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)