Merge pull request #153 from MetaCell/feature/152

#152 Update to netpyne 0.9.6

Author: filippomc

.dockerignore

@@ -13,4 +13,7 @@ Dockerfile_dev
 netpyne_workspace
 webapp/node_modules
 webapp/build
-webapp/geppetto-client
+webapp/geppetto-client
+k8s
+src
+x86_64

.gitignore

@@ -1,6 +1,7 @@
 .ipynb_checkpoints/
 netpyne-ui.log
 log.file
+src
 *.pyc
 *.egg-info
 .DS_Store
@@ -20,3 +21,4 @@ npm*
 app.log
 utilities/x86_64
 .idea
+x86_64

.travis.yml

@@ -11,4 +11,4 @@ notifications:
 services:
   - docker  
 script:
-  - travis_retry docker build -t="netpyne-ui" --build-arg branch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
+  - travis_retry docker build -t="netpyne-ui" --build-arg branch=$TRAVIS_BRANCH .

Dockerfile

@@ -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 --NotebookApp.disable_check_xsrf=True"
+CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"

Dockerfile_dev

@@ -1,5 +1,6 @@
 [![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/updated_documentation/docs/netpyne.png" width="350px"/>
 </p>
@@ -21,6 +22,24 @@ 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
 ```
 git clone https://github.com/MetaCell/NetPyNE-UI.git
 cd utilities

README.md

@@ -1,4 +1,4 @@
-FROM jupyterhub/k8s-hub:0.9.0-beta.4
+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

k8s/Dockerfile

@@ -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

k8s/README.md

@@ -0,0 +1,62 @@
+version: "1.0"
+stages:
+  - "clone"
+  - "build"
+  - "deploy"
+steps:
+  main_clone:
+    type: "git-clone"
+    description: "Cloning main repository..."
+    repo: "MetaCell/NetPyNE-UI"
+    revision: "${{CF_BRANCH}}"
+    stage: "clone"
+    when:
+      branch:
+        only:
+          - "${{CF_BRANCH}}"
+  BuildingNetPyNE-UI:
+    title: Building NetPyNE-UI
+    type: build
+    stage: build
+    image_name: netpyne-ui
+    working_directory: ${{main_clone}}
+    tag: '${{CF_SHORT_REVISION}}'
+    build_arguments:
+      - branch=${{CF_BRANCH}}
+    registry: ${{REGISTRY}}
+    when:
+      branch:
+        only:
+          - "${{CF_BRANCH}}"
+  BuildingHub:
+    title: Building Hub
+    type: build
+    stage: "build"
+    image_name: netpyne-hub
+    working_directory: k8s
+    tag: '${{CF_SHORT_REVISION}}'
+    registry: ${{REGISTRY}}
+    when:
+      branch:
+        only:
+          - "${{CF_BRANCH}}"
+  installing_chart:
+    type: helm
+    stage: deploy
+    title: "Deploy chart"
+    working_directory: NetPyNE-UI/k8s
+    arguments:
+      action: install
+      chart_name: jupyterhub
+      release_name: ${{RELEASE_NAME}}
+      helm_version: 3.0.2
+      chart_repo_url: 'https://jupyterhub.github.io/helm-chart/'
+      chart_version: '0.9.0'
+      kube_context: ${{CLUSTER_NAME}}
+      namespace: ${{NAMESPACE}}
+      custom_value_files: 
+        - 'cf_values.yaml'
+      custom_values:
+        - 'hub_image_tag=${{CF_SHORT_REVISION}}'
+        - 'singleuser_image_tag=${{CF_SHORT_REVISION}}'
+        - 'proxy_secretToken=${{SECRET_TOKEN}}'