AMICI v0.21.0

Deprecations

• Moved PEtab-related functionality from amici.petab_* to the
  petab-subpackage amici.petab.*. The old public functions are still
  available but will be removed in a future release.
  by @dweindl in #2205, #2211, #2252

Features

• Handle events occurring at fixed timepoints without root-finding.
  This avoids event-after-reinitialization errors in many cases brings a
  slight performance improvement.
  by @dweindl in #2227
• Added PetabProblem class for handling PEtab-defined simulation conditions,
  making it easier to perform customized operations based on PEtab-defined
  simulation conditions.
  by @dweindl in #2255
• code-gen: Simplified switch statements, leading to reduced file sizes and
  faster compilation for certain models.
  by @dweindl in #2240
• Made Model and ModelPtr deepcopyable
  by @dweindl in #2247
• Made Solver and SolverPtr deepcopyable
  by @dweindl in #2245
• Added a debugging helper get_model_for_preeq for debugging simulation
  issues during pre-equilibration.
  by @dweindl in #2250
• Added SwigPtrView fields to dir() outputs
  by @dweindl in #2244
• Use proper labels for in plotting functions if IDs are available in
  ReturnData.
  by @dweindl in #2249
• Added ExpData::clear_observations to set all measurements/sigmas to NaN
  by @dweindl in #2258

Fixes

• Fixed AMICI hiding all warnings. Previously, importing amici resulted
  in all warnings being hidden in the rest of the program.
  by @dweindl in #2243
• CMake: Fixed model debug builds
  by @dweindl in #2222
• Fixed CMake potentially using incorrect Python library for building model
  extension
  by @dweindl in #2220
• CMake: fixed cxx flag check
  by @dweindl in #2225
• Fixed potential out-of-bounds read in Model::checkFinite for
  matlab-imported models
  by @dweindl in #2232
• Fixed piecewise/Heaviside handling
  by @dweindl in #2234
• Deterministic order of event assignments
  by @dweindl in #2242
• Proper error message in case of unsupported state-dependent sigmas
  by @dweindl in #2239
• Fixed swig shadow warning + other linting issues
  by @dweindl in #2261
• Fixed SwigPtrView.__getattr__
  by @dweindl in #2259
• simulate_petab: Avoid warning when simulating with default parameters
  by @dweindl in #2265

Documentation

• Updated Python package installation instructions for Arch Linux
  by @willov in #2212
• Updated ExpData documentation
  by @dweindl in #2254
• Documented simulation starting time t0
  by @dweindl in #2263
• Updated PEtab example
  by @dweindl in #2255

...

Full Changelog: v0.20.0...v0.21.0