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Merge pull request #949 from OpenSourceBrain/jupyterhub-update
Jupyterhub updates to PG test branch
2 parents 45358ef + 458f95d commit 58640a7

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‎.github/workflows/docker-netpyne.yml‎

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steps:
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- uses: actions/checkout@v3
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- name: Clone Netpyne UI dependencies
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run: |
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mkdir -p applications/netpyne/dependencies
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git clone --branch 1.1.0 https://github.com/MetaCell/NetPyNE-UI.git applications/netpyne/dependencies/NetPyNE-UI
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- name: Build the Docker image
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run: |

‎.github/workflows/docker-nwbe.yml‎

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- name: Clone NWB Explorer dependencies
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run: |
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mkdir -p applications/nwb-explorer/dependencies
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git clone https://github.com/MetaCell/nwb-explorer.git applications/nwb-explorer/dependencies/nwb-explorer
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git clone --branch development https://github.com/MetaCell/nwb-explorer.git applications/nwb-explorer/dependencies/nwb-explorer
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- name: Build the Docker image
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run: |

‎applications/accounts/docker-compose.yaml‎

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POSTGRES_USER: keycloak
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POSTGRES_PASSWORD: password
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keycloak:
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image: quay.io/keycloak/keycloak:16.1.0
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image: osb/accounts
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environment:
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DB_VENDOR: POSTGRES
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DB_ADDR: postgres

‎applications/jupyterlab/overrides/index.html‎

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<!doctype html>
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<html lang="en">
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<head><meta charset="utf-8"><title>JupyterLab</title><meta name="viewport" content="width=device-width,initial-scale=1">{# Copy so we do not modify the page_config with updates. #} {% set page_config_full = page_config.copy() %} {# Set a dummy variable - we just want the side effect of the update. #} {% set _ = page_config_full.update(baseUrl=base_url, wsUrl=ws_url) %}<script id="jupyter-config-data" type="application/json">{{ page_config_full | tojson }}</script>{% block favicon %}<link rel="icon" type="image/x-icon" href="{{ base_url | escape }}static/favicons/favicon.ico" class="idle favicon"><link rel="" type="image/x-icon" href="{{ base_url | escape }}static/favicons/favicon-busy-1.ico" class="busy favicon">{% endblock %}<script defer="defer" src="{{page_config.fullStaticUrl}}/main.006c51afc5ba8822ed23.js?v=006c51afc5ba8822ed23"></script></head>
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<head><meta charset="utf-8"><title>JupyterLab</title><meta name="viewport" content="width=device-width,initial-scale=1">{# Copy so we do not modify the page_config with updates. #} {% set page_config_full = page_config.copy() %} {# Set a dummy variable - we just want the side effect of the update. #} {% set _ = page_config_full.update(baseUrl=base_url, wsUrl=ws_url) %}<script id="jupyter-config-data" type="application/json">{{ page_config_full | tojson }}</script>{% block favicon %}<link rel="icon" type="image/x-icon" href="{{ base_url | escape }}static/favicons/favicon.ico" class="idle favicon"><link rel="" type="image/x-icon" href="{{ base_url | escape }}static/favicons/favicon-busy-1.ico" class="busy favicon">{% endblock %} {% if custom_css %}<link rel="stylesheet" href="{{ base_url | escape }}custom/custom.css">{% endif %}<script defer="defer" src="{{page_config.fullStaticUrl}}/main.ea7277c9c015ae398545.js?v=ea7277c9c015ae398545"></script></head>
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<body>
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<body class="jp-ThemedContainer">
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<script>/* Remove token from URL. */
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(function () {
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var location = window.location;

