Fix jlab deployment

Author: filippomc

applications/jupyterlab/Dockerfile

@@ -4,24 +4,22 @@ USER root
 
 ####  General packages via apt-get
 
-RUN apt-get update &&  apt-get install graphviz openjdk-11-jre-headless git vim htop ncdu make cmake libncurses-dev g++ -y
-
+RUN apt-get update &&  apt-get install -y graphviz openjdk-11-jre-headless git vim htop ncdu make cmake libncurses-dev g++ \
+    #LFPy dependencies
+    libopenmpi-dev \ 
+    #  Octave etc.
+    octave octave-statistics
 ################################################################################
 
 
-#### Install needed linux packages
-
-USER root
-# LFPy
-RUN apt-get update && apt-get install libopenmpi-dev -y
-
-####  Octave etc.
-RUN apt-get update && apt-get install octave octave-statistics -y
 
 #### Install Python packages
 USER jovyan
 COPY requirements.txt requirements.txt  
-RUN pip install -r requirements.txt --upgrade --no-cache-dir
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip setuptools &&\
+    pip install -r requirements.txt --upgrade --no-cache-dir
+
+RUN conda install pytorch torchvision cpuonly -c pytorch
 
 ####  General Python packages
 ####RUN jupyter labextension install plotlywidget
@@ -77,14 +75,9 @@ RUN wget --no-verbose -P `pip show LFPykit | grep "Location:" | awk '{print $2"/
 ARG NOCACHE
 
 USER root
-# LFPy 
-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_VER=3.8
 ENV NEST_HOME=/opt/conda/nest
 RUN cd /tmp && \
     wget -nv https://github.com/nest/nest-simulator/archive/v$NEST_VER.tar.gz && \
@@ -103,7 +96,7 @@ USER jovyan
 
 #### Install Python packages
 
-RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip && \ 
     pip install backports.tarfile>=1.2 # temp fix for error: ImportError: cannot import name 'tarfile' from 'backports'
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
     pip install -r requirements.txt --upgrade --no-cache-dir
@@ -117,14 +110,15 @@ RUN git clone https://github.com/NeuroML/NeuroML2
 # Install XPP
 RUN git clone https://github.com/NeuroML/xppaut
 USER root
-RUN apt install -y libx11-dev && cd xppaut && make -j4
+RUN apt-get update && apt install -y libx11-dev && cd xppaut && make -j4
 USER jovyan
 ENV XPP_HOME=/home/jovyan/xppaut
 ENV PATH=$PATH:$XPP_HOME
 
 #########################################################################
 # fix for https://github.com/jupyter/notebook/issues/7048
-RUN pip install traitlets==5.9.0
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
+    pip install traitlets==5.9.0
 
 COPY --chown=jovyan:users overrides/* /opt/conda/share/jupyter/lab/static/
 RUN cp /opt/conda/share/jupyter/lab/static/main*.js /opt/conda/share/jupyter/lab/static/main.js

applications/jupyterlab/requirements.txt

@@ -1,13 +1,9 @@
-setuptools>=80.9.0
-# temporary fix until new NEST releases are made with the fix: https://github.com/nest/nest-simulator/issues/3495
-cython<3.1.0
-
 pyneuroml
 pyelectro
 git+https://github.com/NeuralEnsemble/neurotune.git
 
 ####  NEURON & NetPyNE
-neuron==8.2.6
+neuron==8.2.7
 
 # Install specific version of NetPyNE
 git+https://github.com/Neurosim-lab/netpyne.git@osbv2#egg=netpyne
@@ -44,9 +40,6 @@ seaborn
 
 ####  Machine learning libs
 
-# 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==2.3.0+cpu
 
 # For MDF
 modeci_mdf
@@ -71,8 +64,8 @@ plotly
 
 
 #### Install OMV
-OSBModelValidation==0.3.5
+OSBModelValidation==0.3.8
 
 
 ####  Final updates
-numpy  # Removes some issues with LFPy...
+numpy>=2.0.0  # Removes some issues with LFPy...