Update imports/exports (#3092)

Simplify some imports. Fix type annotations. Import extension types only where necessary.

Author: dweindl

python/sdist/amici/importers/pysb/__init__.py

@@ -14,9 +14,7 @@
 import sys
 from collections.abc import Callable, Iterable
 from pathlib import Path
-from typing import (
-    Any,
-)
+from typing import Any
 
 import numpy as np
 import pysb

python/sdist/amici/importers/sbml/__init__.py

@@ -82,7 +82,6 @@
 
 SymbolicFormula = dict[sp.Symbol, sp.Expr]
 
-
 default_symbols = {symbol: {} for symbol in SymbolId}
 
 ConservationLaw = dict[str, str | sp.Expr]

python/sdist/amici/importers/sbml/conserved_quantities_rref.py

@@ -1,15 +1,13 @@
 """Find conserved quantities deterministically"""
 
-from typing import Literal
-
 import numpy as np
 
 __all__ = ["nullspace_by_rref", "rref"]
 
 
 def rref(
-    mat: np.array, round_ndigits: Literal[False] | int | None = None
-) -> np.array:
+    mat: np.ndarray, round_ndigits: bool | int | None = None
+) -> np.ndarray:
     """
     Bring matrix ``mat`` to reduced row echelon form
 
@@ -69,7 +67,7 @@ def _round(mat):
     return mat
 
 
-def pivots(mat: np.array) -> list[int]:
+def pivots(mat: np.ndarray) -> list[int]:
     """Get indices of pivot columns in ``mat``, assumed to be in reduced row
     echelon form"""
     pivot_cols = []
@@ -83,7 +81,7 @@ def pivots(mat: np.array) -> list[int]:
     return pivot_cols
 
 
-def nullspace_by_rref(mat: np.array) -> np.array:
+def nullspace_by_rref(mat: np.ndarray) -> np.ndarray:
     """Compute basis of the nullspace of ``mat`` based on the reduced row
     echelon form"""
     rref_mat = rref(mat)

python/sdist/amici/sim/sundials/_numpy.py

@@ -491,7 +491,7 @@ def __repr__(self):
 
     def by_id(
         self, entity_id: str, field: str = None, model: Model = None
-    ) -> np.array:
+    ) -> np.ndarray:
         """
         Get the value of a given field for a named entity.
 
@@ -635,7 +635,7 @@ def _entity_type_from_id(
     raise KeyError(f"Unknown symbol {entity_id}.")
 
 
-def evaluate(expr: StrOrExpr, rdata: ReturnDataView) -> np.array:
+def evaluate(expr: StrOrExpr, rdata: ReturnDataView) -> np.ndarray:
     """Evaluate a symbolic expression based on the given simulation outputs.
 
     :param expr:

python/sdist/amici/sim/sundials/gradient_check.py

@@ -15,7 +15,7 @@
     ExpData,
     Model,
     ParameterScaling,
-    ReturnData,
+    ReturnDataView,
     SensitivityMethod,
     SensitivityOrder,
     Solver,
@@ -272,8 +272,8 @@ def check_derivatives(
 
 
 def _check_close(
-    result: np.array,
-    expected: np.array,
+    result: np.ndarray,
+    expected: np.ndarray,
     atol: float,
     rtol: float,
     field: str,
@@ -342,7 +342,11 @@ def _check_close(
 
 
 def _check_results(
-    rdata: ReturnData, field: str, expected: np.array, atol: float, rtol: float
+    rdata: ReturnDataView,
+    field: str,
+    expected: np.ndarray,
+    atol: float,
+    rtol: float,
 ) -> None:
     """
     Checks whether rdata[field] agrees with expected according to provided

python/sdist/amici/sim/sundials/petab/v1/__init__.py

@@ -1,4 +1,8 @@
-from ._conditions import create_edatas, create_parameterized_edatas
+from ._conditions import (
+    create_edatas,
+    create_parameterized_edatas,
+    fill_in_parameters,
+)
 from ._petab_problem import PetabProblem
 from ._simulations import (
     EDATAS,
@@ -31,4 +35,5 @@
     "PetabSimulator",
     "create_edatas",
     "create_parameterized_edatas",
+    "fill_in_parameters",
 ]

python/sdist/amici/sim/sundials/petab/v1/_simulations.py

@@ -60,6 +60,8 @@
     "SRES",
     "RDATAS",
     "EDATAS",
+    "rdatas_to_measurement_df",
+    "rdatas_to_simulation_df",
 ]
 
 

python/sdist/amici/testing/models.py

@@ -1,8 +1,11 @@
 """Test models used by AMICI."""
 
+from __future__ import annotations
+
 import sys
 import tempfile
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 import libsbml
 import sympy as sp
@@ -11,7 +14,9 @@
 from amici.importers.antimony import antimony2amici, antimony2sbml
 from amici.importers.sbml.splines import CubicHermiteSpline
 from amici.importers.utils import amici_time_symbol
-from amici.sim.sundials import AmiciModel, Model
+
+if TYPE_CHECKING:
+    from amici.sim.sundials import AmiciModel, Model
 
 model_dirac_ant = r"""
 p1 = 1;

python/tests/util.py

@@ -6,14 +6,14 @@
 
 import numpy as np
 import pandas as pd
-from amici import import_model_module
 from amici.importers.sbml import SbmlImporter
 from amici.sim.sundials import (
     AMICI_SUCCESS,
     AmiciModel,
     ExpData,
     SensitivityMethod,
     SensitivityOrder,
+    import_model_module,
     run_simulation,
 )
 from amici.sim.sundials.gradient_check import _check_close