Updates to Jupyterlab: uses osbv2 netpyne branch & add scripts

Author: pgleeson

.github/workflows/docker-jupyterlab.yml

@@ -1,4 +1,4 @@
-name: Docker Image Build Jupyterlab
+name: Docker Image Build JupyterLab
 
 on:
   push:
@@ -13,17 +13,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Build the Docker image
       run: |
         cd applications/jupyterlab
-        docker build -t myjlab -f Dockerfile --no-cache .
+        ./build_local.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 myjlab  -c "pip3 list"
+        cd applications/jupyterlab
+        ./pip_omv_info.sh

applications/jupyterlab/build_local.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+set -ex
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+time DOCKER_BUILDKIT=1 docker build $platform_flag -t myjlab -f Dockerfile .
+

applications/jupyterlab/pip_omv_info.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e
+
+# A script to print info versions of packages in the JupyterLab container
+
+docker run -t --rm --entrypoint /bin/bash myjlab  -c "pip3 list"
+echo "--------------------------------------------------------"
+docker run -t --rm --entrypoint /bin/bash myjlab  -c "omv list -V"

applications/jupyterlab/rebuild_local.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+set -ex
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+time DOCKER_BUILDKIT=1 docker build $platform_flag -t myjlab -f Dockerfile  --no-cache .
+

applications/jupyterlab/requirements.txt

@@ -6,7 +6,7 @@ neurotune
 neuron
 
 # Install specific version of NetPyNE
-git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne
+git+https://github.com/Neurosim-lab/netpyne.git@osbv2-dev#egg=netpyne
 
 ####  Other simulators
 

applications/jupyterlab/run_local.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e
+
+# A script to run the JupyterLab container locally (build it first with ./build_local.sh)
+
+docker run --network host -it --rm  --name myjupyterlab myjlab 
+
+