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.

Release 0.76

This release fixes an issue where returning simulation results from run_time_course could not be obtained if multiple model elements were named Time. If this issue is encountered:

• basico will no longer try to set the index, and instead issue a warning Duplicate column names in time series consider using use_sbml_id=True, or running ensure_unique_names()
• the new function ensure_unique_names() appends a count to the name ensuring uniqueness

This fixes #60 .

Release 0.75

This release adds a workaround when dealing with the following issues:

• when resolving references from display names for reactions containing ')', these are now correctly found.
• for testing, added function import_sbml that optionally can modify the XML before loading it. This function is experimental and might be removed in the future.

Release 0.74

This is a bugfix release, renaming the parameter for run_lyapunov to calculate_divergence.

Release 0.73

This release adds initial support for calculating lyapunov exponents and can be used like:

        >>> load_example('brusselator')
        >>> exponents, sums, divergence = run_lyapunov(num_exponents=2)
        >>> print(exponents)
        [-0.0007025645113957691, -2.6051942604518477]

Release 0.72

This release adds a set_parameters function the basico PetabSimulator, with that it will be possible to reevaluate many parameters without requiring a reload.

Release 0.71

This release adds support for the new output specifications for scan tasks to get_scan_settings and set_scan_settings. That way more precise control can be gained as to when output is selected.