Move the amici.swig_wrappers.ExpData logic into the swig-generated …

…`ExpData`.

This avoids shading the `ExpData` class by  `amici.swig_wrappers.ExpData`.
The old implementation prevented using e.g. `isinstance(x, amici.ExpData)`.

This required also:
* Moving some annotation types and `_get_ptr` from `amici.swig_wrappers` to the swig-generated `amici.py`
* Some smaller changes to allow for using `from __future__ import annotations` in `amici.py`

Closes AMICI-dev#2380

documentation/conf.py

@@ -558,15 +558,15 @@ def fix_typehints(sig: str) -> str:
     sig = sig.replace("sunindextype", "int")
     sig = sig.replace("H5::H5File", "object")
 
-    # remove const
-    sig = sig.replace(" const ", r" ")
-    sig = re.sub(r" const$", r"", sig)
+    # remove const / const&
+    sig = sig.replace(" const&? ", r" ")
+    sig = re.sub(r" const&?$", r"", sig)
 
     # remove pass by reference
     sig = re.sub(r" &(,|\))", r"\1", sig)
     sig = re.sub(r" &$", r"", sig)
 
-    # turn gsl_spans and pointers int Iterables
+    # turn gsl_spans and pointers into Iterables
     sig = re.sub(r"([\w.]+) \*", r"Iterable[\1]", sig)
     sig = re.sub(r"gsl::span< ([\w.]+) >", r"Iterable[\1]", sig)
 

python/sdist/amici/__init__.py

@@ -134,8 +134,6 @@ def get_model(self) -> amici.Model:
             """Create a model instance."""
             ...
 
-    AmiciModel = Union[amici.Model, amici.ModelPtr]
-
 
 class add_path:
     """Context manager for temporarily changing PYTHONPATH"""

python/sdist/amici/swig_wrappers.py

@@ -4,11 +4,16 @@
 import warnings
 from contextlib import contextmanager, suppress
 from typing import Any, Optional, Union
-from collections.abc import Sequence
 
 import amici
 import amici.amici as amici_swig
-
+from amici.amici import (
+    _get_ptr,
+    AmiciExpData,
+    AmiciExpDataVector,
+    AmiciModel,
+    AmiciSolver,
+)
 from . import numpy
 from .logging import get_logger
 
@@ -18,25 +23,12 @@
 __all__ = [
     "runAmiciSimulation",
     "runAmiciSimulations",
-    "ExpData",
     "readSolverSettingsFromHDF5",
     "writeSolverSettingsToHDF5",
     "set_model_settings",
     "get_model_settings",
-    "AmiciModel",
-    "AmiciSolver",
-    "AmiciExpData",
-    "AmiciReturnData",
-    "AmiciExpDataVector",
 ]
 
-AmiciModel = Union["amici.Model", "amici.ModelPtr"]
-AmiciSolver = Union["amici.Solver", "amici.SolverPtr"]
-AmiciExpData = Union["amici.ExpData", "amici.ExpDataPtr"]
-AmiciReturnData = Union["amici.ReturnData", "amici.ReturnDataPtr"]
-AmiciExpDataVector = Union["amici.ExpDataPtrVector", Sequence[AmiciExpData]]
-
-
 try:
     from wurlitzer import sys_pipes
 except ModuleNotFoundError:
@@ -54,36 +46,6 @@ def _capture_cstdout():
             yield
 
 
-def _get_ptr(
-    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData],
-) -> Union[
-    "amici_swig.Model",
-    "amici_swig.ExpData",
-    "amici_swig.Solver",
-    "amici_swig.ReturnData",
-]:
-    """
-    Convenience wrapper that returns the smart pointer pointee, if applicable
-
-    :param obj:
-        Potential smart pointer
-
-    :returns:
-        Non-smart pointer
-    """
-    if isinstance(
-        obj,
-        (
-            amici_swig.ModelPtr,
-            amici_swig.ExpDataPtr,
-            amici_swig.SolverPtr,
-            amici_swig.ReturnDataPtr,
-        ),
-    ):
-        return obj.get()
-    return obj
-
-
 def runAmiciSimulation(
     model: AmiciModel,
     solver: AmiciSolver,
@@ -128,32 +90,6 @@ def runAmiciSimulation(
     return numpy.ReturnDataView(rdata)
 
