Merge pull request #167 from MetaCell/release/0.6.0

Release/0.6.0

Author: tarelli

.dockerignore

@@ -0,0 +1,19 @@
+org.geppetto.frontend.jupyter
+pygeppetto
+.vscode
+.ipynb_checkpoints
+netpyne_ui/geppetto
+*.egg-info
+notebook.ipynb
+.git
+netpyne
+Dockerfile
+Dockerfile_base
+Dockerfile_dev
+netpyne_workspace
+webapp/node_modules
+webapp/build
+webapp/geppetto-client
+k8s
+src
+x86_64

.gitignore

@@ -1,11 +1,23 @@
 .ipynb_checkpoints/
 netpyne-ui.log
 log.file
+src
 *.pyc
 *.egg-info
 .DS_Store
 pygeppetto/
 netpyne/
 org.geppetto.frontend.jupyter/
 *.ipynb
-init.py
+init.py
+webapp/node_modules
+webapp/geppetto-client
+webapp/build
+netpyne_workspace
+Dockerfile_mini
+npm*
+.vscode
+app.log
+utilities/x86_64
+.idea
+x86_64

.gitmodules

@@ -1,76 +1,26 @@
 language: python
 os: linux
-sudo: false
-dist: trusty
-bundler_args: --retry 5
+python:
+  - "3.7"
 node_js:
-  - "7"
+  - "12"
 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 $TRAVIS_BRANCH does not exist for the dependent bundle, checking out development ..." && git checkout development; fi
-- cd ..
-- npm install --silent -g phantomjs
-- npm install --silent -g casperjs
-- npm install --silent -g slimerjs
-- npm install --silent -g gl
-python:
-  - "2.7"
-  - "3.5"
-edge: true
+    - secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
+    - DEFAULT_BRANCH: development
+    - LANDING_PAGE: "http://localhost:8888/geppetto"
 notifications:
   slack: metacell:5ALSeoP88DqIhORUJvxE56sq
-services:
-  - docker
-addons:
-  firefox: "58.0"
-  apt:
-    packages:
-    - mesa-utils
-    - xvfb
-    - libgl1-mesa-dri
-    - libglapi-mesa
-    - libosmesa6
-
-before_script:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - export SLIMERJSLAUNCHER=/home/travis/firefox-58.0/firefox/firefox
-  - export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
-    
+install:
+  - sudo apt-get install libgnutls28-dev
+  - sudo apt install libcurl4-openssl-dev libssl-dev
+  - sudo apt-get install python3-dev  
 script:
-  - travis_retry docker build -t="netpyne-ui" --build-arg netpyneuiBranch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
-  - travis_retry docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
-  - cd $TRAVIS_BUILD_DIR/ && ls
-  - cd geppetto-netpyne && ls
-  - cd tests
-  - bash utilities/netpyne-server-status.sh
-  - sleep 30
-  - http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
+
+  - python utilities/install.py 
+  - ./NetPyNE-UI &
+  - http_status=$(curl -s -I $1 $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'})
   - echo "$http_status"
-  - while [ "$http_status" == "404" ]; do
-      echo "Restart run";
-      echo "Printing logs for debugging purposes";
-      docker stop $(docker ps -a -q);
-      docker rm $(docker ps -a -q);
-      docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
-      bash utilities/netpyne-server-status.sh
-      sleep 30;
-      http_status=$(curl -s -I $1 http://localhost:8888/geppetto | grep HTTP/1.1 | awk {'print $2'})
-      echo "Done restarting";
-      echo "$http_status";
-    done;
-  - http_status=$(curl -s -I $1 http://localhost:28081 | grep HTTP/1.1 | awk {'print $2'})
-  - echo "$http_status";
-  - "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
-  - 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)
+  - cd webapp
+  - travis_retry npm run test -- --verbose --colors
+  - exit 0

.travis.yml

@@ -1,26 +1,17 @@
-FROM metacell/jupyter-neuron:latest
+FROM frodriguez4600/jupyter-neuron:v7.8.0
 USER $NB_USER
 
-ARG netpyneuiBranch=development 
-ENV netpyneuiBranch=${netpyneuiBranch}  
-RUN echo "$netpyneuiBranch";
+ARG branch=development 
+RUN echo "$branch";
 
-ARG INCUBATOR_VER=unknown
-RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install 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"
+ENV INSTALLATION_FOLDER=/home/jovyan/work/NetPyNE-UI
+WORKDIR /home/jovyan/work
 
