To NRN=8.2.7, BRIAN2=2.9.0, NEST 3.7 & latest pyneuroml & omv

.github/workflows/docker-image.yml

@@ -53,3 +53,7 @@ jobs:
     - name: Print info on docker images
       run: |
         docker images
+
+    - name: Test a number of repos from OSB
+      run: |
+        docker run -t  neuralensemble/osb   /bin/bash -c "git clone https://github.com/OpenSourceBrain/PyNNShowcase.git && cd PyNNShowcase && omv find && omv all -V" 

.gitignore

@@ -1,5 +1,5 @@
 .idea
-/base/generate.sh
 /simulationx/runLocal.sh
 /simulationx/regenerateAll.sh
 /base/runLocal.sh
+.DS_Store

base/Dockerfile

@@ -3,16 +3,17 @@
 #
 
 FROM neurodebian:jammy
-MAINTAINER [email protected]
+LABEL org.opencontainers.image.authors="[email protected],[email protected]"
+LABEL org.opencontainers.image.description="A base Docker image for Python-based computational neuroscience and neurophysiology"
 
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
 ENV LANG=C.UTF-8
 
-RUN apt-get update; apt-get install -y automake libtool build-essential openmpi-bin libopenmpi-dev git vim  \
-                       wget python3 libpython3-dev libncurses5-dev libreadline-dev libgsl0-dev cython3 \
-                       python3-numpy python3-scipy python3-matplotlib python3-jinja2 python3-mock \
-                       ipython3 python3-httplib2 python3-docutils python3-yaml \
-                       subversion python3-venv python3-mpi4py python3-tables python3-h5py cmake zlib1g-dev
+RUN apt-get update
+RUN apt-get install -y automake libtool build-essential openmpi-bin libopenmpi-dev git vim  \
+                       wget python3 libpython3-dev libncurses5-dev libreadline-dev libgsl0-dev \
+                       ipython3 \
+                       subversion python3-venv python3-mpi4py cmake zlib1g-dev
 
 RUN useradd -ms /bin/bash docker
 USER docker
@@ -26,5 +27,5 @@ ENV VENV=$HOME/env/neurosci
 RUN python3 -m venv $VENV && python3 -m venv --system-site-packages $VENV
 
 RUN $VENV/bin/pip3 install --upgrade pip
-RUN $VENV/bin/pip3 install parameters quantities neo django==1.8.19 django-tagging future hgapi gitpython sumatra nixio
+RUN $VENV/bin/pip3 install parameters quantities neo django-tagging future hgapi gitpython sumatra nixio
 RUN $VENV/bin/pip3 install --upgrade nose ipython

base/generate.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -ex
+
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+
+docker build  $platform_flag -t neuralensemble/base .

osb/Dockerfile

@@ -9,7 +9,8 @@
 #FROM neuralensemble/simulationx:py2_pynn094
 # For local testing
 FROM neuralensemble/simulationx
-MAINTAINER [email protected]
+LABEL org.opencontainers.image.authors="[email protected],[email protected]"
+LABEL org.opencontainers.image.description="A Docker image for running neuronal models from Open Source Brain. This image extends the basic simulationx image by adding support for libraries required for OSB models"
 
 USER root
 
@@ -23,9 +24,9 @@ RUN /bin/bash -c "source ~/env/neurosci/bin/activate"
 #### Set versions
 
 # This will set the versions of simulators installed with 'omv install ...'
-ENV OMV_VER=v0.3.3
+ENV OMV_VER=v0.3.10
 
-ENV PYNEUROML_VER=1.3.8
+ENV PYNEUROML_VER=1.3.21
 ENV NETPYNE_VER=1.0.6
 # omv install arbor with 0.9.0 throwing 'Illegal instruction'..?
 ENV ARBOR_VER=0.8.1  
@@ -38,15 +39,13 @@ RUN $VENV/bin/pip install pyNeuroML==$PYNEUROML_VER # will set versions of libNe
 
 # Install OMV
 
+RUN $VENV/bin/pip install scipy tables pythran pandas numexpr --upgrade 
 RUN $VENV/bin/pip install git+https://github.com/OpenSourceBrain/osb-model-validation@${OMV_VER}
 RUN sed -i -e s/'\/usr\/bin\/python'/'\/home\/docker\/env\/neurosci\/bin\/python'/g $VENV/bin/omv
 
 
 # Install jNeuroML, PyLEMS & NeuroML2
 
-RUN $VENV/bin/omv install jNeuroML  
-ENV JNML_HOME=$HOME/jnml/jNeuroMLJar
-
 RUN $VENV/bin/omv install jLEMS
 ENV LEMS_HOME=$HOME/jLEMS
 
@@ -109,7 +108,6 @@ USER root
 
 RUN which python
 
-RUN $VENV/bin/pip install 'numpy<2.0.0' # as there are still some packages not compliant with this 
 
 # Some aliases
 

osb/generateAll.sh

@@ -0,0 +1,16 @@
+set -e
+
+cd ../base
+./generate.sh
+
+cd ../simulation
+./generate.sh
+
+cd ../simulationx
+
+./generate.sh
+
+cd ../osb
+
+./generate.sh
+

simulation/Dockerfile

@@ -3,18 +3,21 @@
 #
 
 FROM neuralensemble/base
-MAINTAINER [email protected]
+LABEL org.opencontainers.image.authors="[email protected],[email protected]"
+LABEL org.opencontainers.image.description="A Docker image for running neuronal network simulations"
 
 RUN ln -s /usr/bin/2to3-3.5 $VENV/bin/2to3
 
 
 #### Set versions
 
-ENV NEST_VER=3.5
-ENV NRN_VER=8.2.2
-ENV BRIAN2_VER=2.5.4
+ENV NEST_VER=3.7
+ENV NRN_VER=8.2.7
+ENV BRIAN2_VER=2.9.0
 ENV PYNN_VER=0.11.0
 
+RUN $VENV/bin/pip install scipy tables pythran pandas numexpr matplotlib --upgrade 
+RUN $VENV/bin/pip install "cython<3.1.0"
 
 #### Install NEST
 
@@ -43,7 +46,7 @@ RUN mkdir $NEST; \
           -DPYTHON_LIBRARY=$VENV/lib/libpython3.8.so \
           -DPYTHON_INCLUDE_DIR=/usr/include/python3.8 \
           $HOME/packages/$NEST; \
-    make -j4; make install
+    make -j7; make install
 
 
 #### Install NEURON

simulationx/Dockerfile

@@ -6,7 +6,8 @@
 #
 
 FROM neuralensemble/simulation
-MAINTAINER [email protected]
+LABEL org.opencontainers.image.authors="[email protected],[email protected]"
+LABEL org.opencontainers.image.description="A Docker image for running neuronal network simulations. This image extends the basic simulation image by adding support for SSH access and Xwindows."
 
 USER root