 
-def ExpData(*args) -> "amici_swig.ExpData":
-    """
-    Convenience wrapper for :py:class:`amici.amici.ExpData` constructors
-
-    :param args: arguments
-
-    :returns: ExpData Instance
-    """
-    if not args:
-        return amici_swig.ExpData()
-
-    if isinstance(args[0], numpy.ReturnDataView):
-        return amici_swig.ExpData(_get_ptr(args[0]["ptr"]), *args[1:])
-
-    if isinstance(args[0], (amici_swig.ExpData, amici_swig.ExpDataPtr)):
-        # the *args[:1] should be empty, but by the time you read this,
-        # the constructor signature may have changed, and you are glad this
-        # wrapper did not break.
-        return amici_swig.ExpData(_get_ptr(args[0]), *args[1:])
-
-    if isinstance(args[0], (amici_swig.Model, amici_swig.ModelPtr)):
-        return amici_swig.ExpData(_get_ptr(args[0]))
-
-    return amici_swig.ExpData(*args)
-
-
 def runAmiciSimulations(
     model: AmiciModel,
     solver: AmiciSolver,

swig/amici.i

@@ -341,6 +341,8 @@ def __repr__(self):
 
 // Handle AMICI_DLL_DIRS environment variable
 %pythonbegin %{
+from __future__ import annotations
+
 import sys
 import os
 
@@ -353,19 +355,52 @@ if sys.platform == 'win32' and (dll_dirs := os.environ.get('AMICI_DLL_DIRS')):
 // import additional types for typehints
 // also import np for use in __repr__ functions
 %pythonbegin %{
-from typing import TYPE_CHECKING, Iterable, Sequence
+from typing import TYPE_CHECKING, Iterable, Union
+from collections.abc import Sequence
 import numpy as np
 if TYPE_CHECKING:
     import numpy
 %}
 
 %pythoncode %{
 
+AmiciModel = Union[Model, ModelPtr]
+AmiciSolver = Union[Solver, SolverPtr]
+AmiciExpData = Union[ExpData, ExpDataPtr]
+AmiciReturnData = Union[ReturnData, ReturnDataPtr]
+AmiciExpDataVector = Union[ExpDataPtrVector, Sequence[AmiciExpData]]
+
+
+def _get_ptr(
+    obj: AmiciModel | AmiciExpData | AmiciSolver | AmiciReturnData,
+) -> Model | ExpData | Solver | ReturnData:
+    """
+    Convenience wrapper that returns the smart pointer pointee, if applicable
+
+    :param obj:
+        Potential smart pointer
+
+    :returns:
+        Non-smart pointer
+    """
+    if isinstance(
+        obj,
+        (
+            ModelPtr,
+            ExpDataPtr,
+            SolverPtr,
+            ReturnDataPtr,
+        ),
+    ):
+        return obj.get()
+    return obj
+
 
 __all__ = [
     x
     for x in dir(sys.modules[__name__])
     if not x.startswith('_')
     and x not in {"np", "sys", "os", "numpy", "IntEnum", "enum", "pi", "TYPE_CHECKING", "Iterable", "Sequence"}
 ]
+
 %}

swig/edata.i

@@ -8,6 +8,24 @@ using namespace amici;
 
 %ignore ConditionContext;
 
+%feature("pythonprepend") amici::ExpData::ExpData %{
+    """
+    Convenience wrapper for :py:class:`amici.amici.ExpData` constructors
+
+    :param args: arguments
+
+    :returns: ExpData Instance
+    """
+    if args:
+        from amici.numpy import ReturnDataView
+
+        # Get the raw pointer if necessary
+        if isinstance(args[0], (ExpData, ExpDataPtr, Model, ModelPtr)):
+            args = (_get_ptr(args[0]), *args[1:])
+        elif isinstance(args[0], ReturnDataView):
+            args = (_get_ptr(args[0]["ptr"]), *args[1:])
+%}
+
 // ExpData.__repr__
 %pythoncode %{
 def _edata_repr(self: "ExpData"):