Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

To NEST_VER=3.5, NRN_VER=8.2.2, BRIAN2_VER=2.5.4, PYNN_VER=0.11.0 #17

Open
wants to merge 17 commits into
base: test_pynn011
Choose a base branch
from
Open

To NEST_VER=3.5, NRN_VER=8.2.2, BRIAN2_VER=2.5.4, PYNN_VER=0.11.0 #17

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
dae4453
To pynn 0.11.0
pgleeson Sep 21, 2023
162941e
Initial tests...
pgleeson Sep 21, 2023
3730c37
Updated to use neurodebian:jammy
pgleeson Sep 22, 2023
80b6718
Tweak for ca1 model
pgleeson Sep 22, 2023
c0d472f
Update omv & brian versions
pgleeson Sep 26, 2023
16fa25c
Update gha version
pgleeson May 1, 2024
10e67a0
Merge pull request #8 from NeuralEnsemble/master
pgleeson May 2, 2024
1ca478a
Merge branch 'master' into test_pynn011
pgleeson May 2, 2024
a504baf
Update to latest omv versions
pgleeson May 2, 2024
4370374
Test latest omv
pgleeson Jun 11, 2024
cfcba0b
Bump version of pyneuroml to use
pgleeson Jun 11, 2024
0e83ed8
Ensure numpy<2.0.0
pgleeson Jun 17, 2024
f98bcb7
Merge branch 'test_pynn011' of github.com:pgleeson/neuralensemble-doc…
pgleeson Jun 17, 2024
b807c84
Use latest omv and pyneuroml
pgleeson Jun 18, 2024
2c0a370
Use pip install...
pgleeson Aug 19, 2024
c033049
Update versions of pynml & omv
pgleeson Aug 20, 2024
7909b8b
Merge branch 'test_pynn011' of github.com:pgleeson/neuralensemble-doc…
pgleeson Aug 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/docker-image.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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: |
Expand Down
2 changes: 1 addition & 1 deletion base/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
19 changes: 10 additions & 9 deletions osb/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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

Expand Down
3 changes: 2 additions & 1 deletion osb_models/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
8 changes: 4 additions & 4 deletions simulation/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down