-WORKDIR /home/jovyan
-RUN git clone --branch v0.5 https://github.com/Neurosim-lab/netpyne_workspace
-WORKDIR /home/jovyan/netpyne_workspace
+COPY --chown=1000:1000 . NetPyNE-UI
+WORKDIR ${INSTALLATION_FOLDER}/utilities
 
-# Uncomment to run travis using this Dockerfile
-# Clone the source code and creates a symlink to the test folder
-WORKDIR /home/jovyan/work
-RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
-RUN unzip $netpyneuiBranch.zip 
-WORKDIR /home/jovyan/netpyne_workspace
-RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/netpyne_ui/tests tests
+RUN python install.py branch $branch
+
+WORKDIR ${INSTALLATION_FOLDER}
 
-CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"
+CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"

Dockerfile

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

NetPyNE-UI

@@ -1,10 +1,11 @@
 [![Docker Automated buil](https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg)](https://hub.docker.com/r/metacell/netpyne-ui/)
-
+[![Build Status](https://travis-ci.org/MetaCell/NetPyNE-UI.svg?branch=master)](https://travis-ci.org/MetaCell/NetPyNE-UI)
+[![Codefresh build status]( https://g.codefresh.io/api/badges/pipeline/tarelli/NetPyNE-UI%2Ftest?branch=master&key=eyJhbGciOiJIUzI1NiJ9.NWFkNzMyNDIzNjQ1YWMwMDAxMTJkN2Rl.-gUEkJxH6NCCIRgSIgEikVDte-Q0BsGZKEs4uahgpzs&type=cf-1)]( https%3A%2F%2Fg.codefresh.io%2Fpipelines%2Ftest%2Fbuilds%3FrepoOwner%3DMetaCell%26repoName%3DNetPyNE-UI%26serviceName%3DMetaCell%252FNetPyNE-UI%26filter%3Dtrigger%3Abuild~Build%3Bbranch%3Amaster%3Bpipeline%3A5e5bbecc6c98a1209fc7bca3~test)
 <p align="center">
-    <img src="https://raw.githubusercontent.com/MetaCell/NetPyNE-UI/master/docs/netpyne.png" width="350px"/>
+    <img src="https://github.com/MetaCell/NetPyNE-UI/raw/documentation/docs/netpyne.png" width="350px"/>
 </p>
 
-![Screenshot](https://github.com/metacell/netpyne-ui/raw/master/docs/netpyneui.png)
+![Screenshot](https://github.com/MetaCell/NetPyNE-UI/raw/documentation/docs/netpyneui.png)
 
 This repository hosts the User Interface for [NetPyNE](http://www.neurosimlab.org/netpyne/). NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
 
@@ -21,15 +22,36 @@ If you are familiar with NEURON and have already NEURON installed in your machin
 </p>
 
