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.

Release 0.70

This release fixes an issue (#56 ) where mapping a number to a reaction parameter would only work if that parameter was in the first position. Additionally, time course settings are now restored when retrieving simulation results for experiments, issue (#54).

Release 0.69

This release fixes an issue where notes / annotations could not be set on all elements. This fixes #53 .

Release 0.68

This release fixes an issue that corrupted expressions when replacing CNs with display names. #52

Release 0.67

This release fixes an issue if NaNs are in the list of affected experiments.