Release notes¶
0.0 series¶
0.0.12 (2020-04-06)¶
- Add typehints to global functions and classes.
- Add PetabImporter.rdatas_to_simulation_df function (all #235).
- Adapt y scale in waterfall plot if convergence was too good (#236).
- Clarify that Objective is of type negative log-posterior, for minimization (#243).
- Tidy up AmiciObjective.parameter_mapping as implemented in AMICI now (#247).
- Add MultiThreadEngine implementing multi-threading aside the MultiProcessEngine implementing multi-processing (#254).
- Fix copying and pickling of AmiciObjective (#252, #257).
- Remove circular dependence history-objective (#254).
- Fix problem of visualizing results with failed starts (#249).
- Rework history: make thread-safe, use factory methods, make context-specific (#256).
- Improve PEtab usage example (#258).
- Define history base contract, enabling different backends (#260).
- Store optimization results to HDF5 (#261).
- Simplify tests (#263).
Breaking changes:
- HistoryOptions passed to pypesto.minimize instead of Objective (#256).
- GlobalOptimizer renamed to PyswarmOptimizer (#235).
0.0.11 (2020-03-17)¶
- Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_objective routines (#209, #219, #225).
- Implement petab test suite checks (#228).
- Various error fixes, in particular regarding PEtab and visualization.
- Improve trace structure.
- Fix conversion between fval and chi2, fix FIM (all #223).
0.0.10 (2019-12-04)¶
- Only compute FIM when sensitivities are available (#194).
- Fix documentation build (#197).
- Add support for pyswarm optimizer (#198).
- Run travis tests for documentation and notebooks only on pull requests (#199).
0.0.9 (2019-10-11)¶
- Update to AMICI 0.10.13, fix API changes (#185).
- Start using PEtab import from AMICI to be able to import constant species (#184, #185)
- Require PEtab>=0.0.0a16 (#183)
0.0.8 (2019-09-01)¶
- Add logo (#178).
- Fix petab API changes (#179).
- Some minor bugfixes (#168).
0.0.7 (2019-03-21)¶
- Support noise models in Petab and Amici.
- Minor Petab update bug fixes.
0.0.6 (2019-03-13)¶
- Several minor error fixes, in particular on tests and steady state.
0.0.5 (2019-03-11)¶
- Introduce AggregatedObjective to use multiple objectives at once.
- Estimate steady state in AmiciObjective.
- Check amici model build version in PetabImporter.
- Use Amici multithreading in AmiciObjective.
- Allow to sort multistarts by initial value.
- Show usage of visualization routines in notebooks.
- Various fixes, in particular to visualization.
0.0.4 (2019-02-25)¶
- Implement multi process parallelization engine for optimization.
- Introduce PrePostProcessor to more reliably handle pre- and post-processing.
- Fix problems with simulating for multiple conditions.
- Add more visualization routines and options for those (colors, reference points, plotting of lists of result obejcts)
0.0.3 (2019-01-30)¶
- Import amici models and the petab data format automatically using pypesto.PetabImporter.
- Basic profiling routines.
0.0.2 (2018-10-18)¶
- Fix parameter values
- Record trace of function values
- Amici objective to directly handle amici models
0.0.1 (2018-07-25)¶
- Basic framework and implementation of the optimization