....

documentation/conf.py

@@ -9,19 +9,33 @@
 import subprocess
 import sys
 from enum import EnumType
-
-# need to import before setting typing.TYPE_CHECKING=True, fails otherwise
-import amici
 import exhale.deploy
-import exhale_multiproject_monkeypatch
 from unittest import mock
-import pandas as pd
 import sphinx
-import sympy as sp
 from exhale import configs as exhale_configs
 from sphinx.transforms.post_transforms import ReferencesResolver
 
-exhale_multiproject_monkeypatch, pd, sp  # to avoid removal of unused import
+try:
+    import exhale_multiproject_monkeypatch  # noqa: F401
+except ModuleNotFoundError:
+    # for unclear reasons, the import of exhale_multiproject_monkeypatch
+    #  fails on some systems, because the the location of the editable install
+    #  is not automatically added to sys.path ¯\_(ツ)_/¯
+    from importlib.metadata import Distribution
+    import json
+    from urllib.parse import unquote_plus, urlparse
+
+    dist = Distribution.from_name("sphinx-contrib-exhale-multiproject")
+    url = json.loads(dist.read_text("direct_url.json"))["url"]
+    package_dir = unquote_plus(urlparse(url).path)
+    sys.path.append(package_dir)
+    import exhale_multiproject_monkeypatch  # noqa: F401
+
+# need to import before setting typing.TYPE_CHECKING=True, fails otherwise
+import amici
+import pandas as pd  # noqa: F401
+import sympy as sp  # noqa: F401
+
 
 # BEGIN Monkeypatch exhale
 from exhale.deploy import _generate_doxygen as exhale_generate_doxygen

python/sdist/amici/swig.py

@@ -159,7 +159,7 @@ def _annotation_from_docstring(self, node: ast.FunctionDef):
     @staticmethod
     def extract_type(line: str) -> tuple[str, str] | tuple[None, None]:
         """Extract argument name and type string from ``:type:`` docstring line."""
-        match = re.match(r"\s*:type\s+(\w+):\s+(.+)\s*$", line)
+        match = re.match(r"\s*:type\s+(\w+):\s+(.+)(?:, optional)?\s*$", line)
         if not match:
             return None, None
 

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
+from amici.amici import (
+    _get_ptr,
+    AmiciExpData,
+    AmiciExpDataVector,
+    AmiciModel,
+    AmiciSolver,
+)
 from . import numpy
 from .logging import get_logger
 
@@ -22,20 +27,8 @@
     "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:

swig/amici.i

@@ -355,7 +355,8 @@ 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
+from collections.abc import Sequence
 import numpy as np
 if TYPE_CHECKING:
     import numpy
@@ -371,6 +372,11 @@ __all__ = [
     and x not in {"np", "sys", "os", "numpy", "IntEnum", "enum", "pi", "TYPE_CHECKING", "Iterable", "Sequence"}
 ]
 
+AmiciModel = Model | ModelPtr
+AmiciSolver = Solver | SolverPtr
+AmiciExpData = ExpData | ExpDataPtr
+AmiciReturnData = ReturnData | ReturnDataPtr
+AmiciExpDataVector = ExpDataPtrVector | Sequence[AmiciExpData]
 
 def _get_ptr(
     obj: AmiciModel | AmiciExpData | AmiciSolver | AmiciReturnData,

swig/misc.i

@@ -4,6 +4,8 @@
 %ignore amici::regexErrorToString;
 %ignore amici::writeSlice;
 %ignore ContextManager;
+%ignore amici::scaleParameters;
+%ignore amici::unscaleParameters;
 
 // Add necessary symbols to generated header
 %{