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Installs NEST, OMV, sbml libs, updates mdf, pytorch in jupyterlab environment #915

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Mar 6, 2024
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Installs NEST, OMV, sbml libs, updates mdf, pytorch in jupyterlab environment #915

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072e346
Update Arbor, torch and mdf
pgleeson Mar 5, 2024
9d2377a
Installs NEST, OMV, sbml libs
pgleeson Mar 5, 2024
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28 changes: 26 additions & 2 deletions applications/jupyterlab/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@ RUN pip install -r requirements.txt --upgrade --no-cache-dir
RUN jupyter labextension install plotlywidget



##############

USER root
Expand All @@ -44,6 +43,10 @@ RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeu
RUN chmod +x /opt/conda/bin/jnml
ENV JNML_HOME=/opt/conda/bin

### Set up lems, reusing pynml jar
RUN echo -e '#!/bin/bash\n#Reusing the jNeuroML jar from the pip installed pyNeuroML for the lems command\n\njava -classpath /opt/conda/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-*-jar-with-dependencies.jar org.lemsml.jlems.viz.VizMain $@' >> /opt/conda/bin/lems
RUN chmod +x /opt/conda/bin/lems

RUN cat ~/.bashrc


Expand Down Expand Up @@ -84,13 +87,34 @@ RUN apt-get update && apt-get install libopenmpi-dev -y
# Octave etc.
RUN apt-get update && apt-get install octave octave-statistics -y

# NEST
ENV NEST_VER=3.5
ENV NEST_HOME=/opt/conda/nest
RUN cd /tmp && \
wget -nv https://github.com/nest/nest-simulator/archive/v$NEST_VER.tar.gz && \
tar xvzf v$NEST_VER.tar.gz && \
mv nest-simulator-$NEST_VER nest && \
cd nest && \
mkdir $NEST_HOME && \
apt-get install libgsl-dev -y && \
cmake -DCMAKE_INSTALL_PREFIX:PATH=$NEST_HOME -DPYTHON_EXECUTABLE:FILEPATH=/opt/conda/bin/python -DPYTHON_INCLUDE_DIR=/opt/conda/include/python3.9 . && \
make -j7 && \
make install
ENV PYTHONPATH=$NEST_HOME/lib/python3.9/site-packages
ENV PATH=$PATH:$NEST_HOME/bin

USER jovyan
#### Install Python packages
RUN pip install -r requirements.txt --upgrade --no-cache-dir

# Compile NEURON mod files for PyNN
RUN cd /opt/conda/lib/python3.9/site-packages/pyNN/neuron/nmodl && nrnivmodl
# See https://github.com/OpenSourceBrain/osb-model-validation/issues/91 for status of this
RUN pip install 'numpy<=1.23.0' # temp fix for https://levelup.gitconnected.com/fix-attributeerror-module-numpy-has-no-attribute-float-d7d68c5a4971

#########################################################################
# fix for https://github.com/jupyter/notebook/issues/7048

RUN pip install traitlets==5.9.0

COPY --chown=jovyan:users overrides/* /opt/conda/share/jupyter/lab/static/
WORKDIR /opt/workspace
16 changes: 13 additions & 3 deletions applications/jupyterlab/requirements.txt
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Expand Up @@ -11,7 +11,7 @@ git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne
#### Other simulators

# Arbor
arbor==0.6.0
arbor==0.9.0

# EDEN
eden-simulator==0.2.1
Expand Down Expand Up @@ -42,10 +42,10 @@ seaborn

# Note: this just installs pytorch for cpu, the default install adds a v large cuda lib
-f https://download.pytorch.org/whl/torch_stable.html
torch==1.11.0+cpu
torch==2.1.2+cpu

# For MDF
modeci_mdf==0.4.5 # big jump in size of image...
modeci_mdf==0.4.8 # big jump in size of image...

scikit-learn # Required for some Neuromatch Academy material
fasttext # Required for some Neuromatch Academy material
Expand All @@ -57,8 +57,18 @@ tvb-data
ipympl


#### SBML/COMBINE packages
python-libsbml
tellurium


#### General Python packages
plotly


#### Install OMV
git+https://github.com/OpenSourceBrain/[email protected]


#### Final updates
numpy # Removes some issues with LFPy...
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