Installation

Conda

lsmgridtrack is designed for use with conda package manager, or its optimized fork mamba. There are multiple packages that provide conda. Currently, the smallest, fastest, and thus recommended package is mambaforge.

To install the current release

lsmgridtrack depends on packages outside of the default conda channels, so we need to add these. The order also matters, because this determines channel priority.

conda config --add channels SimpleITK
conda config --add channels siboles
conda config --add channels conda-forge

Note

If mambaforge or miniforge is used, conda-forge, will be added by default, in which case the last line will have no effect.

In a conda environment

By installing lsmgridtrack into its own conda environment it is guaranteed to not interfere with your system or other environments. Therefore, this approach is the most recommended. This can be accomplished in one command line entry.

mamba create -n [ENVIRONMENT_NAME] lsmgridtrack

Note

This assumes mambaforge. Substitute conda for mamba if another manager was installed.

This creates an environment named whatever you replace [ENVIRONMENT_NAME] with. By providing the last argument, lsmgridtrack, the package will be installed into the newly created environment along with all the dependencies it requires.

To use lsmgridtrack this environment will need to be active. In a command terminal, type:

conda activate [ENVIRONMENT_NAME]

You should see the command prompt change to include (ENVIRONMENT_NAME) in parentheses.

To change to a different environment type the above command with the new environment name. To deactivate the environment type:

conda deactivate

To install the latest code from the github repository

The source code can be downloaded from GitHub or if git is installed cloned with:

git clone https://github.com/siboles/lsmgridtrack.git

It is recommended to follow the prior instructions to create a conda environment from the released version first. With this environment active, navigate to the root level of the cloned repository where setup.py is located. Then install with:

python -m pip install -vv

If you have previously cloned the git repository, it can be updated to the latest version with:

git pull