AMICI v1.1.0

BREAKING CHANGES

• PetabSimulationResult.res (PEtab v2) is a property now, for consistency
  with PetabSimulationResult.llh. Replace result.res() by result.res.
• Require Python >= 3.12, following NEP 29
  (#3180).

Features

• The PEtab v2 simulator now aggregates the residual sensitivities of all
  experiments: PetabSimulationResult.sres contains the sensitivities of the
  residuals returned by PetabSimulationResult.res with respect to the
  estimated PEtab problem parameters.
• Added a checkpoints parameter to the JAX PEtab simulation interface
  (run_simulation/run_simulations), controlling the number of checkpoints
  diffrax's RecursiveCheckpointAdjoint uses for reverse-mode gradients.
  Defaults to None (diffrax's automatic choice), preserving previous
  behavior (#3217).
• PEtab SciML: added support for importing equinox modules (#3179).
• PEtab SciML: implemented additional PyTorch-style layer types
  (BatchNorm, InstanceNorm, AlphaDropout, Bilinear) (#3176).
• PEtab SciML: updated support to PEtab v2 (#3165).
• Sped up parallel model import (AMICI_IMPORT_NPROCS > 1) considerably.
  Previously, a new worker pool was created for every parallelized operation,
  and every worker of every pool had to import sympy and amici from scratch.
  Now, a single pool is created lazily and reused, and its workers are forked
  from a forkserver process that performs these imports only once. For small
  operations, where the inter-process communication overhead outweighs any
  speed-up, processing stays serial. Previously, parallel import could be
  slower than serial import for all but the largest models.

Fixes

• Fixed both simulation backends selecting the wrong branch of a piecewise
  expression whose condition depends on the value of another piecewise
  expression. The Heaviside variables were initialized in a single pass, so
  the outer condition was evaluated using the not-yet-updated value of the
  inner expression. They are now iterated to a fixed point, which also makes
  the result independent of the (previously differing) value the Heaviside
  variables happened to be seeded with in either backend (#3233).
• Demote the module import mtime check during sundials model import to a
  warning, as it can lead to false positives in some environments
  (e.g., when using network file systems with not synchronized clocks).
  If you encounter this warning, and you are sure that the model was not
  modified since the last import, you can safely ignore it.
• Fixed SBML import constant-folding a parameter out of the initial conditions
  when that parameter both carried an initialAssignment with a numeric
  right-hand side and defined a species' initial value. The parameter remained
  in the free-parameter list, so its (initial-condition) sensitivity was
  silently reported as zero (e.g. init_STAT in jakstat_adjoint). This also
  covers the transitive case, where such a parameter is reached through a chain
  of parameter initial assignments (#3214).
• Fixed the JAX model exporter writing floating-point numbers with only 15
  significant digits, which is not enough to round-trip a double. Values were
  silently perturbed in the last bits, which mattered wherever a model compares
  values exactly (e.g. a parameter with value pi no longer tested equal to
  pi).
• amici.sim.sundials.petab.PetabSimulator.simulate no longer fails for
  PEtab v2 problems with non-Gaussian noise models or for the
  RDataReporting.residuals reporting mode. The respective unavailable
  aggregated results (sllh, s2llh, res, sres) are None now.
  Experiments without measurements no longer suppress the residuals of all
  other experiments.
• The residuals (ReturnData.res), their sensitivities (ReturnData.sres)
  and the Fisher information matrix (ReturnData.FIM) of failed simulations
  are invalidated now. Previously, the residuals of the timepoints that were
  not reached stayed at their initial value of 0.0, i.e., they looked like a
  perfect fit, and the FIM contained a partial sum.
• PetabSimulationResult.res (PEtab v2) returns None if any experiment
  failed to simulate.
• Fixed SBML import turning a parameter into a constant state when its
  initialAssignment referenced another parameter that becomes an AMICI
  expression. Such chains are now resolved to a fixed point, so those
  parameters stay expressions instead of inflating the state vector (e.g.
  C2ss/C3ss in calvetti).
• Fixed an AttributeError when importing a model module without having
  first imported something else from amici.sim.sundials (#3200).
• Fixed PEtab problem flattening not substituting the old observable ID in
  the noise formula; updated the error message shown when importing a
  non-flattened PEtab problem that requires flattening (#3177).
• Fixed a spurious AssertionError from the conservation-law computation for
  models with condition-dependent compartment sizes, caused by comparing a
  simplified and an unsimplified but mathematically equivalent expression
  (#3202).
• Fixed a NameError in JAX-exported models when an explicit
  (time-triggered) event trigger depends on a model expression (w) rather
  than only on parameters (#3195).
• JAX PEtab backend: fixed condition-name-based preequilibration detection,
  which only worked for AMICI's own synthetic condition names and produced
  incorrect or crashing results for PEtab problems using arbitrary condition
  names for preequilibration (#3205).
• JAX PEtab backend: fixed JAXProblem.save()/load(), which no longer
  matched the current petab.v2 API (#3204).
• JAX PEtab backend: fixed condition-table state-reinitialization lookup,
  noise-distribution handling, and differentiability of condition-table
  target values (#3207).
• JAX PEtab backend: fixed discontinuity stepping, PEtab v1 problems (now
  auto-upgraded to v2), noise/observable placeholder substitution, and event
  assignments silently dropped for models with an odd number of roots
  (#3196).
• JAX PEtab backend: fixed measurement/override parsing and parameter-scaling
  bugs that caused JAX benchmark simulations to fail or diverge from
  SUNDIALS (#3210).

Performance

• Reduced JAX PEtab gradient-compilation time for benchmark models with
  large repeated subexpressions (e.g. analytic steady-state initial values)
  by adding common-subexpression elimination to the JAX code printer and
  switching to ImplicitAdjoint (#3212).
• Avoided unnecessary JAX recompilation caused by diffrax.steady_state_event()
  returning a new closure (compared by identity) on every call; equivalent
  settings now share the compiled executable (#3197).
• Sped up importing/building models with CMake, most noticeably when
  importing many independent models in one go (e.g. test suites, benchmark
  collections, or PEtab batch imports): skip redundant HDF5 (#3220) and
  compiler-flag (#3221) detection that was previously repeated on every
  single model configure.

Documentation

• Added a PEtab SciML example notebook demonstrating problem loading,
  simulation, and a basic training loop, using the Dandekar PEtab SciML
  benchmark (#3208).

Full Changelog: v1.0.1...v1.1.0