 ## Install NetPyNE User Interface from sources (for developers)
+
+### Python Dependencies
+
+We recommend the use of a new python 3 virtual environment:
+
+```bash
+python3 -m venv npenv
+source npenv/bin/activate
+```
+
+Or, with conda
+
+```bash
+conda create -n netpyne python=3.7
+conda activate netpyne
 ```
+
+### Run install script
+
+```bash
 git clone https://github.com/MetaCell/NetPyNE-UI.git
 cd utilities
 python install.py
 cd ..
 ./NetPyNE-UI
 ```
-### To update sources:
-```
+
+### To update sources
+
+```bash
 python update.py
 ```
 

README.md

@@ -0,0 +1,12 @@
+FROM jupyterhub/jupyterhub:latest
+
+# feature_jupyterhub
+ARG netpyneuiBranch=feature_jupyterhub 
+ENV netpyneuiBranch=${netpyneuiBranch}  
+RUN echo "$netpyneuiBranch";
+
+# Install authenticator and spawner + jupyter_client
+RUN pip install jupyterhub-tmpauthenticator dockerspawner jupyter_client
+
+# Overwrite jupyterhub_config
+RUN wget https://raw.githubusercontent.com/MetaCell/NetPyNE-UI/$netpyneuiBranch/jupyterhub/jupyterhub_config.py -q

docs/gif1.gif

@@ -1,10 +1,18 @@
 FROM metacell/jupyter-neuron:latest
+
+USER root
+RUN conda install -c conda-forge nodejs configurable-http-proxy
+
 USER $NB_USER
 
-ARG netpyneuiBranch=development 
+# feature_jupyterhub
+ARG netpyneuiBranch=feature_jupyterhub  
 ENV netpyneuiBranch=${netpyneuiBranch}  
 RUN echo "$netpyneuiBranch";
 
+ARG INCUBATOR_VER=unknown
+RUN /bin/bash -c "INCUBATOR_VER=${INCUBATOR_VER} source activate snakes && pip install jupyterhub==0.9.4"
+
 # Clone NetPyNE-UI and install the development version
 RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip -q
 RUN unzip $netpyneuiBranch.zip
@@ -15,4 +23,8 @@ WORKDIR /home/jovyan
 RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
 RUN ln -sfn /home/jovyan/work/NetPyNE-UI-$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"
+
+# Copy jupyterhub_config
+# RUN cp /home/jovyan/work/NetPyNE-UI-$netpyneuiBranch/jupyterhub_config.py .
+
+CMD /bin/bash -c "source activate snakes && exec jupyterhub-singleuser --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

docs/netpyneui.png

@@ -0,0 +1,38 @@
+## Class for authenticating users.
+#  
+#  This should be a class with the following form:
+#  
+#  - constructor takes one kwarg: `config`, the IPython config object.
+#  
+#  with an authenticate method that:
+#  _class
+#  - is a coroutine (asyncio or tornado)
+#  - returns username on success, None on failure
+#  - takes two arguments: (handler, data),
+#    where `handler` is the calling web.RequestHandler,
+#    and `data` is the POST form data from the login page.
+#c.JupyterHub.authenticator_class = 'jupyterhub.auth.PAMAuthenticator'
+# c.JupyterHub.authenticator_class = 'dummyauthenticator.DummyAuthenticator'
+# c.DummyAuthenticator.password = "dummypassword"
+c.JupyterHub.authenticator_class = 'tmpauthenticator.TmpAuthenticator'
+
+## The class to use for spawning single-user servers.
+#  
+#  Should be a subclass of Spawner.
+#c.JupyterHub.spawner_class = 'jupyterhub.spawner.LocalProcessSpawner'
+c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner'
+from jupyter_client.localinterfaces import public_ips
+ip = public_ips()[0]
+c.JupyterHub.hub_ip = ip
+c.DockerSpawner.image = 'netpyne_ui_jupyterspawner'
+c.DockerSpawner.remove_containers = True
+c.DockerSpawner.remove = True
+c.DockerSpawner.debug = True
+c.DockerSpawner.network_name='jupyterhub_network'
+
+## Extra arguments to be passed to the single-user server. Only works for the LocalProcessSpawner
+#  
+#  Some spawners allow shell-style expansion here, allowing you to use
+#  environment variables here. Most, including the default, do not. Consult the
+#  documentation for your spawner to verify!
+# c.Spawner.args = ['--library=netpyne_ui', '--NotebookApp.default_url=/geppetto', '--NotebookApp.token=''']

docs/wiki1-1.png

@@ -0,0 +1,14 @@
+FROM jupyterhub/k8s-hub:0.9.0
+    
+COPY --chown=1000:1000 templates/page.html /usr/local/share/jupyterhub/templates/page.html
+COPY --chown=1000:1000 templates/404.html /usr/local/share/jupyterhub/templates/404.html
+COPY --chown=1000:1000 templates/spawn_pending.html /usr/local/share/jupyterhub/templates/spawn_pending.html
+COPY --chown=1000:1000 static/jupyter.png /usr/local/share/jupyterhub/static/images/jupyter.png
+COPY --chown=1000:1000 static/jupyter.png /usr/local/share/jupyterhub/static/images/jupyterhub-80.png
+COPY --chown=1000:1000 static/favicon.ico /usr/local/share/jupyterhub/static/favicon.ico
+COPY --chown=1000:1000 static/favicon.ico /usr/local/share/jupyterhub/static/images/favicon.ico
+COPY --chown=1000:1000 auth.py /usr/local/lib/python3.6/dist-packages/tmpauthenticator/__init__.py
+COPY --chown=1000:1000 js/EventSource.js /usr/local/share/jupyterhub/static/js/EventSource.js
+
+
+CMD ["jupyterhub", "--config", "/srv/jupyterhub_config.py"]

docs/wiki1-2.png

@@ -0,0 +1,16 @@
+# k8s deployment
+
+- Deploy on minikube runnig
+
+```bash
+kubectl create -ns netpyne
+helm upgrade netpyne jupyterhub --install --reset-values --repo https://jupyterhub.github.io/helm-chart/ --version 0.9.0 --namespace netpyne --values minikube_values.yaml --force --debug
+```
+
+- Access the hub by running
+
+```bash
+minikube service list
+```
+
+and use the url corresponding to nepyne proxy-public on port 80