Release 0.51

This release introduces a new method run_scheduled_tasks and the general run_task command, that executes tasks, and aims to produce the output specified. For now basic plotting is implemented, but will be refined in the next versions.

It also includes a number of bugfixes (fixes #34, #35 , #36), thanks to @ayush9pandey for reporting. This should produce more applicable error messages when running simulations, sort an issue where Miriam information could not be retrieved when using python-copasi > 4.35 and clarify issues in the notebooks.

Full Changelog: v0.50...v0.51

Release 0.50

This release upgrades the support for petab_select, cleans up logging (not using the root logger anymore), and also supports observable transformations for PEtab problems. Additionally it exposes the Hybrid Runge Kutta method (fixes #33 ) to the run_time_course / run_time_course_with_output functions.

Release 0.49

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.

New in this release is support for advanced event flags, such as:

• fire_at_initial_time: to indicate that an event should trigger at time = t0, (default False)
• persistent: to indicate that an event has to remain true between trigger time and delay (default False)
• delay_calculation: to indicate that not just the assignment, but also the calculation of the assignment expression should be delayed
• priority: a priority expression that decides which event will get priority if multiple ones trigger at the same time (default random)

Release 0.48

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.

New in this release is the plotting for profile likelihood profiles. Have a look at the updated example, by default we draw the 68% and 95% threshold.

Release 0.47

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.

New in this release is the capability to create / edit / update / remove model parameter sets. Have a look at the tutorial:

• https://basico.readthedocs.io/en/latest/notebooks/Working_with_ParameterSets.html

This release also fixes some more issue, when using relative filenames for experimental data.

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.