From 0f961d676cbda261c32360463cc2245e957ff600 Mon Sep 17 00:00:00 2001
From: Polina Lakrisenko <p.lakrisenko@gmail.com>
Date: Mon, 4 Mar 2024 14:14:34 +0100
Subject: [PATCH 1/3] Fix missing import in `amici/petab/petab_import.py`
 (#2342)

fixes
```
Traceback (most recent call last):
  File "//./mnt/src/optimize.py", line 557, in <module>
    model, model_petab_problem = _model_import(
  File "/mnt/src/util.py", line 44, in _model_import
    model = amici.petab_import.import_petab_problem(
  File "/usr/local/lib/python3.10/dist-packages/amici/petab/petab_import.py", line 79, in import_petab_problem
    warn(
NameError: name 'warn' is not defined
```
---
 python/sdist/amici/petab/petab_import.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python/sdist/amici/petab/petab_import.py b/python/sdist/amici/petab/petab_import.py
index 902bf837ef..cb896b39e3 100644
--- a/python/sdist/amici/petab/petab_import.py
+++ b/python/sdist/amici/petab/petab_import.py
@@ -10,6 +10,7 @@
 import shutil
 from pathlib import Path
 from typing import Union
+from warnings import warn
 
 import amici
 import petab

From 1ab1d555feb1162b9e5be9876ecd14bede374019 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Mon, 4 Mar 2024 15:22:08 +0100
Subject: [PATCH 2/3] Fix ReturnDataView AttributeError: messages (#2341)

* Make log messages from ReturnData available through ReturnDataView.
* Add `LogItem.__repr__`

Closes #2331.
---
 python/sdist/amici/numpy.py      | 9 +++++++--
 python/tests/test_sbml_import.py | 2 +-
 swig/amici.i                     | 8 ++++++++
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index 6e2966ba4b..f75d927b7b 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -9,7 +9,7 @@
 import itertools
 from typing import Literal, Union
 from collections.abc import Iterator
-
+from numbers import Number
 import amici
 import numpy as np
 import sympy as sp
@@ -238,6 +238,7 @@ class ReturnDataView(SwigPtrView):
         "numnonlinsolvconvfailsB",
         "cpu_timeB",
         "cpu_time_total",
+        "messages",
     ]
 
     def __init__(self, rdata: Union[ReturnDataPtr, ReturnData]):
@@ -440,7 +441,11 @@ def _field_as_numpy(
     attr = getattr(data, field)
     if field_dim := field_dimensions.get(field, None):
         return None if len(attr) == 0 else np.array(attr).reshape(field_dim)
-    return float(attr)
+
+    if isinstance(attr, Number):
+        return float(attr)
+
+    return attr
 
 
 def _entity_type_from_id(
diff --git a/python/tests/test_sbml_import.py b/python/tests/test_sbml_import.py
index 74a51d020a..ecf21f1f95 100644
--- a/python/tests/test_sbml_import.py
+++ b/python/tests/test_sbml_import.py
@@ -368,7 +368,7 @@ def test_solver_reuse(model_steadystate_module):
         assert rdata1.status == amici.AMICI_SUCCESS
 
         for attr in rdata1:
-            if "time" in attr:
+            if "time" in attr or attr == "messages":
                 continue
 
             val1 = getattr(rdata1, attr)
diff --git a/swig/amici.i b/swig/amici.i
index 3518b296fe..1ef076fe33 100644
--- a/swig/amici.i
+++ b/swig/amici.i
@@ -235,6 +235,14 @@ def __repr__(self):
 %}
 };
 
+%extend amici::LogItem {
+%pythoncode %{
+def __repr__(self):
+    return (f"{self.__class__.__name__}(severity={self.severity}, "
+        f"identifier={self.identifier!r}, message={self.message!r})")
+%}
+};
+
 
 // Convert integer values to enum class
 // defeats the purpose of enum class, but didn't find a better way to allow for

From e8852be21a25b9fa79fc2fa2bbd44a4c83edabb6 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Mon, 4 Mar 2024 15:23:00 +0100
Subject: [PATCH 3/3] Fix swig/std_unique_ptr.i (#2343)

Fixes some `used without template arguments` errors when running swig with `-builtin` or `-keyword`.
---
 swig/std_unique_ptr.i | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/swig/std_unique_ptr.i b/swig/std_unique_ptr.i
index c44513bcee..f73babfd9e 100644
--- a/swig/std_unique_ptr.i
+++ b/swig/std_unique_ptr.i
@@ -17,7 +17,7 @@ namespace std {
 
      pointer operator-> () const;
      pointer release ();
-     void reset (pointer __p=pointer());
+     void reset (pointer __p=std::unique_ptr<Type>::pointer());
      void swap (unique_ptr &__u);
      pointer get () const;
      operator bool () const;