Release 0.46

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 with setting up timecourses, where inputs are now automatically converted to the types needed by the C++ api. This allows duration to work also with an np.float value
• save_experiments_to_dict, save_model_and_data now use relative filenames for the experiment files. So the files will work readily after copying them to other environments.

Release 0.45

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 has further improvements on the profile likelihood generation. It adds a new convenience function get_profiles_for_model that generates all profiles for the currently loaded model. Additionally processing results now allows for a max_time parameter that stops the calculation of results after the specified timeout in seconds. The example has been updated to reflect that.

When using callbacks it is also possible to specify a max_time argument to automatically cancel longer running operations.

Release 0.44

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 with the validation of reaction mappings. It also adds the option to automatically add separators for non-table reports.

Full Changelog: v0.43...v0.44

Release 0.43

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 version adds a function wrap_copasi_string, that makes it easier to add reports with literal strings in report headers. It also fixes an issue with generating separators. Additionally when mapping model elements to reaction kinetics, these values will now be validated.

Full Changelog: v0.42...v0.43

Release 0.42

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 version fixes an issue, where changing kinetic functions of reaction would fail, even if a mapping was supplied. Additionally there are minor improvements in plotting profiles.

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)