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Dev netpyne updates #993

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31c958d
Test build OSB forrk/branch
pgleeson Aug 21, 2025
fd8842e
Update requirements for latest netpyne and neuroml libraries
pgleeson Aug 21, 2025
be36305
Quicker download of head model
pgleeson Aug 21, 2025
557d7ec
Merge pull request #992 from OpenSourceBrain/develop
pgleeson Aug 22, 2025
3e5593b
Revert change netpyne branch
filippomc Aug 22, 2025
08ef3cd
Merge branch 'develop' into dev_netpyne_updates
filippomc Aug 22, 2025
1860ff5
Consolidated download of nyhead.mat into one line
pgleeson Aug 26, 2025
6892d43
Allow a local directory, shared, to be accessed inside the docker con…
pgleeson Aug 26, 2025
2331908
Remove netpyne gatekeeper
filippomc Aug 26, 2025
f480acb
Merge branch 'dev_netpyne_updates' of github.com:OpenSourceBrain/OSBv…
filippomc Aug 26, 2025
9e54bfd
Merge branch 'dev_netpyne_updates' of github.com:OpenSourceBrain/OSBv…
pgleeson Aug 26, 2025
05ba58a
Minor changes in Dockerfile to aid admin bash scripting
pgleeson Aug 27, 2025
fa93fc8
Update About box: Add Gleeson lab, full url to logos
pgleeson Aug 27, 2025
94a9954
Patch keycloak bootstrap issue
filippomc Aug 28, 2025
3d54f1c
feat(local-script): do not make a skaffold failure stop minikube
sanjayankur31 Aug 28, 2025
f44774e
Updates to Jupyterlab: uses osbv2 netpyne branch & add scripts
pgleeson Aug 28, 2025
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6 changes: 4 additions & 2 deletions applications/netpyne/Dockerfile
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Expand Up @@ -16,7 +16,9 @@ RUN yarn build-dev
### Download on a separate stage to run in parallel with buildkit
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
RUN apt-get update -qq && apt-get install aria2 -y
RUN aria2c -j10 -x 10 https://www.parralab.org/nyhead/sa_nyhead.mat
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@filippomc filippomc Aug 22, 2025

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download and move are better done in one single command, as otherwise the file is present in 2 separate layers, increasing the image size

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@pgleeson pgleeson Aug 26, 2025

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Ok, have made that change. Use of aria2c seems to increase the speed of downloading, sometimes wget would be stuck for ages with the download.

RUN mv sa_nyhead.mat /nyhead.mat

###
FROM quay.io/jupyter/base-notebook:python-3.12
Expand Down Expand Up @@ -87,7 +89,7 @@ RUN ln -s /opt/workspace workspace

# RUN jupyter labextension disable @jupyterlab/hub-extension

COPY --from=downloads --chown=1000:1000 /nyhead.mat $NP_LFPYKIT_HEAD_FILE
COPY --from=downloads --chown=1000:1000 nyhead.mat $NP_LFPYKIT_HEAD_FILE
COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build

RUN chown -R $NB_UID /home/jovyan/.jupyter
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4 changes: 2 additions & 2 deletions applications/netpyne/deploy/values.yaml
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Expand Up @@ -21,8 +21,8 @@ harness:
hard:
- jupyterhub
git:
- url: https://github.com/MetaCell/NetPyNE-UI.git
branch_tag: 1.1.0
- url: https://github.com/OpenSourceBrain/NetPyNE-UI.git
branch_tag: osbv2_tests
singleuser:
cpu:
limit: 1
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10 changes: 5 additions & 5 deletions applications/netpyne/overrides/requirements.txt
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Expand Up @@ -71,7 +71,7 @@ jupyterthemes==0.20.0
kiwisolver==1.4.8
lesscpy==0.15.1
LFPykit==0.5.1
libNeuroML==0.5.1
libNeuroML==0.6.7
lxml==5.3.1
MarkupSafe==1.1.1
matplotlib==3.10.0
Expand All @@ -88,9 +88,9 @@ nbconvert==5.6.1
nbformat==5.2.0
ndindex==1.9.2
nest-asyncio==1.6.0
netpyne @ git+https://github.com/Neurosim-lab/netpyne.git@3d633bcda9a3ab3fe4a90b7c705cd3692a729185
netpyne @ git+https://github.com/Neurosim-lab/netpyne.git@osbv2-dev#egg=netpyne
networkx==3.4.2
neuromllite==0.5.4
neuromllite==0.6.1
NEURON==8.2.6
notebook==6.4.5
notebook_shim==0.2.3
Expand All @@ -117,9 +117,9 @@ pycparser==2.22
pyecore==0.15.2
pygeppetto==0.9.0
Pygments==2.19.1
PyLEMS==0.5.9
PyLEMS==0.6.8
pymongo==4.11.1
pyNeuroML==1.0.10
pyNeuroML==1.3.21
pyparsing==3.2.1
pytest==6.2.5
python-dateutil==2.9.0.post0
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4 changes: 2 additions & 2 deletions deployment/codefresh-dev.yaml
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Expand Up @@ -30,8 +30,8 @@ steps:
clone_NetPyNE-UI_git_netpyne:
title: Cloning NetPyNE-UI.git repository...
type: git-clone
repo: https://github.com/MetaCell/NetPyNE-UI.git
revision: dev_netpyne_updates
repo: https://github.com/OpenSourceBrain/NetPyNE-UI.git
revision: osbv2_tests
working_directory: applications/netpyne/dependencies/
git: github
clone_nwb-explorer_git_nwb-explorer:
Expand Down
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