Command Line Interface (CLI)¶

OpenCOR can be used from the CLI using the OpenCOR script, as illustrated below. Python-related scripts are also provided.

Help¶

$ ./OpenCOR -h
Usage: OpenCOR [-a|--about] [-c|--command [<plugin>]::<command> [<argument> ...]] [-e|--exclude <plugins>] [-h|--help] [-i|--include <plugins>] [-p|--plugins] [-r|--reset] [-s|--status] [-v|--version] [<files>]
 -a, --about     Display some information about OpenCOR
 -c, --command   Send a command to one or all the CLI plugins
 -e, --exclude   Exclude the given plugin(s)
 -h, --help      Display this help information
 -i, --include   Include the given plugin(s)
 -p, --plugins   Display all the CLI plugins
 -r, --reset     Reset all your settings
 -s, --status    Display the status of all the plugins
 -v, --version   Display the version of OpenCOR

About¶

$ ./OpenCOR -a
OpenCOR Version 0.7
macOS 13.0
Copyright 2011-2022

OpenCOR is a cross-platform modelling environment, which can be used to organise, edit, simulate and analyse CellML files.

Command¶

$ ./OpenCOR -c ::help
Commands supported by the CellMLTextView plugin:
 * Display the commands supported by the CellMLTextView plugin:
      help
 * Export a CellML Text <file> to CellML:
      export <file>
 * Import a CellML <file> to the CellML Text format:
      import <file>

Commands supported by the CellMLTools plugin:
 * Display the commands supported by the CellMLTools plugin:
      help
 * Export <file> to a given <format> or a given <language>:
      export <file> <format>|<language>
   <format> can take one of the following values:
      cellml_1_0: to export a CellML 1.1 file to CellML 1.0
   <language> can take one of the following values:
      c: to export a CellML file to C
      fortran_77: to export a CellML file to FORTRAN 77
      matlab: to export a CellML file to MATLAB
      python: to export a CellML file to Python
 * Validate <file>:
      validate <file>

Commands supported by the JupyterKernel plugin:
 * Display the commands supported by the JupyterKernel plugin:
      help
 * Start the OpenCOR Jupyter kernel:
      kernel <connectionFile>

Commands supported by the PythonShell plugin:
 * Display the commands supported by the PythonShell plugin:
      help
 * Run an interactive Python shell in OpenCOR's environment:
      [python] [<option> ...] [-c <command> | -m <module> | <file> | -] [<argument> ...]
   where
      -c <command> executes a program passed in as a string
      -m <module> runs a library module as a script
      <file> runs a program read from a script file
      - runs a program read from the standard input

$ ./OpenCOR -c CellMLTools::help
Commands supported by the CellMLTools plugin:
 * Display the commands supported by the CellMLTools plugin:
      help
 * Export <file> to a given <format> or a given <language>:
      export <file> <format>|<language>
   <format> can take one of the following values:
      cellml_1_0: to export a CellML 1.1 file to CellML 1.0
   <language> can take one of the following values:
      c: to export a CellML file to C
      fortran_77: to export a CellML file to FORTRAN 77
      matlab: to export a CellML file to MATLAB
      python: to export a CellML file to Python
 * Validate <file>:
      validate <file>

Exclude¶

$ ./OpenCOR -e Core HelpWindow Unknown
 - Core: cannot be directly excluded.
 - HelpWindow: excluded from the GUI version of OpenCOR.
 - Unknown: unknown plugin.

Include¶

$ ./OpenCOR -i Core HelpWindow Unknown
 - Core: cannot be directly included.
 - HelpWindow: included to the GUI version of OpenCOR.
 - Unknown: unknown plugin.

Plugins¶

$ ./OpenCOR -p
The following CLI plugins are available:
 - CellMLTextView: a plugin to edit CellML files using the CellML Text format.
 - CellMLTools: a plugin to access various CellML-related tools.
 - JupyterKernel: the Jupyter kernel plugin.
 - PythonShell: the Python shell plugin.

Reset¶

$ ./OpenCOR -r
All your settings have been reset.

Status¶

$ ./OpenCOR -s
The following plugins are available:
 - CellMLAPI: the plugin is loaded and fully functional.
 - CellMLEditingView: the plugin is loaded and fully functional.
 - CellMLSupport: the plugin is loaded and fully functional.
 - CellMLTextView: the plugin is loaded and fully functional.
 - CellMLTools: the plugin is loaded and fully functional.
 - COMBINESupport: the plugin is loaded and fully functional.
 - Compiler: the plugin is loaded and fully functional.
 - Core: the plugin is loaded and fully functional.
 - CVODESolver: the plugin is loaded and fully functional.
 - DataStore: the plugin is loaded and fully functional.
 - EditingView: the plugin is loaded and fully functional.
 - EditorWidget: the plugin is loaded and fully functional.
 - ForwardEulerSolver: the plugin is loaded and fully functional.
 - FourthOrderRungeKuttaSolver: the plugin is loaded and fully functional.
 - HeunSolver: the plugin is loaded and fully functional.
 - JupyterKernel: the plugin is loaded and fully functional.
 - KINSOLSolver: the plugin is loaded and fully functional.
 - libNuML: the plugin is loaded and fully functional.
 - libSBML: the plugin is loaded and fully functional.
 - libSEDML: the plugin is loaded and fully functional.
 - LLVMClang: the plugin is loaded and fully functional.
 - MathMLViewerWidget: the plugin is loaded and fully functional.
 - Python: the plugin is loaded and fully functional.
 - PythonPackages: the plugin is loaded and fully functional.
 - PythonQt: the plugin is loaded and fully functional.
 - PythonQtSupport: the plugin is loaded and fully functional.
 - PythonShell: the plugin is loaded and fully functional.
 - PythonSupport: the plugin is loaded and fully functional.
 - QScintilla: the plugin is loaded and fully functional.
 - QScintillaWidget: the plugin is loaded and fully functional.
 - Qwt: the plugin is loaded and fully functional.
 - SecondOrderRungeKuttaSolver: the plugin is loaded and fully functional.
 - SEDMLSupport: the plugin is loaded and fully functional.
 - SimulationSupport: the plugin is loaded and fully functional.
 - StandardSupport: the plugin is loaded and fully functional.
 - SUNDIALS: the plugin is loaded and fully functional.
 - ZIPSupport: the plugin is loaded and fully functional.
 - zlib: the plugin is loaded and fully functional.

Version¶

$ ./OpenCOR -v
OpenCOR Version 0.7