From 35f9baef8cf405322b9502c7708062f5759c19fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20K=C3=B6nig?= <konigmatt@googlemail.com>
Date: Fri, 31 Jan 2025 11:33:50 +0100
Subject: [PATCH] fixing inf issues

---
 setup.cfg                       | 9 +++++----
 src/sbmlsim/fit/helpers.py      | 5 ++++-
 src/sbmlsim/fit/objects.py      | 4 ++--
 src/sbmlsim/fit/optimization.py | 4 ++--
 4 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 34962db..4473474 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -28,8 +28,9 @@ classifiers =
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 	Operating System :: OS Independent
-	Programming Language :: Python :: 3.8
-	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+
 	Programming Language :: Python :: Implementation :: CPython
 	Topic :: Scientific/Engineering
 	Topic :: Scientific/Engineering :: Bio-Informatics
@@ -49,8 +50,8 @@ zip_safe = True
 python_requires = >=3.11
 install_requires =
     sbmlutils>=0.8.7
-    numpy>=1.26.4
-    libroadrunner>=2.7.0
+    numpy>=2.2
+    libroadrunner>=2.8.0
     scipy>=1.12.0
     pint>=0.23
 
diff --git a/src/sbmlsim/fit/helpers.py b/src/sbmlsim/fit/helpers.py
index 1f2c436..4929ef5 100644
--- a/src/sbmlsim/fit/helpers.py
+++ b/src/sbmlsim/fit/helpers.py
@@ -108,8 +108,11 @@ def f_fitexp(
 
     return fit_experiments
 
+
 def filter_empty(fit_mapping_key: str, fit_mapping: FitMapping) -> bool:
     """Return all experiments/mappings."""
     return True
 
-
+def filter_outlier(fit_mapping_key: str, fit_mapping: FitMapping) -> bool:
+    """Return non outlier experiments."""
+    return not fit_mapping.metadata.outlier
diff --git a/src/sbmlsim/fit/objects.py b/src/sbmlsim/fit/objects.py
index 1ff7913..3888496 100644
--- a/src/sbmlsim/fit/objects.py
+++ b/src/sbmlsim/fit/objects.py
@@ -224,8 +224,8 @@ def __init__(
         self,
         pid: str,
         start_value: float = None,
-        lower_bound: float = -np.Inf,
-        upper_bound: float = np.Inf,
+        lower_bound: float = -np.inf,
+        upper_bound: float = np.inf,
         unit: str = None,
     ):
         """Initialize FitParameter.
diff --git a/src/sbmlsim/fit/optimization.py b/src/sbmlsim/fit/optimization.py
index a219202..34908fc 100644
--- a/src/sbmlsim/fit/optimization.py
+++ b/src/sbmlsim/fit/optimization.py
@@ -43,8 +43,8 @@ class RuntimeErrorOptimizeResult:
     status: str = "-1"
     success: bool = False
     duration: float = -1.0
-    cost: float = np.Inf
-    optimality: float = np.Inf
+    cost: float = np.inf
+    optimality: float = np.inf
 
 
 class OptimizationProblem(ObjectJSONEncoder):