fixing numpy 2 issues

Author: matthiaskoenig

misc/xpp/xpp_models.py

@@ -194,9 +194,9 @@ def simulate(sbml_file):
             traceback.print_exc(file=sys.stdout)
             print()
             success = False
-            valid = np.NaN
-            simulates = np.NaN
-            Nall, Nerr, Nwarn = np.NaN, np.NaN, np.NaN
+            valid = np.nan
+            simulates = np.nan
+            Nall, Nerr, Nwarn = np.nan, np.nan, np.nan
 
             Nfail += 1
         results.append([xpp_file, success, valid, simulates, Nall, Nerr, Nwarn])

src/sbmlutils/examples/reaction.py

@@ -20,7 +20,7 @@
     + templates.terms_of_use,
     creators=templates.creators,
     compartments=[
-        Compartment(sid="c", name="cytosol", value=np.NaN),
+        Compartment(sid="c", name="cytosol", value=np.nan),
     ],
     species=[
         Species(
@@ -102,10 +102,10 @@
             sid="v4",
             equation=ReactionEquation(
                 reactants=[
-                    EquationPart(species="x", stoichiometry=np.NaN, sid="v4_x"),
+                    EquationPart(species="x", stoichiometry=np.nan, sid="v4_x"),
                 ],
                 products=[
-                    EquationPart(species="y", stoichiometry=np.NaN, sid="v4_y"),
+                    EquationPart(species="y", stoichiometry=np.nan, sid="v4_y"),
                 ],
                 reversible=False,
             ),

src/sbmlutils/factory.py

@@ -42,7 +42,7 @@
 import libsbml
 import numpy as np
 import xmltodict  # type: ignore
-from numpy import NaN
+from numpy import nan as NaN
 from pint import UndefinedUnitError, UnitRegistry
 from pydantic import BaseModel, ConfigDict
 from pymetadata.core.creator import Creator
@@ -1088,7 +1088,7 @@ def create_sbml(self, model: libsbml.Model) -> libsbml.Parameter:
         obj: libsbml.Parameter = model.createParameter()
         self._set_fields(obj, model)
         if self.value is None:
-            obj.setValue(np.NaN)
+            obj.setValue(np.nan)
 
         elif type(self.value) is str:
             try:
@@ -1160,7 +1160,7 @@ def create_sbml(self, model: libsbml.Model) -> libsbml.Compartment:
         self._set_fields(obj, model)
 
         if self.value is None:
-            obj.setSize(np.NaN)
+            obj.setSize(np.nan)
         elif type(self.value) is str:
             try:
                 # check if number

src/sbmlutils/resources/converters/odefac_template.pytemp

@@ -49,7 +49,7 @@ x0 = np.array([
 # -------------------
 p = np.array([
 {% for id in pids %}
-    {{ 'np.NaN' if p.get(id)|string == 'nan' else p[id] }},     # [{{ loop.index0 }}] {{ id }} [{{units[id]}}] {{names[id]}}
+    {{ 'np.nan' if p.get(id)|string == 'nan' else p[id] }},     # [{{ loop.index0 }}] {{ id }} [{{units[id]}}] {{names[id]}}
 {% endfor %}
 ])
 

tests/test_factory.py

@@ -25,7 +25,7 @@
         {"compartments": 1, "parameters": 0, "initial_assignments": 0, "rules": 0},
     ),
     (
-        np.NaN,
+        np.nan,
         True,
         {"compartments": 1, "parameters": 0, "initial_assignments": 0, "rules": 0},
     ),
@@ -103,7 +103,7 @@ def test_compartment_value(
 parameter_value_data = [
     (1.0, True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
     (1, True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
-    (np.NaN, True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
+    (np.nan, True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
     ("1.0", True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
     ("1", True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),
     ("NaN", True, {"parameters": 1, "initial_assignments": 0, "rules": 0}),