Building a python environment for kaiju on Ubuntu 20.04

Introduction

This file describes how to set up a python 3.8-based conda environment on an Intel-based machine running Ubuntu 20.04 which can be used to run the kaiju code.

These steps assume that pip (only) is used for installing additional packages, and packages are only taken from PyPI (and the default conda repository, if needed) - no other repositories are used.

A NOTE OF EXPLANATION: These instructions install miniconda3 into a Ubuntu 20.04-specific subdirectory of the home directory, to maintain compatibility with instructions for other systems. Feel free to install miniconda3 wherever is convenient.

Building the python environment

# Download the installer.
cd $HOME
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

# Run the installer.
# Install into $HOME/ubuntu-20.04/miniconda3, use all defaults.
bash ./Miniconda3-latest-MacOSX-x86_64.sh

# NOTE: This installation *should* run "conda init", which *should*
# add the conda setup code to ~/.bashrc or ~/.bash_profile.

# NOTE: This installation creates ~/.conda/environments.txt, but
# nothing else. This file just contains the path to the miniconda3
# installation directory.

# Turn off auto-activation of base environment.
# NOTE: This command creates ~/.condarc.
conda config --set auto_activate_base false

# Update everything to latest version.
conda update --all

# NOTE: This creates the directory ~/.cache/conda.

# Now create the environment for kaiju, specifying only the python version.
conda create -n kaiju-3.8 python=3.8

# NOTE: This adds the path to the new environment in
# ~/.conda/environments.txt.

# Activate the new environment.
conda activate kaiju-3.8

# Update everything to latest version.
conda update --all

# IMPORTANT: Use a pip cache specific to this machine.
export PIP_CACHE_DIR=$HOME/ubuntu-20.04/pip_cache

# Make sure CDF, HDF5, and GEOS have been built and installed.

# Install packages required by kaipy.
pip install -r requirements.txt

# Save the environment description.
conda list >& kaiju-3.8-ubuntu-20.04-YYYYMMDD.env

Where requirements.txt is a text file containing:

ai.cdas
alive_progress
cartopy
cdasws
cdflib
configparser
dataclasses_json
h5py
jinja2
matplotlib
netCDF4
progressbar
pyhdf
pytest
scipy
spacepy
sunpy
xarray

Using the python environment

Once your python environment is created, you must activate it for use with the kaiju software:

conda activate kaiju-3.8   # or whatever name you used for the python environment