From 072e346d82a17c8ea1c4326e1de62722b212464c Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 5 Mar 2024 11:41:51 +0000
Subject: [PATCH 1/2] Update Arbor, torch and mdf

---
 applications/jupyterlab/requirements.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/applications/jupyterlab/requirements.txt b/applications/jupyterlab/requirements.txt
index c822378c..20718921 100644
--- a/applications/jupyterlab/requirements.txt
+++ b/applications/jupyterlab/requirements.txt
@@ -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
@@ -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

From 9d2377a9c93200f52e1c92b859e1e7e45088ae28 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 5 Mar 2024 18:07:47 +0000
Subject: [PATCH 2/2] Installs NEST, OMV, sbml libs

---
 applications/jupyterlab/Dockerfile       | 28 ++++++++++++++++++++++--
 applications/jupyterlab/requirements.txt | 10 +++++++++
 2 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/applications/jupyterlab/Dockerfile b/applications/jupyterlab/Dockerfile
index 151473ad..ecf6a4e4 100644
--- a/applications/jupyterlab/Dockerfile
+++ b/applications/jupyterlab/Dockerfile
@@ -31,7 +31,6 @@ RUN pip install -r requirements.txt --upgrade --no-cache-dir
 RUN jupyter labextension install plotlywidget
 
 
-
 ##############
 
 USER root
@@ -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
 
 
@@ -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
diff --git a/applications/jupyterlab/requirements.txt b/applications/jupyterlab/requirements.txt
index 20718921..9f0bb0c5 100644
--- a/applications/jupyterlab/requirements.txt
+++ b/applications/jupyterlab/requirements.txt
@@ -57,8 +57,18 @@ tvb-data
 ipympl
 
 
+####  SBML/COMBINE packages
+python-libsbml
+tellurium
+
+
 ####  General Python packages
 plotly
 
+
+#### Install OMV
+git+https://github.com/OpenSourceBrain/osb-model-validation.git@v0.2.15
+
+
 ####  Final updates
 numpy  # Removes some issues with LFPy...
\ No newline at end of file