Release 0.61

This release contains further improvements in translating expressions with names to expressions of CNs as expected by the COPASI C++ API.

Release 0.60

Another bug fix release, this time with setting the expressions for a different than the current model. With that species / parameters can now be cloned from dictionary like so:

        # get from one model 
        species = basico.as_dict(basico.get_species())
        params = basico.as_dict(basico.get_parameters())
        # start new model 
        dm = basico.new_model()

        # ensure we have all species
        for s in species:
            basico.add_species(s['name'], s['compartment'])

        for p in params:
            basico.add_parameter(p['name'], p['value'])

        # now set all values as we had them
        for s in species:
            basico.set_species(exact=True, **s)

        for p in params:
            basico.set_parameters(exact=True, **p)

Release 0.59

This release fixes an issue, where get_parameters or get_species would return expressions from the current model, rather than from the model that has been passed in. Additionally upon request get functions now return the display_name of elements additionally rather than just the name. Also transition_time is now returned when calling get_species which might be of interest after bringing the model to steady state.

Full Changelog: v0.58...v0.59

Release 0.58

This release fixes an issue with get_reaction_mappings that on some systems would fail to provide the complete mapping of a reaction element. Additionally an issue is fixed when set_task_settings is used to change Duration / StepNumber of time courses, which unfortunately would sometimes not be correct. Also added two new methods:

• get_model_name returns the name of the current model
• remove_loaded_models removes all loaded models

Release 0.57

This release fixes an issue in the plotting subroutine for the profile likelihood method.

Release 0.56

This release ensures that parameter estimation tasks are executed, even if errors have been previously logged.

Release 0.55

This is a bug fix release, that solves an issue (#39) where creating a parameter set could cause other tasks to not run anymore.

Release 0.54

This release fixes compatibility with python 3.12. Additionally it supports parameter scans over parameter sets, as was introduced with COPASI 4.42. It fixes issues when creating events with multiple assignments, and ensures that parametersets are correctly created from the current model state.

Examples:

• Working with Parameter Sets

Release 0.53

This release adds support for the MCA task to basico, for an example on how to use it see:

• MCA Example

Release 0.52

Basico is a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.

This release adds support for using constraints when running optimization or parameter estimation tasks. They do make things much more difficult to solve, so use with care. I've updated the examples to show how to use them:

• Parameter estimation example
• Optimization example

Full Changelog: v0.51...v0.52