/MetaCell/HNN-UI>`__
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info!
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Installation
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============
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.. code-block:: bash
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pip install hnn_ui
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jupyter nbextension enable --py jupyter_geppetto
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Usage
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=====
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.. code-block:: bash
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HNN-UI
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or
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.. code-block:: bash
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jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token=''
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‎docs/wiki1.png‎

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‎docs/wiki10.png‎

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