Release 0.86

This release fixes an issue with changing the mapping of a reaction parameter using for example:

• set_reaction_parameters('(R2).k1', mapped_to='global1')

this would fail occasionally. It was also not possible to remove a mapping, this can now be done using None.

It is also possible to change the mapping directly based on dictionaries.

Thanks to Marc Lefranc for reporting.

Full Changelog: v0.85...v0.86

Release 0.85

This release fixes an issue with the profile likelihood graphs. Additionally, an issue is fixed that made it impossible to overwrite the CopasiSE executable to be used by the processing functions.

Additional new features allow the plotting engine for plots to be specified (QWT / QCustomPlot).

Finally all events of a model can be removed quickly using remove_all_events.

Release 0.84

This release fixes an issue where the LNA task would give a confusing error message, when no steady state was found. It also works around an incompativility when using python-copasi compiled with SWIG 4.3.0.

Release 0.83

This release updates basico to work with the latest version of petab_select. All changes are in the backend, and do not influence how to perform model selection:

• Model selection example

Release 0.82

This release upgrades the implementation of the PEtab select package to the latest version. Nothing on the external API has changed, for an example see:

• FAMOS Model Selection

Release 0.81

This is a bug fix release silencing a misleading error message coming from the steady state task

Release 0.80

This release adds access to the results of the Linear Noise Approximation Task. (it requires an python-copasi > 4.44). For an example of running the task see the:

• LNA Task Example

Generally, the LNA is computed runing run_lna the optional argument return_results (default False) indicates whether the full result is returned, or only the status of the computation. To retrieve the results after a computation of the LNA the following methods may be used:

• get_lna_status returns the status of the last computation
• get_lna_covariance_matrix returns the full covariance matrix
• get_lna_reduced_covariance_matrix returns the reduced covariance matrix
• get_lna_reduced_b_matrix returns the reduced b Matrix
• get_lna_solution returns the tuple: (status, covariance matrix, reduced covariance matrix, reduced b matrix)

Release 0.79

This issue changes the behavior when running time courses, obtaining values only at specified time points. Previously the first value might have been the first value specified or an earlier time point if the model was not currently at the time. This release changes that behavior to set the output start time to the first specified value.

Additionally, the previously private collect_data method can now be used to obtain values from the current model state using either display names or cns.

This resolves issue #61.

Release 0.78

This is a bugfix release that fixes an issue that occurs if basico is used with the python-copasi package 4.45 and using optimisation constraints.

Release 0.77

This release fixes an issue with load_model_from_string, where specific SBML models were mistakenly imported as COPASI models.