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pgleeson wants to merge 3 commits into from
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Some netpyne updates #991

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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
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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
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 @@ -19,8 +19,8 @@ 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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