libtbx.program_template: Standard Program Template for CCTBX Programs

Program Template

The “program” is the actual task to be performed without any user interfaces. The user interfaces (command-line and graphical) build the “data_manager” and “params” objects for the program. The “data_manager” handles all file input and “params” handles all the program settings.

The required methods break up the calling order into discrete phases

  • constructor: minimal set up

  • validate: check that the inputs (files and parameters) are valid and consistent

  • run: run the actual task

  • get_results: return the desired output from the program

The optional methods provide some extra tweaking

  • custom_init: called at the end of the constructor, additional initialization

  • clean_up: if temporary files are written in the course of running the program,

    this step should remove those files.

class libtbx.program_template.ProgramTemplate(data_manager, params, master_phil=None, logger=None)
__init__(data_manager, params, master_phil=None, logger=None)

Common constructor for all programs

This is supposed to be lightweight. Custom initialization, if necessary, should be handled by the custom_init function. Developers should not need to override this function.

Parameters:

  • data_manager – An instance of the DataManager (libtbx/data_manager.py) class containing data structures from file input

  • params – An instance of PHIL

  • logger – Standard Python logger (from logging module), optional. A logger will be created if it is not provided.

clean_up()
custom_init()

Optional initialization step

Developers should override this function if additional initialization is needed. There should be no arguments because all necessary information should be in self.data_manager (file input) and self.params (phil parameters)

Parameters:

None

get_results()
run()
validate()