‎applications/netpyne/Dockerfile‎

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FROM gcr.io/metacellllc/netpyne-ui:1.1.1
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COPY overrides/requirements.txt overrides/requirements.txt
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FROM node:18 as jsbuild
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ARG APP_DIR=dependencies/NetPyNE-UI
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ENV FOLDER=netpyne
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WORKDIR $FOLDER/webapp
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COPY $APP_DIR/webapp/package.json .
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COPY $APP_DIR/webapp/yarn.lock .
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RUN yarn install --network-timeout 1000000000
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COPY $APP_DIR/webapp .
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RUN yarn build-dev
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### Download on a separate stage to run in parallel with buildkit
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FROM quay.io/jupyter/base-notebook:latest as downloads
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USER root
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RUN wget --no-check-certificate -O /nyhead.mat https://www.parralab.org/nyhead/sa_nyhead.mat
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###
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FROM quay.io/jupyter/base-notebook:latest
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ARG APP_DIR=dependencies/NetPyNE-UI
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ENV NB_UID=jovyan
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ENV FOLDER=netpyne
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ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
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USER root
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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 conda install python=3.7 -y
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WORKDIR $FOLDER
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COPY overrides/requirements.txt ./requirements.txt
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RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
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pip install -r overrides/requirements.txt
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pip install -r requirements.txt
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# ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default
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# and thus removes the frame ancestor cors settings
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RUN rm -f ~/.jupyter/*.json
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RUN chown $NB_UID .
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RUN chown $NB_UID /opt
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RUN rm -Rf workspace
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# sym link workspace pvc to $FOLDER
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RUN mkdir -p /opt/workspace
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RUN mkdir -p /opt/user
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COPY $APP_DIR/netpyne_ui netpyne_ui
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COPY $APP_DIR/utilities utilities
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COPY $APP_DIR/setup.py .
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COPY $APP_DIR/tests tests
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COPY $APP_DIR/NetPyNE-UI .
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COPY $APP_DIR/README.rst .
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COPY $APP_DIR/requirements-test.txt .
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USER $NB_UID
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ENV NEURON_HOME=/opt/conda
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USER root
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RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
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RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
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RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
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ARG BUILD_ARGS=""
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ARG WORKSPACE_VERSION=master
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RUN --mount=type=cache,target=/home/jovyan/.cache python -m pip install --upgrade pip &&\
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python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION --npm-skip --no-test
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RUN mv workspace /opt/workspace/tutorials
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RUN chown -R $NB_UID /opt/workspace
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RUN ln -s /opt/workspace workspace
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# RUN jupyter labextension disable @jupyterlab/hub-extension
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COPY --from=downloads --chown=1000:1000 /nyhead.mat $NP_LFPYKIT_HEAD_FILE
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COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build
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RUN chown -R $NB_UID /home/jovyan/.jupyter
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RUN touch app.log && chown $NB_UID app.log
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USER $NB_UID
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EXPOSE 8888
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EXPOSE 8888
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CMD jupyter notebook --NotebookApp.default_url=/geppetto --ServerApp.token='' --ServerApp.notebook_dir=workspace --library=netpyne_ui --ServerApp.disable_check_xsrf=True

‎applications/netpyne/dependencies/NetPyNE-UI‎

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Subproject commit 73c357ce07c9ddc6b2a77bfa32fd5e511e389818

‎applications/netpyne/deploy/values.yaml‎

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deployment:
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auto: false
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jupyterhub:
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args: ["--NotebookApp.default_url=/geppetto", "--library=netpyne_ui", "--NotebookApp.notebook_dir=/opt/workspace", "--NotebookApp.disable_check_xsrf=True"]
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args: ["--ServerApp.default_url=/geppetto", "--library=netpyne_ui", "--NotebookApp.notebook_dir=/opt/workspace", "--NotebookApp.disable_check_xsrf=True", '--NotebookApp.tornado_settings={"headers":{"Content-Security-Policy": "frame-ancestors *;"}}']
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applicationHook: "osb_jupyter.change_pod_manifest"
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extraConfig:
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timing: |
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dependencies:
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hard:
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- jupyterhub
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git:
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- url: https://github.com/MetaCell/NetPyNE-UI.git
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branch_tag: 1.1.0
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singleuser:
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cpu:
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limit: 1

