From 28b2611cc10c91f2d781944e9166b7d1e65341cf Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Fri, 19 Apr 2024 22:26:09 +0200
Subject: [PATCH 1/2] SwigPtrView: look up unhandled attributes in _swigptr
 (#2405)

So far, only the explicitly listed attributes are accessible directly via SwigPtrView.
Things like ReturnData.ny are only available through ReturnDataView.ptr.ny, which is inconvenient.
Let's just look all non-private attributes that are not already explicitly handled by SwigPtrView
on _swigptr and return them as is.
---
 python/sdist/amici/numpy.py         | 17 ++++++++++-------
 python/sdist/amici/plotting.py      |  2 +-
 python/tests/test_swig_interface.py |  3 +++
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index c1aef949c6..f40d0f4c6e 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -55,15 +55,18 @@ def __getitem__(self, item: str) -> Union[np.ndarray, float]:
         if item in self._cache:
             return self._cache[item]
 
-        if item == "id":
-            return getattr(self._swigptr, item)
+        if item in self._field_names:
+            value = _field_as_numpy(
+                self._field_dimensions, item, self._swigptr
+            )
+            self._cache[item] = value
 
-        if item not in self._field_names:
-            self.__missing__(item)
+            return value
+
+        if not item.startswith("_") and hasattr(self._swigptr, item):
+            return getattr(self._swigptr, item)
 
-        value = _field_as_numpy(self._field_dimensions, item, self._swigptr)
-        self._cache[item] = value
-        return value
+        self.__missing__(item)
 
     def __missing__(self, key: str) -> None:
         """
diff --git a/python/sdist/amici/plotting.py b/python/sdist/amici/plotting.py
index d27f2994ce..19dbe05f89 100644
--- a/python/sdist/amici/plotting.py
+++ b/python/sdist/amici/plotting.py
@@ -109,7 +109,7 @@ def plot_observable_trajectories(
     if not ax:
         fig, ax = plt.subplots()
     if not observable_indices:
-        observable_indices = range(rdata["y"].shape[1])
+        observable_indices = range(rdata.ny)
 
     if marker is None:
         # Show marker if only one time point is available,
diff --git a/python/tests/test_swig_interface.py b/python/tests/test_swig_interface.py
index f214519f26..b5063ca3cc 100644
--- a/python/tests/test_swig_interface.py
+++ b/python/tests/test_swig_interface.py
@@ -511,6 +511,9 @@ def test_rdataview(sbml_example_presimulation_module):
     rdata = amici.runAmiciSimulation(model, model.getSolver())
     assert isinstance(rdata, amici.ReturnDataView)
 
+    # check that non-array attributes are looked up in the wrapped object
+    assert rdata.ptr.ny == rdata.ny
+
     # fields are accessible via dot notation and [] operator,
     #  __contains__ and __getattr__ are implemented correctly
     with pytest.raises(AttributeError):

From e8493cf32773847078151954754b8a33eaa5047d Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sat, 20 Apr 2024 00:49:20 +0200
Subject: [PATCH 2/2] cmake: set sundials path hint for python package (#2397)

So far, CMakeLists.txt only provided a path hint for sundials for the
standalone c++ library, but not for the python package. The latter
should be added to ensure the right sundials version is found. There
have been issues with system installations of sundials.

Closes #2394
---
 CMakeLists.txt | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 744847930d..d8a1109d90 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -133,9 +133,16 @@ elseif(AMICI_TRY_ENABLE_HDF5)
 endif()
 
 set(VENDORED_SUNDIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/sundials)
-set(VENDORED_SUNDIALS_BUILD_DIR ${VENDORED_SUNDIALS_DIR}/build)
-set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
 set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
+# Handle different sundials build/install dirs, depending on whether we are
+#  building the Python extension only or the full C++ interface
+if(AMICI_PYTHON_BUILD_EXT_ONLY)
+  set(VENDORED_SUNDIALS_BUILD_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+  set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
+else()
+  set(VENDORED_SUNDIALS_BUILD_DIR ${VENDORED_SUNDIALS_DIR}/build)
+  set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
+endif()
 find_package(
   SUNDIALS REQUIRED PATHS
   "${VENDORED_SUNDIALS_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake/sundials/")