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pgleesonpgleeson
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Merge branch 'dev_netpyne_updates' into feature/repo_updates_via_api2
2 parents 0494f8e + f44774e commit ba82101

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‎.github/workflows/docker-jupyterlab.yml‎

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name: Docker Image Build Jupyterlab
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name: Docker Image Build JupyterLab
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on:
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push:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Build the Docker image
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run: |
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cd applications/jupyterlab
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docker build -t myjlab -f Dockerfile --no-cache .
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./build_local.sh
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- name: Info on Docker image sizes
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run: |
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docker images
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- name: Run the Docker container and list python installs
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run: |
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docker run -t --rm --entrypoint /bin/bash myjlab -c "pip3 list"
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cd applications/jupyterlab
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./pip_omv_info.sh

‎applications/accounts/deploy/resources/realm.json‎

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]
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},
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"clients": [
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{
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"id": "18893fbb-8252-4aaa-bc9b-60799ceb9932",
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"clientId": "account-console",
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"name": "${client_account-console}",
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"rootUrl": "${authBaseUrl}",
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"baseUrl": {{ printf "/realms/%s/account" .Values.namespace | quote }},
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"surrogateAuthRequired": false,
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"enabled": true,
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"alwaysDisplayInConsole": false,
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"clientAuthenticatorType": "client-secret",
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"redirectUris": [
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{{ printf "/realms/%s/account/*" .Values.namespace | quote }}
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],
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"webOrigins": [],
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"notBefore": 0,
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"bearerOnly": false,
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"consentRequired": false,
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"standardFlowEnabled": true,
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"implicitFlowEnabled": false,
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"directAccessGrantsEnabled": false,
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"serviceAccountsEnabled": false,
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"publicClient": true,
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"frontchannelLogout": false,
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"protocol": "openid-connect",
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"attributes": {
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"realm_client": "false",
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"post.logout.redirect.uris": "+",
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"pkce.code.challenge.method": "S256"
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},
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"authenticationFlowBindingOverrides": {},
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"fullScopeAllowed": false,
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"nodeReRegistrationTimeout": 0,
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"protocolMappers": [
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{
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"id": "9a68ec2d-943d-49cb-9fdd-cd821d606210",
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"name": "audience resolve",
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"protocol": "openid-connect",
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"protocolMapper": "oidc-audience-resolve-mapper",
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"consentRequired": false,
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"config": {}
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}
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],
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"defaultClientScopes": [
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"service_account",
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"web-origins",
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"acr",
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"address",
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"administrator-scope",
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"phone",
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"profile",
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"roles",
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"microprofile-jwt",
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"basic",
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"email"
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],
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"optionalClientScopes": []
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},
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{
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"id": "9a6a2560-c6be-4493-8bd5-3fdc4522d82b",
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"clientId": {{ .Values.apps.accounts.client.id | quote }},

‎applications/jupyterlab/build_local.sh‎

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

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

‎applications/jupyterlab/rebuild_local.sh‎

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

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neuron
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# Install specific version of NetPyNE
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git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne
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git+https://github.com/Neurosim-lab/netpyne.git@osbv2-dev#egg=netpyne
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#### Other simulators
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‎applications/jupyterlab/run_local.sh‎

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#!/bin/bash
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set -e
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# A script to run the JupyterLab container locally (build it first with ./build_local.sh)
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docker run --network host -it --rm --name myjupyterlab myjlab
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‎applications/netpyne/Dockerfile‎

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USER root
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### Some helpful aliases
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RUN echo -e '\n\nalias cd..="cd .." \nalias h=history \nalias ll="ls -alt" \n' >> ~/.bashrc
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RUN rm -rf /var/lib/apt/lists
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RUN apt-get update -qq &&\
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apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
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RUN apt-get install openjdk-11-jre-headless -y
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RUN apt-get install openjdk-11-jre-headless htop ncdu -y
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# RUN conda install python=3.7 -y
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‎applications/netpyne/deploy/values.yaml‎

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harness:
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subdomain: netpyne
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secured: true
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secured: false
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uri_role_mapping: []
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service:
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auto: false

‎applications/osb-portal/src/components/MainDrawer/MainDrawer.tsx‎

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<ListItemIcon>
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<HomeIcon />
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</ListItemIcon>
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<ListItemText primary="Main site" />
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<ListItemText primary="OSB homepage" />
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</ListItemButton>
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<ListItemButton

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