pyPESTO 0.1.0

Objective

• Write solver settings to stream to enable serialization for distributed
  systems (#308)
• Refactor objective function (#347)
  • Removes necessity for all of the nasty binding/undbinding in AmiciObjective
  • Substantially reduces the complexity of the AggregatedObjective class
  • Aggregation of functions with inconsistent sensi_order/mode support
  • Introduce ObjectiveBase as an abstract Objective class
  • Introduce FunctionObjective for objectives from functions
• Implement priors with gradients, integrate with PEtab (#357)
• Fix minus sign in AmiciObjective.get_error_output (#361)
• Implement a prior class, derivatives for standard models, interface with
  PEtab (#357)
• Use amici.import_model_module to resolve module loading failure (#384)

Problem

• Tidy up problem vectors using properties (#393)

Optimization

• Interface IpOpt optimizer (#373)

Profiles

• Tidy up profiles (#356)
• Refactor profiles; add locally approximated profiles (#369)
• Fix profiling and visualization with fixed parameters (#393)

Sampling

• Geweke test for sampling convergence (#339)
• Implement basic Pymc3 sampler (#351)
• Make theano for pymc3 an optional dependency (allows using pypesto without
  pymc3) (#356)
• Progress bar for MCMC sampling (#366)
• Fix Geweke test crash for small sample sizes (#376)
• In parallel tempering, allow to only temperate the likelihood, not the prior
  (#396)

History and storage

• Allow storing results in a pre-filled hdf5 file (#290)
• Various fixes of the history (reduced vs. full parameters, read-in from file,
  chi2 values) (#315)
• Fix proper dimensions in result for failed start (#317)
• Create required directories before creating hdf5 file (#326)
• Improve storage and docs documentation (#328)
• Fix storing x_free_indices in hdf5 result (#334)
• Fix problem hdf5 return format (#336)
• Implement partial trace extraction, simplify History API (#337)
• Save really all attributes of a Problem to hdf5 (#342)

Visualization

• Customizable xLabels and tight layout for profile plots (#331)
• Fix non-positive bottom ylim on a log-scale axis in waterfall plots (#348)
• Fix "palette list has the wrong number of colors" in sampling plots (#372)
• Allow to plot multiple profiles from one result (#399)

Logging

• Allow easier specification of only logging for submodules (#398)

Tests

• Speed up travis build (#329)
• Update travis test system to latest ubuntu and python 3.8 (#330)
• Additional code quality checks, minor simplifications (#395)

pyPESTO 0.0.13

• 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).

pyPESTO 0.0.12

• 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).

pyPESTO 0.0.11

• 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).

pyPESTO 0.0.10

• 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).

pyPESTO 0.0.9

• 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)

pyPESTO 0.0.8

• Add logo (#178).
• Fix petab API changes (#179).
• Some minor bugfixes (#168).

v0.0.7

• Support noise models in Petab and Amici.
• Minor Petab update bug fixes.

v0.0.6

• Several minor error fixes, in particular on tests and steady state.

v0.0.5

• 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.