How to install Brain Modeling Toolkit (BMTK) on Ubuntu 24.04 LTS on VMWare Fusion Pro

Author: Mari Iura (M1), Yamazaki Lab.

This is a produre that I installed Brain Modeling Toolkit on a virtual machine of Ubuntu 24.04 LTS on VMWare Fusion Pro.

Environment

VMWare Fusion 13 Pro

Version

$ lsb_release -a
Distributor ID:    Ubuntu
Description:    Ubuntu 24.04 LTS
Release:    24.04
Codename:    noble

$ python3 -V
Python 3.12.3

Installation

Installed necessary packages as follows:

$ sudo apt install -y make build-essential zlib1g-dev git libssl-dev pkg-config libx11-dev bison flex automake libtool libxext-dev libncurses-dev xfonts-100dpi libopenmpi-dev libffi-dev libhdf5-dev python3-pip cython3 python3-dev python3-scipy neuron neuron-dev python3.12-venv

Built a virtual environment of Python:

$ python3 -m venv ~/bmtk_env

Activated the virtual environment:

$ source ~/bmtk_env/bin/activate

Installed further necessary packages:

(bmtk_env)$ pip3 install --upgrade pip setuptools wheel cython pkgconfig
(bmtk_env)$ pip3 install neuron numpy==1.26.4 h5py

Installed BMTK:

(bmtk_env)$ git clone https://github.com/AllenInstitute/bmtk.git 
(bmtk_env)$ cd bmtk
(bmtk_env)$ python3 setup.py install

Details of the installed BMTK

$ pip3 show bmtk
Name: bmtk
Version: 1.1.0
Summary: Brain Modeling Toolkit
Home-page: https://github.com/AllenInstitute/bmtk
Author: Kael Dai
Author-email: kaeld@alleninstitute.org
License: 
Location: /home/hogehoge/bmtk_env/lib/python3.12/site-packages/bmtk-1.1.0-py3.12.egg
Requires: h5py, jsonschema, matplotlib, numpy, pandas, pynrrd, scikit-image, scipy, six, sympy
Required-by: 

How to deactivate/reactivate the virtual environment of Python

Can deactivate the virtual environment of Python:

(bmtk_env)$ deactivate

Can reactivate the virtual environment:

$ source ~/bmtk_env/bin/activate