From dae4453e17b7d034ce8d385028dadc6ecccf8725 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 21 Sep 2023 12:38:52 +0100 Subject: [PATCH 01/13] To pynn 0.11.0 --- simulation/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/simulation/Dockerfile b/simulation/Dockerfile index e019262..4ad0d48 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -13,7 +13,7 @@ RUN ln -s /usr/bin/2to3-3.5 $VENV/bin/2to3 ENV NEST_VER=3.3 ENV NRN_VER=8.1.0 ENV BRIAN2_VER=2.5.1 -ENV PYNN_VER=0.10.1 +ENV PYNN_VER=0.11.0 #### Install NEST From 162941eebc36eda4bd63e9751529a342b85f295e Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 21 Sep 2023 19:39:54 +0100 Subject: [PATCH 02/13] Initial tests... --- simulation/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/simulation/Dockerfile b/simulation/Dockerfile index 4ad0d48..821bdaf 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -10,8 +10,8 @@ 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 NEST_VER=3.5 +ENV NRN_VER=8.2.2 ENV BRIAN2_VER=2.5.1 ENV PYNN_VER=0.11.0 From 3730c37b2899eb2045e8ce9918d2ae78d65d9264 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 22 Sep 2023 10:07:32 +0100 Subject: [PATCH 03/13] Updated to use neurodebian:jammy --- base/Dockerfile | 2 +- osb/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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 8ed7e85..5929f44 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 From 80b6718ad7c6c850e6a01b8d3c74237d10147e8b Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 22 Sep 2023 14:26:35 +0100 Subject: [PATCH 04/13] Tweak for ca1 model --- osb_models/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 From c0d472f78dbc341e77400c900df5bf5894f0d442 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 26 Sep 2023 10:06:07 +0100 Subject: [PATCH 05/13] Update omv & brian versions --- osb/Dockerfile | 4 ++-- simulation/Dockerfile | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 5929f44..8eef81a 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -23,7 +23,7 @@ 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=v0.2.12 +ENV OMV_VER=v0.2.13 ENV PYNEUROML_VER=1.1.1 ENV NETPYNE_VER=1.0.5 @@ -37,7 +37,7 @@ RUN $VENV/bin/pip install pyNeuroML==$PYNEUROML_VER # will set versions of libNe # Install OMV -RUN $VENV/bin/pip install git+https://github.com/OpenSourceBrain/osb-model-validation@v0.2.11 +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 diff --git a/simulation/Dockerfile b/simulation/Dockerfile index 821bdaf..d43b3db 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -12,7 +12,7 @@ RUN ln -s /usr/bin/2to3-3.5 $VENV/bin/2to3 ENV NEST_VER=3.5 ENV NRN_VER=8.2.2 -ENV BRIAN2_VER=2.5.1 +ENV BRIAN2_VER=2.5.4 ENV PYNN_VER=0.11.0 From 16fa25c9e08313f3d8ad8394b7dc6604c6ab3acc Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 1 May 2024 17:39:11 +0100 Subject: [PATCH 06/13] Update gha version --- .github/workflows/docker-image.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 4625688..21c182f 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Build the base Docker image run: | From a504baf4467588c4373248ec37d1d272fbbe88a2 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 2 May 2024 15:19:25 +0100 Subject: [PATCH 07/13] Update to latest omv versions --- osb/Dockerfile | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 8eef81a..a189124 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -23,11 +23,12 @@ RUN /bin/bash -c "source ~/env/neurosci/bin/activate" #### Set versions # This will set the versions of simulators installed with 'omv install ...' -ENV OMV_VER=v0.2.13 +ENV OMV_VER=v0.2.21 -ENV PYNEUROML_VER=1.1.1 -ENV NETPYNE_VER=1.0.5 -ENV EDEN_VER=0.2.2 +ENV PYNEUROML_VER=1.2.12 +ENV NETPYNE_VER=1.0.6 +# omv install arbor with 0.9.0 throwing 'Illegal instruction'..? +ENV ARBOR_VER=0.8.1 # Install NeuroML Python libraries @@ -97,18 +98,18 @@ RUN omv install moose # Install Arbor -RUN omv install arbor +RUN omv install arbor:$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<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 # Some aliases From 4370374617198d4b95c5bc6375420d49f2fdbfd6 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 11 Jun 2024 18:35:46 +0100 Subject: [PATCH 08/13] Test latest omv --- osb/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index a189124..210bf8b 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -23,7 +23,7 @@ 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=v0.2.21 +ENV OMV_VER=v0.2.22 ENV PYNEUROML_VER=1.2.12 ENV NETPYNE_VER=1.0.6 From cfcba0bd04dc3f2effec0c55b7770d3a94cbc54a Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 11 Jun 2024 19:02:44 +0100 Subject: [PATCH 09/13] Bump version of pyneuroml to use --- osb/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 210bf8b..5af296d 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -25,7 +25,7 @@ RUN /bin/bash -c "source ~/env/neurosci/bin/activate" # This will set the versions of simulators installed with 'omv install ...' ENV OMV_VER=v0.2.22 -ENV PYNEUROML_VER=1.2.12 +ENV PYNEUROML_VER=1.3.0 ENV NETPYNE_VER=1.0.6 # omv install arbor with 0.9.0 throwing 'Illegal instruction'..? ENV ARBOR_VER=0.8.1 From 0e83ed8d1e5e6414c336050d3af23a2649108081 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 17 Jun 2024 17:34:47 +0100 Subject: [PATCH 10/13] Ensure numpy<2.0.0 --- osb/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 210bf8b..a645edb 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -109,7 +109,7 @@ 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 From b807c84060e0a3469fc4d4b9534f2e4f9bdba9a9 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 18 Jun 2024 17:36:40 +0100 Subject: [PATCH 11/13] Use latest omv and pyneuroml --- osb/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 087b29c..298fd02 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -23,9 +23,9 @@ 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=v0.2.22 +ENV OMV_VER=v0.3.2 -ENV PYNEUROML_VER=1.3.0 +ENV PYNEUROML_VER=1.3.2 ENV NETPYNE_VER=1.0.6 # omv install arbor with 0.9.0 throwing 'Illegal instruction'..? ENV ARBOR_VER=0.8.1 From 2c0a37094374d5b3c7affc8b0d14d8535a79471a Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 19 Aug 2024 10:47:29 +0100 Subject: [PATCH 12/13] Use pip install... --- osb/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 298fd02..843eccf 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -83,7 +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 From c033049afc5de521fd9d3ae5283a40f85e101bf0 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 20 Aug 2024 16:09:04 +0100 Subject: [PATCH 13/13] Update versions of pynml & omv --- osb/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/osb/Dockerfile b/osb/Dockerfile index 298fd02..d8eef63 100644 --- a/osb/Dockerfile +++ b/osb/Dockerfile @@ -23,9 +23,9 @@ 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=v0.3.2 +ENV OMV_VER=v0.3.3 -ENV PYNEUROML_VER=1.3.2 +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 @@ -83,7 +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