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pyPESTO 0.1.0
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@yannikschaelte yannikschaelte released this 17 Jun 17:30
v0.1.0
6b34642
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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)
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