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dweindl merged 2 commits into from
Feb 26, 2026
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Update changelog, bump version #3134

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1daa23c
doc: Update changelog
dweindl Feb 25, 2026
01e7d5d
1.0.0
dweindl Feb 25, 2026
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87 changes: 55 additions & 32 deletions CHANGELOG.md
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Expand Up @@ -8,9 +8,26 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni

**BREAKING CHANGES**

* The package has been reorganized. All importers have been moved to
`amici.importers` subpackages. For example, all functionality from
`amici.sbml_import` is now available in `amici.importers.sbml`.
*Removed functionality*

The following functionality has been removed without replacement:

* The complete MATLAB interface has been removed.
* `amici.sbml_import.species_to_parameters` has been removed.

*API changes*

* For a more consistent API, all function names are now `snake_case` instead of
`camelCase`.
* The package has been reorganized.
* All importers have been moved to `amici.importers` subpackages.
For example, all functionality from `amici.sbml_import` is now available in
`amici.importers.sbml`.
* All simulation-related functionality has been moved to `amici.sim.sundials`
for the SUNDIALS interface, and `amici.sim.jax` for the JAX interface.
* A number of functions and modules have been made private
(i.e., their name starts with `_` or they are excluded from `__all__`),
as they are not intended for public use and may change without deprecation.
* The naming of free and fixed parameters has been harmonized across the API:
AMICI differentiates between parameters with respect to which a model
can compute sensitivities ("free parameters") and parameters with respect to
Expand All @@ -37,21 +54,16 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
* `assignmentRules2observables` has been renamed to
`assignment_rules_to_observables` and now returns `list[MeasurementChannel]`
to be passed to the import functions.
* `assignmentRules2observables` has been renamed to
`assignment_rules_to_observables` and now returns `list[MeasurementChannel]`
to be passed to the import functions.
* `AmiVector::getLength` and `AmiVectorArray::getLength` have been renamed to
`size` to be more consistent with STL containers.
* `amici.petab.petab_import.import_model` has been removed.
Use `amici.petab.petab_import.import_model_sbml` instead.
(The former was just an alias for the latter.)
* For a more consistent API, all function names are now snake_case instead of
camelCase.
* `Model.getSolver` has been renamed to `Model.create_solver`.
Use `amici.importers.petab.v1.import_petab_problem` instead.
* `Model.getSolver` has been renamed to `Model.create_solver`,
emphasizing that a new `Solver` instance is created on each call.
* `amici.runAmiciSimulation` and `amici.runAmiciSimulations` have been renamed
to `amici.run_simulation` and `amici.run_simulations`.
to `amici.sim.sundials.run_simulation` and
`amici.sim.sundials.run_simulations`, respectively.
* The following deprecated functionality has been removed:
* The complete MATLAB interface has been removed.
* `NonlinearSolverIteration::functional` has been removed,
use `NonlinearSolverIteration::fixedpoint` instead.
* The deprecated argument `log_as_log10` to `SbmlImporter.sbml2amici` and
Expand All @@ -62,8 +74,6 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
modules.
* The `force_compile` argument to `import_petab_problem` has been removed.
See the `compile_` argument.
* Removals without deprecation:
* `amici.sbml_import.species_to_parameters` has been removed.
* Model output directory keyword arguments have been harmonized:
What was previously `model_output_dir`, `output_dir`, `outdir` is now
consistently called `output_dir` across the API.
Expand All @@ -72,47 +82,60 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni

**Features**

* Experimental support for the PEtab data format v2.0.0 (draft, see
https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html)
for SBML- and PySB-based problems (see `amici.petab.petab_importer`). The API is subject to change.
* Support for the PEtab data format v2.0.0
([draft](https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html))
for the JAX and SUNDIALS interfaces.

See `amici.importers.petab.PetabImporter` and examples for
[JAX](https://amici.readthedocs.io/en/latest/examples/example_jax_petab/ExampleJaxPEtab.html)
and [SUNDIALS](https://amici.readthedocs.io/en/latest/examples/example_petab/petab_v2.html).

For JAX-based models, the interface can be considered stable;
for SUNDIALS-based models, the API may still change.

* Current limitations for PySB-based PEtab problems:
* Only species and `pysb.Expression` are supported as condition table
targets.
SBML- and PySB-based PEtab problems are currently supported.
For PySB-based PEtab problems, only species and `pysb.Expression` are
supported as condition table targets (i.e., no parameters yet).

PEtab v1 import for SUNDIALS-based models is still available via
`amici.importers.petab.v1`. Once PEtab v2 import has been stabilized,
PEtab v1 import for SUNDIALS-based models will be removed.
* Many relevant `ReturnData` fields are now available as `xarray.DataArray`
via `ReturnData.xr.{x,y,w,x0,sx,...}`.
`DataArray`s include the identifiers and are often more convenient than the
plain numpy arrays. This allows for easy subselection and plotting of the
results, and conversion to DataFrames.
* `Model.simulate()` has been added as a convenience function to run
simulations without having to create a `Solver` object explicitly.
This is a wrapper for both `amici.run_simulation` and
`amici.run_simulations`, depending on the type of the `edata` argument.
This is a wrapper for both `amici.sim.sundials.run_simulation` and
`amici.sim.sundials.run_simulations`,
depending on the type of the `edata` argument.
It also supports passing some `Solver` options as keyword arguments.
* Improved `pickle` support for `amici.{Model,ModelPtr,Solver,ExpData`.
This is intended for interactive use; for better full control and
performance, it is still recommended to create a `Solver` object and call
`amici.sim.sundials.{run_simulation,run_simulations}` directly.
* Improved `pickle` support for
`amici.sim.sundials.{Model,ModelPtr,Solver,ExpData}`.
Note that AMICI's pickling support is only intended for short-term storage
or inter-process communication.
Reading pickled objects after updating AMICI or the model code will almost
certainly fail.
* `amici.Model`and `amici.ModelPtr` now support sufficient pickling for use
in multi-processing contexts. This works only if the amici-generated model
* `Model`and `ModelPtr` now support sufficient pickling for use
in multiprocessing contexts. This works only if the amici-generated model
package exists in the same file system location and does not change until
unpickling.
* `amici.Solver` is now picklable if amici was built with HDF5 support.
* `Solver` is now picklable if amici was built with HDF5 support.
This only works on shared file systems, as the solver state is stored in a
temporary HDF5 file.
* `amici.ExpData` is now picklable.
* Implemented support for the [PEtab SciML](https://github.com/PEtab-dev/petab_sciml)
extension for the JAX interface.
* `ExpData` is now picklable.
* The import function `sbml2amici`, `pysb2amici`, and `antimony2amici` now
return an instance of the generated model class if called with `compile=True`
(default).
* The default directory for model import changed, and a base directory
can now be specified via the `AMICI_MODELS_ROOT` environment variable.
See `amici.get_model_dir` for details.
* IDs and names of model entities are now not only accessible via `Model`, but
also via `ReturnData`
* IDs and names of model entities are now not only accessible via
`amici.sim.sundials.Model`, but also via `amici.sim.sundials.ReturnData`
(`ReturnData.{free_parameter_ids,observable_ids,...}`,
`ReturnData.{free_parameter_names,observable_names,...}`).

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2 changes: 1 addition & 1 deletion version.txt
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@@ -1 +1 @@
1.0.0.dev
1.0.0
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