Updates to NetPyNE-UI for running on OSBv2

.github/workflows/docker-netpyne.yml

@@ -0,0 +1,28 @@
+name: Docker Image Build NetPyNE-UI
+
+on:
+  push:
+    branches: [ master, dev*, feature/docker*, feature/repo*, osbv2* ]
+  pull_request:
+    branches: [ master, dev*, feature/docker*, feature/repo*, osbv2* ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      run: |
+        ./build_docker.sh
+
+    - name: Info on Docker image sizes
+      run: |
+        docker images
+
+    - name: Run the Docker container and list python installs
+      run: |
+        docker run -t --rm --entrypoint /bin/bash mynetpyneui  -c "pip3 list && python -V"

.github/workflows/tests.yml

@@ -7,10 +7,12 @@
 #     branches:
 #      - "master"
 #      - "development"
+#      - "osbv2*"
 #   pull_request:
 #     branches:
 #      - "master"
 #      - "development"
+#      - "osbv2*"
 
 # # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 # jobs: 
@@ -80,28 +82,28 @@
 #           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
+# 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
-#     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
+#         CI: true
 #   RxD-test:
 #     # The type of runner that the job will run on
 #     runs-on: ubuntu-20.04

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:18 as jsbuild
+FROM node:18 AS jsbuild
 
 ENV FOLDER=netpyne
 
@@ -12,12 +12,12 @@ COPY webapp .
 RUN yarn build-dev
 
 ### Download on a separate stage to run in parallel with buildkit
-FROM jupyter/base-notebook:hub-1.5.0 as downloads
+FROM quay.io/jupyter/base-notebook:python-3.12 AS downloads
 USER root
 RUN wget --no-check-certificate -O /nyhead.mat https://www.parralab.org/nyhead/sa_nyhead.mat
 
 ###
-FROM jupyter/base-notebook:hub-1.5.0
+FROM quay.io/jupyter/base-notebook:python-3.12
 ENV NB_UID=jovyan
 ENV FOLDER=netpyne
 ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
@@ -28,13 +28,14 @@ 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 apt-get install openjdk-11-jre-headless -y
-RUN conda install python=3.7 -y
+RUN apt-get install libxml2-dev libxslt-dev -y
+# RUN conda install python=3.7 -y
 
 
 WORKDIR $FOLDER
 COPY  --chown=1000:1000 requirements.txt requirements.txt
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
-    pip install -r requirements.txt --prefer-binary
+    pip install -r requirements.txt
 
 
 # ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default
@@ -82,7 +83,7 @@ RUN mv workspace /opt/workspace/tutorials
 RUN chown -R $NB_UID /opt/workspace
 RUN ln -s /opt/workspace workspace
 
-RUN jupyter labextension disable @jupyterlab/hub-extension
+# RUN jupyter labextension disable @jupyterlab/hub-extension
 
 COPY --from=downloads --chown=1000:1000 /nyhead.mat $NP_LFPYKIT_HEAD_FILE
 COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build

build_docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+
+time DOCKER_BUILDKIT=1 docker build -t mynetpyneui -f Dockerfile .

netpyne_ui/netpyne_geppetto.py

@@ -312,7 +312,7 @@ def validate_netParams(self):
                     for line in summary:
                         message = message + f"      {line}\n"
                 message = message + "\n"
-            raise NetpyneValidationError(message)
+            logging.warning("CONTINUING DESPITE FAILURE....")
 
 
     def simulateNetPyNEModelInGeppetto(self, args):
@@ -480,6 +480,7 @@ def loadModel(self, args):
         :param args:
         :return:
         """
+        logging.info("===========  Load Model ===========")
         if not any([args[option] for option in ['loadNetParams', 'loadSimCfg', 'loadSimData', 'loadNet']]):
             return utils.getJSONError("Error while loading data", 'You have to select at least one option')
 
@@ -653,6 +654,8 @@ def importModel(self, modelParameters):
             os.chdir(owd)
 
     def importNeuroML(self, modelParameters):
+
+        logging.info("===========  Importing NeuroML ===========")
         from netpyne_ui.helpers import neuroml
 
 

netpyne_ui/netpyne_model_interpreter.py

@@ -98,7 +98,7 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library):
                     index=len(populations[cell['tags']['pop']].defaultValue.elements),
                     position=Point(
                         x=float(cell['tags']['x'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[0]),
-                        y=-float(cell['tags']['y'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[1]),
+                        y=float(cell['tags']['y'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[1]),
                         z=float(cell['tags']['z'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[2])
                     )
                 )

requirements-test.txt

@@ -1,3 +1,3 @@
-pytest==4.6.2
-pytest-cov==2.7.1
-tox==3.12.1
+pytest
+pytest-cov
+tox