Installation

PyPI (pip)

Note

The commands below use $ pip, however $ python -m pip is often a safer choice. It is possible for the $ pip executable to point to a different version of Python than the $ python executable. Using $ python -m pip at least ensures that the package is installed against the Python interpreter in use. The issue is further compounded on systems that also have $ python3 and $ pip3 executables, or executables for specific versions of Python like $ python3.11 and $ pip3.11.

ISOFIT can be installed from the Python Package Index with:

$ pip install isofit

In order to support a wide variety of environments, ISOFIT does not overly constrain its dependencies, however this means that in some cases pip can take a very long time to resolve ISOFIT’s dependency tree. Some users may need to provide constraints for specific packages, or install ISOFIT last. pip also supports installing from a remote git repository – this installs against the main branch:

$ pip install "git+https://github.com/isofit/isofit.git@main"

Manual (GitHub)

We recommend using Mamba to create a virtual environment:

$ git clone https://github.com/isofit/isofit
$ mamba env create -f isofit/recipe/isofit.yml
$ mamba activate isofit_env
$ pip install -e ./isofit

Developers may need to install additional packages provided by alternative YAML files in the recipe directory:

$ micromamba install --name isofit_env --file ISOFIT/recipe/docker.yml

Alternatively, you may also use uv for installing ISOFIT from source:

$ uv sync

The above command will install the default python version and pinned packages that are confirmed to be working with ISOFIT. Once installed, the CLI can be accessed via uv run:

$ uv run isofit --help

Alternatively, activate the virtual environment to skip the uv run command:

$ source .venv/bin/activate
$ isofit --help

For additional packages, such as those required for development:

$ uv sync --extra dev

Advanced users may switch python versions via:

$ uv python pin 3.13
$ uv sync

Downloading Extra Files

Once ISOFIT is installed, the CLI provides an easy way to download additional files that may be useful. These can be acquired via the isofit download command, and the current list of downloads we support is available via isofit download --help. See data for more information.

> _NOTE:_ The default location for downloading extra files is ~/.isofit/. First time invoking the ISOFIT CLI will instantiate this directory and an isofit.ini file for storing the paths to downloaded products.

Setting Environment Variables

Depending on the selected RTM, specific environment variables pointing to the RTM’s base directory have to be set prior to running ISOFIT. In the following, general instructions on how to set these variables on MacOS, Linux and Windows are provided.

MacOS

  • Most MacOS systems load environment variables from the user’s .bash_profile configuration file. Open this file with your preferred text editor, such as vim:

vim ~/.bash_profile

  • Add this line to your .bash_profile:

export VARIABLE_NAME=DIRECTORY (use your actual path)

  • Save your changes and run:

source ~/.bash_profile

Linux

  • Most Linux profiles use either bash or csh/tcsh shells. These shells load environment variables from the user’s .bashrc or .cshrc configuration files.

  • (BASH) Add this parameter to the .bashrc (see MacOS description):

export VARIABLE_NAME=DIRECTORY (use your actual path)

  • (T/CSH) Add this parameter to the .cshrc (see MacOS description):

setenv VARIABLE_NAME=DIRECTORY (use your actual path)

Windows

  • Using a command prompt, type one of the following:

setx /M VARIABLE_NAME "DIRECTORY" (use your actual path)

setx VARIABLE_NAME "DIRECTORY" (use your actual path)

ISOFIT variables

The following environment variables are actively used within ISOFIT:

Variable

Purpose

MKL_NUM_THREADS, OMP_NUM_THREADS

These control the threading of various packages within ISOFIT. It is important to set these to 1 to ensure ISOFIT performs to its fullest capabilities. By default, ISOFIT will insert these into the environment if they are not set and/or not set correctly.

ISOFIT_NO_SET_THREADS

This will disable automatically setting the MKL and OMP environment variables. Only recommended for advanced users that know what they are doing and can mitigate the consequences.

ISOFIT_DEBUG

Disables the ray package across ISOFIT to force single-core execution. Primarily used as a debugging tool by developers and is not recommended for normal use.