motile: Multi-Object Tracker using Integer Linear Equations

motile tracks multiple objects by solving a global optimization problem.

Read all about it in the documentation.

Installation

Motile depends on ilpy, which is currently only available via conda on the funkelab channel. ilpy in turn requires gurobi which is only available via the gurobi channel.

So, to create a new environment with motile:

conda create -n my_env -c conda-forge -c funkelab -c gurobi ilpy
conda activate my_env
pip install motile

or, to install into an existing environment:

conda install -c conda-forge -c funkelab -c gurobi ilpy
pip install motile

Development

git clone https://github.com/funkelab/motile  # or your fork
cd motile

# currently required to build ilpy dependency wheel
conda install scip

pip install -e .[dev]

Testing

pytest

Deployment

note for developers

To deploy a new version, first make sure to bump the version string in motile/__init__.py. Then create an annotated tag, and push it to github. This will trigger the deploy.yaml workflow to upload to PyPI

git tag -a vX.Y.Z -m vX.Y.Z
git push upstream --follow-tags

Building Documentation

pip install -e .[docs]
make docs && open docs/_build/html/index.html

# or to start a live-reloading server
make docs-watch