Potts.jl

Welcome to Potts.jl, a Cellular Potts Model (Potts) simulation ecosystem for Julia.

Potts.jl is a monorepo containing several interconnected packages:

• CorePotts: The core physics and simulation engine for Cellular Potts Models.
• PottsToolkit: High-level utilities and domain-specific language (DSL) for defining simulations.
• MakiePotts: Visualization and interactive dashboard tools built on top of Makie.jl.
• NeuralPotts: Neural network integration for Cellular Potts Models.

Installation

Potts.jl acts as a meta-package that unifies several sub-packages. Because these sub-packages are not yet in the official Julia registry, you must first install them directly from their sub-directories using their GitHub URLs before installing the main Potts package.

Open the Julia REPL, type ] to enter the Pkg prompt, and run:

pkg> add https://github.com/PraneethMerugu/Potts.jl:lib/CorePotts
pkg> add https://github.com/PraneethMerugu/Potts.jl:lib/MakiePotts
pkg> add https://github.com/PraneethMerugu/Potts.jl:lib/NeuralPotts
pkg> add https://github.com/PraneethMerugu/Potts.jl:lib/PottsToolkit
pkg> add https://github.com/PraneethMerugu/Potts.jl

For development, you can clone the repository and develop the packages:

using Pkg
Pkg.develop(path="lib/CorePotts")
Pkg.develop(path="lib/PottsToolkit")
Pkg.develop(path="lib/MakiePotts")
Pkg.develop(path="lib/NeuralPotts")

Documentation

To build the documentation locally:

julia --project=docs/ -e 'using Pkg; Pkg.develop([PackageSpec(path="lib/" * pkg) for pkg in ["CorePotts", "PottsToolkit", "MakiePotts", "NeuralPotts"]]); Pkg.instantiate(); include("docs/make.jl")'

The documentation is built using Documenter.jl and is hosted on GitHub Pages.