Remove deprecated functionality for PEtab import from individual files instead of petab.Problem

python/sdist/amici/petab/sbml_import.py

@@ -5,11 +5,9 @@
 from itertools import chain
 from pathlib import Path
 from typing import Union
-from warnings import warn
 
 import amici
 import libsbml
-import pandas as pd
 import petab
 import sympy as sp
 from _collections import OrderedDict
@@ -31,9 +29,6 @@
 @log_execution_time("Importing PEtab model", logger)
 def import_model_sbml(
     sbml_model: Union[str, Path, "libsbml.Model"] = None,
-    condition_table: str | Path | pd.DataFrame | None = None,
-    observable_table: str | Path | pd.DataFrame | None = None,
-    measurement_table: str | Path | pd.DataFrame | None = None,
     petab_problem: petab.Problem = None,
     model_name: str | None = None,
     model_output_dir: str | Path | None = None,
@@ -52,18 +47,6 @@ def import_model_sbml(
         PEtab SBML model or SBML file name.
         Deprecated, pass ``petab_problem`` instead.
 
-    :param condition_table:
-        PEtab condition table. If provided, parameters from there will be
-        turned into AMICI constant parameters (i.e. parameters w.r.t. which
-        no sensitivities will be computed).
-        Deprecated, pass ``petab_problem`` instead.
-
-    :param observable_table:
-        PEtab observable table. Deprecated, pass ``petab_problem`` instead.
-
-    :param measurement_table:
-        PEtab measurement table. Deprecated, pass ``petab_problem`` instead.
-
     :param petab_problem:
         PEtab problem.
 
@@ -113,31 +96,6 @@ def import_model_sbml(
 
     logger.info("Importing model ...")
 
-    if any([sbml_model, condition_table, observable_table, measurement_table]):
-        warn(
-            "The `sbml_model`, `condition_table`, `observable_table`, and "
-            "`measurement_table` arguments are deprecated and will be "
-            "removed in a future version. Use `petab_problem` instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        if petab_problem:
-            raise ValueError(
-                "Must not pass a `petab_problem` argument in "
-                "combination with any of `sbml_model`, "
-                "`condition_table`, `observable_table`, or "
-                "`measurement_table`."
-            )
-
-        petab_problem = petab.Problem(
-            model=SbmlModel(sbml_model)
-            if isinstance(sbml_model, libsbml.Model)
-            else SbmlModel.from_file(sbml_model),
-            condition_df=petab.get_condition_df(condition_table),
-            observable_df=petab.get_observable_df(observable_table),
-            measurement_df=petab.get_measurement_df(measurement_table),
-        )
-
     if petab_problem.observable_df is None:
         raise NotImplementedError(
             "PEtab import without observables table "

python/sdist/pyproject.toml

@@ -4,13 +4,7 @@
 requires = [
     "setuptools>=61",
     "wheel",
-    # oldest-supported-numpy helps us to pin numpy here to the lowest supported
-    # version to have ABI-compatibility with the numpy version in the runtime
-    # environment. The undesirable alternative would be pinning the setup.py
-    # numpy requirement to the same version as here, which we want to avoid.
-    # cf. discussion at https://github.com/numpy/numpy/issues/5888
-    # (https://github.com/scipy/oldest-supported-numpy/)
-    "oldest-supported-numpy",
+    "numpy>=2.0",
     "cmake-build-extension==0.6.0",
 ]
 build-backend = "setuptools.build_meta"

python/tests/test_preequilibration.py

@@ -32,7 +32,7 @@ def preeq_fixture(pysb_example_presimulation_module):
 
     edata_preeq = amici.ExpData(edata)
     edata_preeq.t_presim = 0
-    edata_preeq.setTimepoints([np.infty])
+    edata_preeq.setTimepoints([np.inf])
     edata_preeq.fixedParameters = edata.fixedParametersPreequilibration
     edata_preeq.fixedParametersPresimulation = ()
     edata_preeq.fixedParametersPreequilibration = ()