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filippomcfilippomc
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Merge deployment fixes
2 parents 6dc1526 + 8496995 commit 35b6d06

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Lines changed: 63 additions & 56 deletions

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‎.dockerignore‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ notebook.ipynb
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Dockerfile
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Dockerfile_base
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Dockerfile_dev
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node_modules
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webapp/node_modules
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webapp/build
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webapp/geppetto-client
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workspace
@@ -23,4 +23,5 @@ app.log
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/.pytest_cache
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.jupyter-config
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**/*.pyc
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**/__pycache__
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**/__pycache__
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app.log

‎Dockerfile‎

Lines changed: 52 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -1,42 +1,66 @@
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FROM frodriguez4600/jupyter-neuron:v7.8.0
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ARG INSTALLATION_FOLDER=/home/jovyan/work/NetPyNE-UI
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ARG NETPYNE_VERSION=development
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ARG WORKSPACE_VERSION=nov2020
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FROM node:13.14 as jsbuild
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WORKDIR /app
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COPY --chown=1000:1000 webapp/package.json .
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COPY --chown=1000:1000 webapp/yarn.lock .
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RUN yarn install --network-timeout 1000000000
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COPY webapp/ .
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RUN yarn build-dev
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RUN mv node_modules/@metacell .
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RUN rm -Rf node_modules/*
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RUN mv @metacell node_modules
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###
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FROM jupyter/base-notebook:hub-1.5.0
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ENV NB_UID=jovyan
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ENV FOLDER=netpyne
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ARG GEPPETTO_VERSION=development
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ARG BUILD_ARGS=""
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USER $NB_USER
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ENV FOLDER=/home/jovyan/work/NetPyNE-UI
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ENV INSTALLATION_FOLDER=$INSTALLATION_FOLDER
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ENV NETPYNE_VERSION=$NETPYNE_VERSION
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ENV WORKSPACE_VERSION=$WORKSPACE_VERSION
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ENV GEPPETTO_VERSION=$GEPPETTO_VERSION
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ENV BUILD_ARGS=$BUILD_ARGS
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# Install openmpi for parallel simulations
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# Important: Have to switch to root to install a package and ensure to switch back to NB user afterwards
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USER root
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RUN apt-get update && apt-get install -y libopenmpi-dev
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USER $NB_USER
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WORKDIR /home/jovyan/work
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COPY --chown=1000:1000 requirements.txt ${INSTALLATION_FOLDER}/requirements.txt
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RUN rm -rf /var/lib/apt/lists
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RUN apt-get update -qq &&\
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apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
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RUN conda install python=3.7 -y
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WORKDIR ${INSTALLATION_FOLDER}
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RUN pip install -r requirements.txt
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WORKDIR $FOLDER
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COPY --chown=1000:1000 requirements.txt requirements.txt
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RUN pip install -r requirements.txt --no-cache-dir --prefer-binary
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COPY --chown=1000:1000 . .
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WORKDIR ${INSTALLATION_FOLDER}/utilities
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COPY --chown=$NB_UID:1000 . .
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COPY --from=jsbuild --chown=$NB_UID:1000 /app webapp
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RUN npm install --global yarn
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RUN npm install --global yalc
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RUN python install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION}
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RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
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RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
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RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --npm-skip
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RUN jupyter labextension disable @jupyterlab/hub-extension
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RUN chown $NB_UID .
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RUN chown -R $NB_UID workspace
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USER $NB_UID
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EXPOSE 8888
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# Temp fixes for eeg plots
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RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
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WORKDIR ${INSTALLATION_FOLDER}
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RUN pip install -r requirements-test.txt
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RUN pytest tests/backend
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CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"
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‎k8s/cf_values.yaml‎

Lines changed: 3 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -2,35 +2,19 @@ hub:
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image:
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name: gcr.io/metacellllc/netpyne-hub
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pullPolicy: IfNotPresent
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allowNamedServers: true
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resources:
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requests:
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cpu: 100m
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memory: 128Mi
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allowNamedServers: true
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namedServerLimitPerUser: 2
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shutdownOnLogout: true
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extraConfig:
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timing: |
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c.JupyterHub.allow_named_servers = True
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c.Spawner.port = 8000
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c.Spawner.http_timeout = 300
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c.Spawner.start_timeout = 300
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c.Spawner.notebook_dir = '/home/jovyan/work/NetPyNE-UI'
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c.Spawner.default_url = '/geppetto'
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c.Spawner.debug = True
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spawner: >-
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c.Spawner.args = ["--library=netpyne_ui", "--NotebookApp.disable_check_xsrf=True"]
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scheduling:
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userScheduler:
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replicas: 1
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auth:
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type: tmp
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c.Spawner.args = ["--library=netpyne_ui"]
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singleuser:
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storage:
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type: none
@@ -54,4 +38,4 @@ cull:
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maxAge: 0
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debug:
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enabled: false
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enabled: false

‎requirements.txt‎

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Original file line numberDiff line numberDiff line change
@@ -23,14 +23,12 @@ jedi==0.17.0
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Jinja2==2.11.2
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jsonpickle==2.1.0
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jsonschema==3.2.0
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jupyter==1.0.0
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jupyter-client==6.1.3
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jupyter-console==6.1.0
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jupyter-core==4.6.3
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jupyter_geppetto==1.1.1
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jupyter-telemetry==0.0.5
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jupyterhub==1.1.0
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jupyterlab==2.1.3
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jupyter-client==7.0.6
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jupyter-core==4.9.1
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jupyter-server==1.11.2
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jupyterhub==1.5.0
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jupyterlab==3.2.4
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jupyterthemes==0.20.0
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kiwisolver==1.2.0
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lesscpy==0.14.0

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