Merge branch 'development' into feature/netpyne-106

Author: enicolasgomez

.github/workflows/tests.yml

@@ -58,6 +58,72 @@ jobs:
           npm run Experiment_Manager_test
       env:
           CI: true
+  Control_Panel-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Control Panel test using Tut#2
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Control Panel test
+          npm run Control_Panel_test
+      env:
+          CI: true
+  Save_and_Open_File-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Test for Opening and Saving a file
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run Control Panel test
+          npm run Save_Open_File_test
+      env:
+          CI: true
+  RxD-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    container: lironavon/docker-puppeteer-container:14.16.0
+    env:
+      CI: true
+    steps:
+    - uses: actions/checkout@v1
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+          node-version: ${{ matrix.node-version }}
+          cache-dependency-path: frontend/e2e/tests/package-lock.json
+    - name: Test for RxD plot
+      run: |
+          cd tests/frontend/e2e
+          #install dependencies
+          npm ci
+          # run RxD Plot test
+          npm run RxD_test
+      env:
+          CI: true
   Tutorial_1-SmokeTest:
     # The type of runner that the job will run on
     runs-on: ubuntu-20.04

.gitignore

@@ -30,4 +30,5 @@ venv
 webapp/build
 webapp/.yalc
 node_modules
-sa_nyhead.mat
+sa_nyhead.mat
+workspace

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:13.14 as jsbuild
+FROM node:14.21.3-bullseye as jsbuild
 
 WORKDIR /app
 
@@ -18,10 +18,10 @@ RUN rm -Rf node_modules/*
 FROM jupyter/base-notebook:hub-1.5.0
 ENV NB_UID=jovyan
 ENV FOLDER=netpyne
-ARG GEPPETTO_VERSION=development
 ARG BUILD_ARGS=""
-ARG NETPYNE_VERSION=master
 ARG WORKSPACE_VERSION=master
+# ARG GEPPETTO_VERSION=development
+# ARG NETPYNE_VERSION=master
 
 ENV FOLDER=/home/jovyan/work/NetPyNE-UI
 
@@ -32,21 +32,20 @@ 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  openjdk-11-jre-headless -y -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
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip && pip install -r requirements.txt --prefer-binary
 
-COPY --chown=$NB_UID:1000 . .
-COPY --from=jsbuild --chown=$NB_UID:1000 /app webapp
+COPY --chown=jovyan:1000 . .
+COPY --from=jsbuild --chown=jovyan: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} --netpyne $NETPYNE_VERSION --workspace WORKSPACE_VERSION --npm-skip
+RUN python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION
 
 RUN jupyter labextension disable @jupyterlab/hub-extension
 
@@ -58,7 +57,8 @@ ENV NEURON_HOME=/opt/conda
 # For lfpykit 0.4
 # RUN wget -P $(pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}') https://www.parralab.org/nyhead/sa_nyhead.mat
 # For lpfykit 0.5
-RUN wget --no-check-certificate -P ${FOLDER}/workspace https://www.parralab.org/nyhead/sa_nyhead.mat
+ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
+RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
 
 USER $NB_UID
 

README.md

@@ -7,7 +7,7 @@
 
 ![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
+This repository hosts the User Interface for [NetPyNE](https://netpyne.v2.opensourcebrain.org/). NetPyNE is a python package
 to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON
 simulator.
 
@@ -116,4 +116,4 @@ docker-compose up --abort-on-container-exit --exit-code-from netpyne-ui-e2e
 ## Additional Notes
 
 NetPyNE-UI is being developed in collaboration with the [Neurosim Lab](http://neurosimlab.org/). See
-the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info!
+the [Wiki](https://github.com/MetaCell/NetPyNE-UI/wiki) for more info!

netpyne_ui/__init__.py

@@ -11,21 +11,23 @@
     "https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6"
 )
 
+HEAD_MODEL_FILE = os.getenv("NP_LFPYKIT_HEAD_FILE", "sa_nyhead.mat")
+
 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
+        NYHeadModel(HEAD_MODEL_FILE) # 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()
-
+if not os.path.exists(HEAD_MODEL_FILE):
+    from multiprocessing import Process
+    thread = Process(target = init_eeg)
+    thread.start()
 
 RouteManager.add_controller(api.NetPyNEController)
 

netpyne_ui/mod_utils.py

@@ -1,3 +1,4 @@
+import logging
 import shutil
 import subprocess
 import os
@@ -26,19 +27,33 @@ def is_loaded_mechanisms():
         return True
 
 
-def loadModMechFiles(compileMod, modFolder):
+def loadModMechFiles(compileMod, modFolder, forceRecompile=False):
     # Create Symbolic link
-    if compileMod:
-        modPath = os.path.join(str(modFolder), "x86_64")
 
-        if os.path.exists(modPath):
-            shutil.rmtree(modPath)
-
-        os.chdir(modFolder)
-        subprocess.call(["nrnivmodl"])
-        os.chdir('..')
-
-    try:
-        neuron.load_mechanisms(str(modFolder))
-    except:
-        raise
+        try:
+
+            owd = os.getcwd()
+            if compileMod:
+                
+                compiledModPath = os.path.join(str(modFolder), "x86_64")
+
+                if os.path.exists(compiledModPath) and forceRecompile:
+                        logging.info("Forcing mod files to recompile in %s" % modFolder)
+                        shutil.rmtree(compiledModPath)
+
+                if not os.path.exists(compiledModPath):
+                    logging.info("Compiling mod files in %s" % modFolder)
+                    os.chdir(modFolder)
+                    subprocess.call(["nrnivmodl"])
+                    os.chdir('..')
+
+            try:
+                neuron.load_mechanisms(str(modFolder))
+            except:
+                logging.exception("Error loading mechanisms")
+                if not forceRecompile:
+                    logging.info("Trying to recompile mod files")
+                    loadModMechFiles(True, modFolder, forceRecompile=True)
+                raise
+        finally:
+            os.chdir(owd)