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Release notes

0.0 series

0.0.13 (2020-05-03)

  • Tidy up and speed up tests (#265 and others).
  • Basic self-implemented Adaptive Metropolis and Adaptive Parallel Tempering sampling routines (#268).
  • Fix namespace sample -> sampling (#275).
  • Fix covariance matrix regularization (#275).
  • Fix circular dependency PetabImporter - PetabAmiciObjective via AmiciObjectBuilder, PetabAmiciObjective becomes obsolete (#274).
  • Define AmiciCalculator to separate the AMICI call logic (required for hierarchical optimization) (#277).
  • Define initialize function for resetting steady states in AmiciObjective (#281).
  • Fix scipy least squares options (#283).
  • Allow failed starts by default (#280).
  • Always copy parameter vector in objective to avoid side effects (#291).
  • Add Dockerfile (#288).
  • Fix header names in CSV history (#299).

Documentation:

  • Use imported members in autodoc (#270).
  • Enable python syntax highlighting in notebooks (#271).

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