Release 0.41

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 brings a first version of performing 1d likelihood profiles along and fixes an issue where setting model values would fail, if a model is passed along to the key value args.

Release 0.40

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 an overload to reset the default handler, that can be used to display status information during long running operations. There is now also an example showing how to use the default handler (that will work of tqdm is installed).

Release 0.39

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 changes the model editing so that the model is not compiled as often. Especially when creating big models, this reduces the runtime of scripts drastically.

basico 0.38

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 changes the behavior of add_reaction / set_reaction, when it comes to assigning a function definition to it. Previously, the reaction scheme would already have to have all modifiers of the function listed, before a function could be assigned. Now this is no longer necessary and modifiers will be automatically added to the reaction scheme, as long as the mapping to all modifiers is specified. See also the Editing reaction kinetics example in the documentation. ( fixes #29 )

basico 0.37

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 fixes an issue, where initial_concentrations would be lost when also setting additional properties using either add_species or get_species. (Issue #28)

Release 0.36

This release updates the PEtab support to the latest libpetab version, and the latest petab_select library. Now also an example for using PEtab problem / selection problems is online:

• https://basico.readthedocs.io/en/latest/notebooks/Working_with_PEtab.html

Release 0.35

This release ensures, that basico is compatible with the latest COPASI version.

Release 0.34

This release adds the option to return the fit statistic for each experiment when get_fit_statistic is called with include_experiments=True . The python-copasi package will have to be version 2.37.263 or higher for this to work.

Release 0.33

This release adds the option of specifying affected experiments to set_fit_parameters.

Release 0.32

This release adds an optional parameter new_name to set_compartments / events / parameters, to allow them being renamed in the same way as species and reactions were.

It also fixes an issue when adding experiments, which sometimes could fail. It also provides more information from the fit statistic.