Copasi-basico

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.

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](https://basico.readthedocs.io/en/latest/notebooks/Using_callbacks.html) showing how to use the default handler (that will work of tqdm is installed).

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 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](https://basico.readthedocs.io/en/latest/notebooks/Editing_Kinetics.html) in the documentation. ( fixes #29 )

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)

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>