Core

initializeModelManager()
initializeModelManager(path_to_project_dir::AbstractString)
initializeModelManager(path_to_physicell::AbstractString, path_to_data::AbstractString)

Initialize the PhysiCellModelManager.jl project model manager, identifying the data folder, PhysiCell folder, and loading the central database.

If no arguments are provided, it assumes that the PhysiCell and data directories are inside the current working directory.

Arguments

• path_to_project_dir::AbstractString: Path to the project directory. Must contain the PhysiCell and data subdirectories.
• path_to_physicell::AbstractString: Path to the PhysiCell directory.
• path_to_data::AbstractString: Path to the data directory.

PCMMException

Abstract supertype of every exception PhysiCellModelManager.jl raises on its own behalf.

Catch this to handle any PCMM-specific failure, or a concrete subtype to handle one condition. Errors raised by Julia itself or by a dependency are not part of this hierarchy.

Examples

try
    runStudio(1)
catch e
    e isa PCMMException || rethrow()   # a PCMM refusal, not a bug
    @info "PCMM could not do that" reason=sprint(showerror, e)
end

PCMMMissingProject(msg::String)

A PhysiCellModelManager.jl project could not be found.

Raised by initializeModelManager when neither the given nor the inferred paths hold a PhysiCell directory and a data directory. Auto-initialization on using PhysiCellModelManager catches this one and prints guidance instead of failing.

Fields

• msg::String: which paths were searched.

Examples

try
    initializeModelManager("not-a-project")
catch e
    e isa PCMMMissingProject && @info "no project there"
end

PCMMStudioLaunchError(cmd::Cmd, cause::Exception)

PhysiCell Studio could not be launched, or exited with an error.

Carries the command that was run and the underlying exception, which differs by failure mode: Base.IOError when the Python executable itself could not be spawned (a wrong PCMM_PYTHON_PATH), and ProcessFailedException when Studio ran and exited non-zero (a wrong PCMM_STUDIO_PATH, or a Studio-side error). Inspect cause to tell those apart.

Fields

• cmd::Cmd: the command PCMM ran.
• cause::Exception: the exception raised by run.

Examples

try
    runStudio(1)
catch e
    e isa PCMMStudioLaunchError || rethrow()
    e.cause isa Base.IOError ? @warn("check PCMM_PYTHON_PATH") : @warn("Studio itself failed")
end