ICB-DCM/pyPESTO: 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)