diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 4625688..21c182f 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Build the base Docker image run: | diff --git a/base/Dockerfile b/base/Dockerfile index e7df23b..8e90170 100644 --- a/base/Dockerfile +++ b/base/Dockerfile @@ -2,7 +2,7 @@ # A base Docker image for Python-based computational neuroscience and neurophysiology # -FROM neurodebian:focal +FROM neurodebian:jammy MAINTAINER andrew.davison@unic.cnrs-gif.fr ENV DEBIAN_FRONTEND noninteractive diff --git a/osb/Dockerfile b/osb/Dockerfile index befbae5..d8eef63 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -14,7 +14,7 @@ MAINTAINER p.gleeson@gmail.com USER root RUN apt-get update -RUN apt-get install -y default-jdk python-tk python-lxml octave maven +RUN apt-get install -y default-jdk python-tk octave maven RUN apt-get install -y htop libxml2-dev libxslt-dev zlib1g-dev RUN apt-get install -y python3-setuptools unzip @@ -23,11 +23,12 @@ 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=v0.2.13 +ENV OMV_VER=v0.3.3 -ENV PYNEUROML_VER=1.1.1 -ENV NETPYNE_VER=1.0.5 -ENV EDEN_VER=0.2.2 +ENV PYNEUROML_VER=1.3.8 +ENV NETPYNE_VER=1.0.6 +# omv install arbor with 0.9.0 throwing 'Illegal instruction'..? +ENV ARBOR_VER=0.8.1 # Install NeuroML Python libraries @@ -82,7 +83,7 @@ RUN $VENV/bin/pip install netpyne==$NETPYNE_VER # Install OSB_API RUN git clone https://github.com/OpenSourceBrain/OSB_API.git -RUN cd OSB_API/python && python setup.py install && cd - +RUN cd OSB_API/python && pip install . && cd - # Install neuroConstruct @@ -97,18 +98,18 @@ RUN omv install moose # Install Arbor -RUN omv install arbor +RUN omv install arbor:$ARBOR_VER # Install EDEN -RUN $VENV/bin/pip install eden-simulator==$EDEN_VER +RUN omv install eden USER root RUN which python -RUN $VENV/bin/pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 +RUN $VENV/bin/pip install 'numpy<2.0.0' # as there are still some packages not compliant with this # Some aliases diff --git a/osb_models/Dockerfile b/osb_models/Dockerfile index d56ca02..1995b06 100644 --- a/osb_models/Dockerfile +++ b/osb_models/Dockerfile @@ -27,7 +27,8 @@ RUN cd coreprojects/SmithEtAl2013-L23DendriticSpikes/NEURON/test && nrnivmodl .. RUN cd coreprojects/L5bPyrCellHayEtAl2011/NEURON/test && nrnivmodl ../mod -RUN cd coreprojects/ca1/NeuroML2 && nrnivmodl .. +# Note: sgate.mod is not required and throws an error on later NEURON versions +RUN cd coreprojects/ca1 && rm sgate.mod && cd NeuroML2 && nrnivmodl .. RUN cd coreprojects/SadehEtAl2017-InhibitionStabilizedNetworks && ./make_tests.sh diff --git a/simulation/Dockerfile b/simulation/Dockerfile index e019262..d43b3db 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -10,10 +10,10 @@ RUN ln -s /usr/bin/2to3-3.5 $VENV/bin/2to3 #### Set versions -ENV NEST_VER=3.3 -ENV NRN_VER=8.1.0 -ENV BRIAN2_VER=2.5.1 -ENV PYNN_VER=0.10.1 +ENV NEST_VER=3.5 +ENV NRN_VER=8.2.2 +ENV BRIAN2_VER=2.5.4 +ENV PYNN_VER=0.11.0 #### Install NEST