From 31c958d81c55ce478a757a18dce155ffbe5c4c4c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 21 Aug 2025 11:44:00 +0100 Subject: [PATCH 1/3] Test build OSB forrk/branch --- applications/netpyne/deploy/values.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/applications/netpyne/deploy/values.yaml b/applications/netpyne/deploy/values.yaml index 69f9a87d5..e55d6abd0 100644 --- a/applications/netpyne/deploy/values.yaml +++ b/applications/netpyne/deploy/values.yaml @@ -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 From fd8842e817176fdb30008489e289cf53e1b2a0ba Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 21 Aug 2025 13:09:38 +0100 Subject: [PATCH 2/3] Update requirements for latest netpyne and neuroml libraries --- applications/netpyne/overrides/requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/applications/netpyne/overrides/requirements.txt b/applications/netpyne/overrides/requirements.txt index 5326f342c..7640ea03c 100644 --- a/applications/netpyne/overrides/requirements.txt +++ b/applications/netpyne/overrides/requirements.txt @@ -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 @@ -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 @@ -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 From be3630504b09ad9d3799204b724ff1aff5239daa Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 21 Aug 2025 14:51:20 +0100 Subject: [PATCH 3/3] Quicker download of head model --- applications/netpyne/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/applications/netpyne/Dockerfile b/applications/netpyne/Dockerfile index eca06eea7..3b1ed003d 100644 --- a/applications/netpyne/Dockerfile +++ b/applications/netpyne/Dockerfile @@ -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 @@ -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