Potts.jl

Potts.jl is a Cellular Potts modeling system for Julia. The repository contains four independently testable Julia packages:

• PottsToolkit: the repository-root biological authoring interface.
• CorePotts: the scientific execution engine and advanced extension interface.
• MakiePotts: native Makie recipes over explicit, host-owned render frames.
• ProcessBigraphs: a domain-neutral runtime for composing multirate scientific processes.

The historical Potts umbrella package and pre-freeze engine have been removed. ProcessBigraphs remains pre-1.0 and is documented independently; its availability does not imply complete Process-Bigraph 2.0 parity.

Installation

Until the package family is registered, install PottsToolkit directly from the repository root:

using Pkg
Pkg.add(url = "https://github.com/PraneethMerugu/Potts.jl", subdir = "lib/ProcessBigraphs")
Pkg.add(url = "https://github.com/PraneethMerugu/Potts.jl", subdir = "lib/CorePotts")
Pkg.add(url = "https://github.com/PraneethMerugu/Potts.jl")

CorePotts is installed explicitly because user scripts import it directly for execution. Add the lib/MakiePotts subdirectory as a direct dependency when using visualization.

For development:

using Pkg
Pkg.develop(path="lib/ProcessBigraphs")
Pkg.develop(path="lib/CorePotts")
Pkg.develop(path=".")

The package family supports Julia 1.12 and later Julia 1.x releases. See CONTRIBUTING.md for the complete development commands.

Documentation

julia --project=docs --startup-file=no -e 'using Pkg; Pkg.instantiate(; julia_version_strict=true)'
julia --project=docs --startup-file=no docs/make.jl

The manual is organized as Learn, Examples, Published Models, Concepts and Guarantees, and API. Documentation builds are strict and executable. API compatibility is assigned by curated inventories and guarantee metadata, not merely by whether a name is exported.