diff --git a/python/sdist/amici/parameter_mapping.py b/python/sdist/amici/parameter_mapping.py deleted file mode 100644 index dc369b448b..0000000000 --- a/python/sdist/amici/parameter_mapping.py +++ /dev/null @@ -1,46 +0,0 @@ -"""Parameter mapping between AMICI and PEtab. - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab.parameter_mapping` instead. -""" - -# some extra imports for backward-compatibility -import warnings - -from .petab.conditions import ( # noqa # pylint: disable=unused-import - fill_in_parameters, - fill_in_parameters_for_condition, -) -from .petab.parameter_mapping import ( # noqa # pylint: disable=unused-import - ParameterMapping, - ParameterMappingForCondition, - SingleParameterMapping, - SingleScaleMapping, - amici_to_petab_scale, - petab_to_amici_scale, - scale_parameter, - scale_parameters_dict, - unscale_parameter, - unscale_parameters_dict, -) - -warnings.warn( - "Importing amici.parameter_mapping is deprecated. Use `amici.petab.parameter_mapping` instead.", - DeprecationWarning, - stacklevel=2, -) - -__all__ = [ - "fill_in_parameters", - "fill_in_parameters_for_condition", - "ParameterMapping", - "ParameterMappingForCondition", - "SingleParameterMapping", - "SingleScaleMapping", - "amici_to_petab_scale", - "petab_to_amici_scale", - "scale_parameter", - "scale_parameters_dict", - "unscale_parameter", - "unscale_parameters_dict", -] diff --git a/python/sdist/amici/petab_import.py b/python/sdist/amici/petab_import.py deleted file mode 100644 index 1bcadaa1d2..0000000000 --- a/python/sdist/amici/petab_import.py +++ /dev/null @@ -1,47 +0,0 @@ -""" -PEtab Import ------------- -Import a model in the :mod:`petab` (https://github.com/PEtab-dev/PEtab) format -into AMICI. - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab` instead. -""" - -import warnings - -warnings.warn( - "Importing amici.petab_import is deprecated. Use `amici.petab` instead.", - DeprecationWarning, - stacklevel=2, -) - -from .petab.import_helpers import ( # noqa # pylint: disable=unused-import - get_observation_model, - petab_noise_distributions_to_amici, - petab_scale_to_amici_scale, -) - -# DEPRECATED - DON'T ADD ANYTHING NEW HERE -from .petab.petab_import import ( # noqa # pylint: disable=unused-import - check_model, - import_model, - import_model_sbml, - import_petab_problem, -) -from .petab.sbml_import import ( # noqa - _get_fixed_parameters_sbml as get_fixed_parameters, -) -from .petab.sbml_import import species_to_parameters # noqa - -__all__ = [ - "get_observation_model", - "petab_noise_distributions_to_amici", - "petab_scale_to_amici_scale", - "check_model", - "import_model", - "import_model_sbml", - "import_petab_problem", - "get_fixed_parameters", - "species_to_parameters", -] diff --git a/python/sdist/amici/petab_import_pysb.py b/python/sdist/amici/petab_import_pysb.py deleted file mode 100644 index 4d73a4bab3..0000000000 --- a/python/sdist/amici/petab_import_pysb.py +++ /dev/null @@ -1,22 +0,0 @@ -""" -PEtab import for PySB models - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab.pysb_import` instead. -""" - -import warnings - -from .petab.pysb_import import * # noqa: F401, F403 - -# DEPRECATED - DON'T ADD ANYTHING NEW HERE - -warnings.warn( - "Importing amici.petab_import_pysb is deprecated. Use `amici.petab.pysb_import` instead.", - DeprecationWarning, - stacklevel=2, -) - -__all__ = [ - "import_model_pysb", -] diff --git a/python/sdist/amici/petab_objective.py b/python/sdist/amici/petab_objective.py deleted file mode 100644 index 6d0dc44d84..0000000000 --- a/python/sdist/amici/petab_objective.py +++ /dev/null @@ -1,54 +0,0 @@ -""" -Evaluate a PEtab objective function. - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab.simulations` instead. -""" - -# THIS FILE IS TO BE REMOVED - DON'T ADD ANYTHING HERE! - -import warnings - -warnings.warn( - f"Importing {__name__} is deprecated. Use `amici.petab.simulations` instead.", - DeprecationWarning, - stacklevel=2, -) - -from .petab.conditions import fill_in_parameters # noqa: F401 -from .petab.parameter_mapping import create_parameter_mapping # noqa: F401 -from .petab.simulations import ( # noqa: F401 - EDATAS, - FIM, - LLH, - RDATAS, - RES, - S2LLH, - SLLH, - SRES, - aggregate_sllh, - create_edatas, - rdatas_to_measurement_df, - rdatas_to_simulation_df, - rescale_sensitivity, - simulate_petab, -) - -__all__ = [ - "EDATAS", - "FIM", - "LLH", - "RDATAS", - "RES", - "S2LLH", - "SLLH", - "SRES", - "aggregate_sllh", - "create_edatas", - "fill_in_parameters", - "create_parameter_mapping", - "rdatas_to_measurement_df", - "rdatas_to_simulation_df", - "rescale_sensitivity", - "simulate_petab", -] diff --git a/python/sdist/amici/petab_simulate.py b/python/sdist/amici/petab_simulate.py deleted file mode 100644 index 5f81d02a93..0000000000 --- a/python/sdist/amici/petab_simulate.py +++ /dev/null @@ -1,21 +0,0 @@ -""" -Simulate a PEtab problem - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab.simulator` instead. -""" -# THIS FILE IS TO BE REMOVED - DON'T ADD ANYTHING HERE! - -import warnings - -warnings.warn( - f"Importing {__name__} is deprecated. Use `amici.petab.simulator` instead.", - DeprecationWarning, - stacklevel=2, -) - -from .petab.simulator import PetabSimulator # noqa: F401 - -__all__ = [ - "PetabSimulator", -] diff --git a/python/sdist/amici/petab_util.py b/python/sdist/amici/petab_util.py deleted file mode 100644 index cf12a7411d..0000000000 --- a/python/sdist/amici/petab_util.py +++ /dev/null @@ -1,24 +0,0 @@ -""" -Various helper functions for working with PEtab problems. - -.. deprecated:: 0.21.0 - Use :mod:`amici.petab.util` instead. -""" - -# THIS FILE IS TO BE REMOVED - DON'T ADD ANYTHING HERE! - -import warnings - -from .petab import PREEQ_INDICATOR_ID # noqa: F401 -from .petab.util import get_states_in_condition_table # noqa: F401 - -warnings.warn( - f"Importing {__name__} is deprecated. Use `amici.petab.util` instead.", - DeprecationWarning, - stacklevel=2, -) - -__all__ = [ - "get_states_in_condition_table", - "PREEQ_INDICATOR_ID", -]