From 21b498214d4eebeb3273f088fd1db061b78b629e Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 3 Jan 2018 22:53:51 +0100 Subject: [PATCH 1/3] For py3, update to NEST 2.14.0, NEURON 7.5, support NixIO --- LICENSE | 2 +- README.md | 2 +- base/Dockerfile | 4 ++-- simulation/Dockerfile | 2 +- simulation/README.md | 2 +- simulationx/README.md | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/LICENSE b/LICENSE index c84bb71..f5a1924 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2015 NeuralEnsemble +Copyright (c) 2015-2018 NeuralEnsemble Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 8fcbe16..b01696e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ## Available images: -- simulation: NEST 2.12, NEURON 7.4, and PyNN 0.9 and the scientific Python stack +- simulation: NEST 2.14, NEURON 7.5, PyNN 0.9 and the scientific Python stack - For **Python 3** use the [master branch](https://github.com/NeuralEnsemble/neuralensemble-docker/tree/master/simulation) - For **Python 2** use the [python2 branch](https://github.com/NeuralEnsemble/neuralensemble-docker/tree/python2/simulation) - simulationx: like "simulation", but with support for X11 forwarding over SSH diff --git a/base/Dockerfile b/base/Dockerfile index 89dac4b..73c6690 100644 --- a/base/Dockerfile +++ b/base/Dockerfile @@ -12,7 +12,7 @@ RUN apt-get update; apt-get install -y automake libtool build-essential openmpi- wget python3 libpython3-dev libncurses5-dev libreadline-dev libgsl0-dev cython3 \ python3-pip python3-numpy python3-scipy python3-matplotlib python3-jinja2 python3-mock \ ipython3 python3-httplib2 python3-docutils python3-yaml \ - subversion python3-venv python3-mpi4py python3-tables cmake + subversion python3-venv python3-mpi4py python3-tables python3-h5py cmake RUN useradd -ms /bin/bash docker USER docker @@ -26,5 +26,5 @@ 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 django-tagging future hgapi gitpython sumatra +RUN $VENV/bin/pip3 install parameters quantities neo django django-tagging future hgapi gitpython sumatra nixio RUN $VENV/bin/pip3 install --upgrade nose ipython diff --git a/simulation/Dockerfile b/simulation/Dockerfile index 432c5db..b62ca2d 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -5,7 +5,7 @@ FROM neuralensemble/base MAINTAINER andrew.davison@unic.cnrs-gif.fr -ENV NEST_VER=2.12.0 NRN_VER=7.4 +ENV NEST_VER=2.14.0 NRN_VER=7.5 ENV NEST=nest-$NEST_VER NRN=nrn-$NRN_VER ENV PATH=$PATH:$VENV/bin RUN ln -s /usr/bin/2to3-3.4 $VENV/bin/2to3 diff --git a/simulation/README.md b/simulation/README.md index 6c2460e..b373dd2 100644 --- a/simulation/README.md +++ b/simulation/README.md @@ -2,7 +2,7 @@ ## What it gives you -* shell environment with NEST 2.12, NEURON 7.4, and PyNN 0.9 installed. +* shell environment with NEST 2.14, NEURON 7.5, and PyNN 0.9 installed. * The Python 2.7 version provides Brian 1.4, the Python 3.4 version provides Brian 2. * IPython, scipy, matplotlib and OpenMPI are also installed. * use directly or as a base for your own project-specific Docker images. diff --git a/simulationx/README.md b/simulationx/README.md index 5edd37c..6a3351a 100644 --- a/simulationx/README.md +++ b/simulationx/README.md @@ -3,7 +3,7 @@ ## What it gives you -* shell environment with NEST 2.12, NEURON 7.4, and PyNN 0.9 installed. +* shell environment with NEST 2.14, NEURON 7.5, and PyNN 0.9 installed. * The Python 2.7 version provides Brian 1.4, the Python 3.4 version provides Brian 2. * IPython, scipy, matplotlib and OpenMPI are also installed. * ssh access, so you can access the container with multiple terminals. From a147914ca3195cd896c087030301c059f224a1eb Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Wed, 3 Jan 2018 23:27:19 +0100 Subject: [PATCH 2/3] Install the correct version of Django for Sumatra --- base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/base/Dockerfile b/base/Dockerfile index 73c6690..2125c9f 100644 --- a/base/Dockerfile +++ b/base/Dockerfile @@ -26,5 +26,5 @@ ENV VENV=$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 django-tagging future hgapi gitpython sumatra nixio +RUN $VENV/bin/pip3 install parameters quantities neo "django<1.9" django-tagging future hgapi gitpython sumatra nixio RUN $VENV/bin/pip3 install --upgrade nose ipython From aebb1f3bfe95e343307da390d5fcae068ec4835e Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Thu, 4 Jan 2018 10:34:20 +0100 Subject: [PATCH 3/3] Roll back to NEURON 7.4, problems building 7.5 in the Docker image. --- simulation/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/simulation/Dockerfile b/simulation/Dockerfile index b62ca2d..b9e95b6 100644 --- a/simulation/Dockerfile +++ b/simulation/Dockerfile @@ -5,7 +5,7 @@ FROM neuralensemble/base MAINTAINER andrew.davison@unic.cnrs-gif.fr -ENV NEST_VER=2.14.0 NRN_VER=7.5 +ENV NEST_VER=2.14.0 NRN_VER=7.4 ENV NEST=nest-$NEST_VER NRN=nrn-$NRN_VER ENV PATH=$PATH:$VENV/bin RUN ln -s /usr/bin/2to3-3.4 $VENV/bin/2to3