Importing a project

If you already have a PhysiCell project in PhysiCell/user_projects/ (or PhysiCell/sample_projects/), import it into your PhysiCellModelManager.jl project with importProject:

julia> importProject(path_to_project_folder)

path_to_project_folder can be an absolute path (recommended) or a path relative to where Julia was launched.

Input files

importProject assumes the standard PhysiCell/user_projects/ layout. The Default directory column is relative to path_to_project_folder.

Input	Default directory	Default name	Key	Optional
config	`config`	`PhysiCell_settings.xml`	`config`
main	`.`	`main.cpp`	`main`
Makefile	`.`	`Makefile`	`makefile`
custom modules	`.`	`custom_modules/`	`custom_modules`
rules	`config`	`cell_rules.{csv,xml}`	`rulesets_collection`	X
cell initial conditions	`config`	`cells.csv`	`ic_cell`	X
substrate initial conditions	`config`	`substrates.csv`	`ic_substrate`	X
ECM initial conditions	`config`	`ecm.csv`	`ic_ecm`	X
DC initial conditions	`config`	`dcs.csv`	`ic_dc`	X
intracellular model	`config`	`intracellular.xml`	`intracellular`	X

If a file is not in its standard location, pass a src dictionary keyed by the table above with paths relative to the Default directory. For example, if the config file is at config/config.xml:

julia> src = Dict("config" => "config.xml")
julia> importProject(path_to_project_folder; src=src)

Add more entries as a comma-separated list in Dict, or later with src[key] = rel_path.

Rulesets collection

The rulesets collection can be the base PhysiCell CSV or the drbergman/PhysiCell XML version. importProject looks for cell_rules.csv first, then cell_rules.xml.

Intracellular models

If the intracellular key is not provided and config/intracellular.xml is not found, importProject reads the config file for any intracellular models and assembles intracellular.xml from them.

Renaming the imported folders

After importing, update scripts/GenerateData.jl to reference the new project folders. By default, folder names come from the project name (with an integer appended if it already exists). To choose different names, pass a dest dictionary keyed as below:

Output	Key
config	`config`
custom code	`custom_code`
rulesets collection	`rulesets_collection`
cell initial conditions	`ic_cell`
substrate initial conditions	`ic_substrate`
ECM initial conditions	`ic_ecm`
DC initial conditions	`ic_dc`
intracellular	`intracellular`