Merge pull request #18 from NeuralEnsemble/test_pynn011

To NEST_VER=3.5, NRN_VER=8.2.2, BRIAN2_VER=2.5.4, PYNN_VER=0.11.0

Author: pgleeson

.github/workflows/docker-image.yml

@@ -10,10 +10,21 @@ jobs:
 
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:        
+        runs-on: [ubuntu-latest ] # macos-13 takes too long to build nest
+
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
+    - name: Setup docker (missing on MacOS)
+      if: runner.os == 'macos'
+      run: |
+        brew install docker colima
+        colima start
     
     - name: Build the base Docker image
       run: |

base/Dockerfile

@@ -2,7 +2,7 @@
 # A base Docker image for Python-based computational neuroscience and neurophysiology
 #
 
-FROM neurodebian:focal
+FROM neurodebian:jammy
 MAINTAINER [email protected]
 
 ENV DEBIAN_FRONTEND noninteractive

base/regenerate.sh

@@ -1 +1,14 @@
-docker build -t neuralensemble/base --no-cache .
+#!/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 --no-cache .

osb/Dockerfile

@@ -14,7 +14,7 @@ MAINTAINER [email protected]
 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
 

osb/generate.sh

@@ -1 +1,14 @@
-docker build -t neuralensemble/osb .
+#!/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/osb .

osb/regenerate.sh

@@ -1,2 +1,15 @@
-docker build -t neuralensemble/osb --no-cache .
+#!/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/osb --no-cache .
 

osb/regenerateAll.sh

@@ -13,3 +13,4 @@ cd ../simulationx
 cd ../osb
 
 ./regenerate.sh
+

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
 

osb_models/generate.sh

@@ -1 +1,14 @@
-docker build -t osb_models_new .
+#!/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 osb_models_new .

osb_models/regenerate.sh

@@ -1 +1,14 @@
-docker build -t osb_models_new --no-cache .
+#!/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 osb_models_new --no-cache .