‎applications/netpyne/overrides/requirements.txt‎

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lfpykit==0.5.1
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pyNeuroML>=0.7.5
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git+https://github.com/Neurosim-lab/netpyne.git@osbv2
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aiofiles==22.1.0
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aiosqlite==0.21.0
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airspeed==0.6.0
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anyio==3.7.1
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argon2-cffi==23.1.0
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argon2-cffi-bindings==21.2.0
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arrow==1.3.0
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asttokens==3.0.0
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attrs==25.1.0
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babel==2.17.0
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beautifulsoup4==4.13.3
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bleach==6.2.0
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blosc2==3.1.1
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bokeh
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cachetools==5.5.2
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cattrs==24.1.2
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certifi==2025.1.31
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cffi==1.17.1
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charset-normalizer==3.4.1
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comm==0.2.2
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contourpy==1.3.1
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cycler==0.12.1
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dacite==1.9.2
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debugpy==1.8.12
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decorator==5.2.1
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defusedxml==0.7.1
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Deprecated==1.2.18
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dnspython==2.7.0
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docstring_parser==0.16
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entrypoints==0.4
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executing==2.2.0
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fastjsonschema==2.21.1
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find_libpython==0.4.0
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fonttools==4.56.0
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fqdn==1.5.1
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future==1.0.0
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future-fstrings==1.2.0
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graphviz==0.20.3
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h11==0.14.0
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h5py==3.13.0
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httpcore==1.0.7
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httpx==0.28.1
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idna==3.10
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iniconfig==2.0.0
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ipykernel==6.20.2
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ipython==8.21.0
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ipython-genutils==0.2.0
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ipywidgets==8.1.5
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isoduration==20.11.0
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jedi==0.19.2
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Jinja2==2.11.2
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json5==0.10.0
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jsonpickle==4.0.2
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jsonpointer==3.0.0
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jsonschema==4.23.0
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jsonschema-specifications==2024.10.1
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jupyter==1.1.1
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jupyter-client==7.0.6
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jupyter-console==6.4.4
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jupyter-core==4.12.0
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# jupyter-events==0.12.0
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jupyter-geppetto==1.1.5
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jupyter-server==1.15.0
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jupyter-ydoc==0.2.5
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jupyter_server_ydoc==0.8.0
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jupyterlab==3.3.4
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jupyterlab_pygments==0.3.0
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jupyterlab-server==2.10.3
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jupyterlab_widgets==3.0.13
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jupyterthemes==0.20.0
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kiwisolver==1.4.8
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lesscpy==0.15.1
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LFPykit==0.5.1
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libNeuroML==0.5.1
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lxml==5.3.1
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MarkupSafe==1.1.1
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matplotlib==3.10.0
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matplotlib-inline==0.1.7
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matplotlib-scalebar==0.9.0
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MEAutility==1.5.2
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mistune==0.8.4
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modelspec==0.3.5
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msgpack==1.1.0
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multimethod==2.0
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nbclassic==0.3.7
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nbclient==0.10.2
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nbconvert==5.6.1
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nbformat==5.2.0
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ndindex==1.9.2
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nest-asyncio==1.6.0
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netpyne @ git+https://github.com/Neurosim-lab/netpyne.git@3d633bcda9a3ab3fe4a90b7c705cd3692a729185
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networkx==3.4.2
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neuromllite==0.5.4
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NEURON==8.2.6
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notebook==6.4.5
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notebook_shim==0.2.3
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numexpr==2.10.2
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numpy==1.26.4
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ordered-set==4.1.0
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packaging==24.2
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pandas==2.2.3
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pandocfilters==1.5.1
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parso==0.8.4
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pexpect==4.9.0
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pillow==11.1.0
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platformdirs==4.3.6
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pluggy==1.5.0
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ply==3.11
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prometheus_client==0.21.1
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prompt_toolkit==3.0.50
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psutil==7.0.0
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ptyprocess==0.7.0
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pure_eval==0.2.3
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py==1.11.0
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py-cpuinfo==9.0.0
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pycparser==2.22
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pyecore==0.15.2
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pygeppetto==0.9.0
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Pygments==2.19.1
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PyLEMS==0.5.9
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pymongo==4.11.1
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pyNeuroML==1.0.10
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pyparsing==3.2.1
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pytest==6.2.5
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python-dateutil==2.9.0.post0
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python-json-logger==3.2.1
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pytz==2025.1
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PyYAML==6.0.2
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pyzmq==26.2.1
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referencing==0.36.2
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requests==2.32.3
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RestrictedPython==8.0
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rfc3339-validator==0.1.4
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rfc3986-validator==0.1.1
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rpds-py==0.23.1
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schema==0.7.7
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scipy==1.15.2
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Send2Trash==1.8.3
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sentry-sdk==1.5.2
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setuptools==75.8.0
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six==1.17.0
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sniffio==1.3.1
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soupsieve==2.6
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stack-data==0.6.3
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tables==3.10.2
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tabulate==0.9.0
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terminado==0.18.1
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testpath==0.6.0
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tinycss2==1.4.0
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toml==0.10.2
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tornado==6.1
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tqdm==4.67.1
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traitlets==5.9.0
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jupyterhub>=4.0.0
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types-python-dateutil==2.9.0.20241206
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typing_extensions==4.12.2
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tzdata==2025.1
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uri-template==1.3.0
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urllib3==2.3.0
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wcwidth==0.2.13
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webcolors==24.11.1
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webencodings==0.5.1
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websocket-client==1.8.0
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wheel==0.45.1
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widgetsnbextension==4.0.13
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wrapt==1.17.2
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xyzservices==2025.1.0
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y-py==0.6.2
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ypy-websocket==0.8.4

‎applications/nfsserver/deploy/values-dev.yaml‎

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nfs:
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useDNS: true
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server:
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diskSize: 40Gi
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diskSize: 80Gi

‎applications/nwb-explorer/dependencies/nwb-explorer‎

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Subproject commit 20e799e0076d0f965154e2a484df1f998f9e1452
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Subproject commit ff44c209b71b119a1d9ede41550d555e362c76e8

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