Remove deprecated functionality

CHANGELOG.md

@@ -8,13 +8,24 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 BREAKING CHANGES
 
-* The MATLAB interface has been removed.
 * `ReturnDataView.posteq_numsteps` and `ReturnDataView.posteq_numsteps` now
   return a one-dimensional array of shape `(num_timepoints,)` instead of a
   two-dimensional array of shape `(1, num_timepoints)`.
 * `ReturnDataView.posteq_status` and `ReturnDataView.preeq_status` now
   return `list[SteadyStateStatus]` instead of an `ndarray[int]` of shape
   `(1, 3)`.
+* 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
+    `SbmlImporter.sbml2jax` has been removed. Just remove this argument, as
+    this never had any effect.
+  * Deprecated imports from `amici.petab.*` in `amici.petab.simulations`
+    have been removed. Import those functions directly from their respective
+    modules.
+  * The `force_compile` argument to `import_petab_problem` has been removed.
+    See the `compile_` argument.
 
 ## v0.X Series
 

include/amici/defines.h

@@ -195,7 +195,6 @@ enum class LinearMultistepMethod {
 
 /** CVODES/IDAS Nonlinear Iteration method */
 enum class NonlinearSolverIteration {
-    functional = 1, /** deprecated */
     fixedpoint = 1,
     newton = 2
 };

python/sdist/amici/petab/petab_import.py

@@ -9,7 +9,6 @@
 import os
 import shutil
 from pathlib import Path
-from warnings import warn
 
 import amici
 import petab.v1 as petab
@@ -82,17 +81,6 @@ def import_petab_problem(
     :return:
         The imported model.
     """
-    if "force_compile" in kwargs:
-        if kwargs["force_compile"]:
-            compile_ = True
-            del kwargs["force_compile"]
-        warn(
-            "The `force_compile` option is deprecated, please use the "
-            "new `compile_` option, which also supports 'do not compile'.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-
     if petab_problem.model.type_id not in (MODEL_TYPE_SBML, MODEL_TYPE_PYSB):
         raise NotImplementedError(
             "Unsupported model type " + petab_problem.model.type_id

python/sdist/amici/petab/simulations.py

@@ -18,24 +18,14 @@
 from .. import AmiciExpData, AmiciModel
 from ..logging import get_logger, log_execution_time
 
-# some extra imports for backward-compatibility
-# DEPRECATED: remove in 1.0
-from .conditions import (  # noqa # pylint: disable=unused-import
-    create_edata_for_condition,
+from .conditions import (
     create_edatas,
-    create_parameterized_edatas,
     fill_in_parameters,
 )
-from .parameter_mapping import (  # noqa # pylint: disable=unused-import
+from .parameter_mapping import (
     ParameterMapping,
     create_parameter_mapping,
-    create_parameter_mapping_for_condition,
 )
-from .util import (  # noqa # pylint: disable=unused-import
-    get_states_in_condition_table,
-)
-
-# END DEPRECATED
 
 try:
     import pysb

python/sdist/amici/sbml_import.py

@@ -293,7 +293,6 @@ def sbml2amici(
         compute_conservation_laws: bool = True,
         simplify: Callable | None = _default_simplify,
         cache_simplify: bool = False,
-        log_as_log10: bool = None,
         generate_sensitivity_code: bool = True,
         hardcode_symbols: Sequence[str] = None,
     ) -> None:
@@ -448,10 +447,6 @@ def sbml2amici(
         :param cache_simplify:
             See :meth:`amici.DEModel.__init__`.
 
-        :param log_as_log10:
-            This option is deprecated and will be removed in a future version.
-            Also, this option never had any effect on model import.
-
         :param generate_sensitivity_code:
             If ``False``, the code required for sensitivity computation will
             not be generated.
@@ -464,16 +459,6 @@ def sbml2amici(
         """
         set_log_level(logger, verbose)
 
-        if log_as_log10 is not None:
-            # deprecated 04/2025
-            warnings.warn(
-                "The `log_as_log10` argument is deprecated and will be "
-                "removed in a future version. This argument can safely be "
-                "dropped without replacement.",
-                category=DeprecationWarning,
-                stacklevel=2,
-            )
-
         ode_model = self._build_ode_model(
             observables=observables,
             event_observables=event_observables,
@@ -521,7 +506,6 @@ def sbml2jax(
         compute_conservation_laws: bool = True,
         simplify: Callable | None = _default_simplify,
         cache_simplify: bool = False,
-        log_as_log10: bool = None,
     ) -> None:
         """
         Generate and compile AMICI jax files for the model provided to the
@@ -585,22 +569,9 @@ def sbml2jax(
 
         :param cache_simplify:
                 see :meth:`amici.DEModel.__init__`
-
-        :param log_as_log10:
-            This option is deprecated and will be removed in a future version.
-            Also, this option never had any effect on model import.
         """
         set_log_level(logger, verbose)
 
-        if log_as_log10 is not None:
-            warnings.warn(
-                "The `log_as_log10` argument is deprecated and will be "
-                "removed in a future version. This argument can safely be "
-                "dropped without replacement.",
-                category=DeprecationWarning,
-                stacklevel=2,
-            )
-
         ode_model = self._build_ode_model(
             observables=observables,
             sigmas=sigmas,