Merge pull request #587 from MetaCell/release/0.8.1

Release/0.8.1 to master

Author: ddelpiano

.dockerignore

@@ -10,7 +10,7 @@ notebook.ipynb
 Dockerfile
 Dockerfile_base
 Dockerfile_dev
-node_modules
+webapp/node_modules
 webapp/build
 webapp/geppetto-client
 workspace
@@ -23,4 +23,5 @@ app.log
 /.pytest_cache
 .jupyter-config
 **/*.pyc
-**/__pycache__
+**/__pycache__
+app.log

Dockerfile

@@ -1,39 +1,67 @@
-FROM frodriguez4600/jupyter-neuron:v7.8.0
-ARG INSTALLATION_FOLDER=/home/jovyan/work/NetPyNE-UI
-ARG NETPYNE_VERSION=development
-ARG WORKSPACE_VERSION=nov2020
+FROM node:13.14 as jsbuild
+
+WORKDIR /app
+
+COPY --chown=1000:1000 webapp/package.json .
+COPY --chown=1000:1000 webapp/yarn.lock .
+
+
+RUN yarn install  --network-timeout 1000000000
+
+COPY webapp/ .
+RUN yarn build-dev
+
+
+RUN mv node_modules/@metacell .
+RUN rm -Rf node_modules/*
+RUN mv @metacell node_modules
+
+###
+FROM jupyter/base-notebook:hub-1.5.0
+ENV NB_UID=jovyan
+ENV FOLDER=netpyne
 ARG GEPPETTO_VERSION=development
 ARG BUILD_ARGS=""
 
-USER $NB_USER
-
-ENV INSTALLATION_FOLDER=$INSTALLATION_FOLDER
-ENV NETPYNE_VERSION=$NETPYNE_VERSION
-ENV WORKSPACE_VERSION=$WORKSPACE_VERSION
-ENV GEPPETTO_VERSION=$GEPPETTO_VERSION
-ENV BUILD_ARGS=$BUILD_ARGS
+ENV FOLDER=/home/jovyan/work/NetPyNE-UI
 
-# Install openmpi for parallel simulations
-# Important: Have to switch to root to install a package and ensure to switch back to NB user afterwards
 USER root
-RUN apt-get update && apt-get install -y libopenmpi-dev
-USER $NB_USER
 
-WORKDIR /home/jovyan/work
-COPY --chown=1000:1000 requirements.txt ${INSTALLATION_FOLDER}/requirements.txt
+RUN rm -rf /var/lib/apt/lists
+RUN apt-get update -qq &&\
+    apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
+RUN conda install python=3.7 -y
+
+
+WORKDIR $FOLDER
+COPY --chown=1000:1000 requirements.txt requirements.txt
+RUN pip install -r requirements.txt --no-cache-dir --prefer-binary
+
+COPY --chown=$NB_UID:1000 . .
+COPY --from=jsbuild --chown=$NB_UID:1000 /app webapp
+
+
+RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
+RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
+RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
+RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
+
+RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --npm-skip
+
+RUN jupyter labextension disable @jupyterlab/hub-extension
+
+RUN chown  $NB_UID .
+RUN chown -R $NB_UID workspace
+
+# Temp fixes for eeg plots
+RUN wget -P `pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}'` https://www.parralab.org/nyhead/sa_nyhead.mat
+
+USER $NB_UID
+
+
+EXPOSE 8888
 
-WORKDIR ${INSTALLATION_FOLDER}
-RUN pip install -r requirements.txt
 
-COPY --chown=1000:1000 . .
-WORKDIR ${INSTALLATION_FOLDER}/utilities
 
-RUN npm install --global yarn
-RUN npm install --global yalc
-RUN python install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION}
 
-WORKDIR ${INSTALLATION_FOLDER}
 
-RUN pip install -r requirements-test.txt
-RUN pytest tests/backend
-CMD /bin/bash -c "jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui --NotebookApp.disable_check_xsrf=True"

k8s/cf_values.yaml

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

netpyne_ui/__init__.py

@@ -1,9 +1,32 @@
+import logging
+import sys
+import os
+
 from jupyter_geppetto.webapi import RouteManager
 from netpyne_ui import api
+from netpyne_ui.constants import HERE
 import sentry_sdk
 
 sentry_sdk.init(
     "https://[email protected]/6"
 )
 
+def init_eeg():
+    import sys
+    from netpyne_ui.constants import HERE
+    # FIXES library asking for input to download
+    sys.stdin = open(os.path.join(HERE, "resources/stdin.txt"),'r') 
+    from lfpykit.eegmegcalc import NYHeadModel
+    try:
+        NYHeadModel() # Downloads the model if does not exist
+    except:
+        logging.error("Error initializing the EEG head model", exc_info=True)
+
+from multiprocessing import Process
+thread = Process(target = init_eeg)
+thread.start()
+
+
 RouteManager.add_controller(api.NetPyNEController)
+
+

netpyne_ui/experiments.py

@@ -74,7 +74,7 @@ def edit_experiment(name: str, experiment: dict):
 
     if exp.state != model.ExperimentState.DESIGN:
         raise ExperimentsError(
-            f"Can only edit experiment in f{model.ExperimentState.DESIGN} state"
+            f"Can only edit experiment in {model.ExperimentState.DESIGN} state"
         )
 
     updated_exp = from_dict(model.Experiment, experiment)