Create a conda environment for working with brain images in Jupyter

create_env.sh

#!/usr/bin/env bash
#
# use the following command to run this script: source ./create_env.sh
#
# ** `source` in the above command is necessary for this script to run correctly **
#
# Created on: May 14, 2021
# Author: Jacob Reinhold ([email protected])

if [[ "$OSTYPE" != "linux-gnu" && "$OSTYPE" != "darwin"* ]]; then
    echo "Operating system must be either linux or OS X"
    return 1
fi

command -v conda >/dev/null 2>&1 || { echo >&2 "anaconda required but not installed. Aborting."; return 1; }

# first make sure conda is up-to-date
conda update -n base conda --yes

packages=(
    jupyterlab
    matplotlib
    nb_conda
    numpy
    pandas
    scikit-image
    scikit-learn
    scipy
)

conda_forge_packages=(
    ipywidgets
    jupyterlab_widgets
    nibabel
    nilearn
)

conda create --override-channels -c defaults -n neuroimage python=3.8 "${packages[@]}" -y
conda activate neuroimage
conda install --override-channels -c defaults -c conda-forge "${conda_forge_packages[@]}" -y
pip install git+git://github.com/jcreinhold/niwidgets # PyPI package seems broken.

echo "create_env.sh script finished"