Avoid bug running python 3.08

Author: joseph-hellerstein

README.md

@@ -28,7 +28,7 @@ pySubnetSB is installed using
 https://github.com/ModelEngineering/pySubnetSB/blob/main/examples/api_basics.ipynb is a Jupyter notebook that demonstrates pySubsetSB capabilities.
 
 # Version History
-* 1.0.4 7/18/2025  Fix install issues with missing modules
+* 1.0.5 7/19/2025  Fix install issues with missing modules
 * 1.0.2 4/10/2025. ModelSpecification API accepts many kinds of model inputs, Antimony, SBML, roadrunner.
 * 1.0.1 4/09/2025. Improved generation of networks with subnets. Use "mapping_pair" in API. Bug fixes.
 * 1.0.0 2/27/2025. First beta release.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pySubnetSB"
-version = "1.0.4"
+version = "1.0.5"
 description = "Python Subnet Discovery for Systems Biology"
 authors = [{ name = "Joseph Hellerstein", email = "joseph.hellerstein@gmail.com" }]
 license = { file = "LICENSE" }

src/pySubnetSB/__init__.py

@@ -5,4 +5,4 @@
 A Network is a representation of a chemical reaction network that includes a NamedMatrix for reactants and products.
 A Constraint describes numerical or categorical charateristics of a network that are organized as one or more NamedMatrix.
 """
-__version__ = "1.0.4"
+__version__ = "1.0.5"

src/pySubnetSB/constraint_option_collection.py

@@ -20,7 +20,8 @@ def __init__(self, **kwargs):
         """
         self.__dict__.update(kwargs)
         self.option_names = list(kwargs.keys())
-        self.long_to_short_dct = {n: self.short_names[i] for i, n in enumerate(self.option_names)}
+        # short_names is defined in subclasses
+        self.long_to_short_dct = {n: self.short_names[i] for i, n in enumerate(self.option_names)} # type: ignore
         self.short_to_long_dct = {v: k for k, v in self.long_to_short_dct.items()}
         self.num_option = len(self.option_names)
 
@@ -42,7 +43,7 @@ def __eq__(self, other)->bool:
     def __repr__(self)->str:
         return str(self.__class__) + ": " + ', '.join(self.getTrueNames())
 
-    def getTrueNames(self)->list[str]:
+    def getTrueNames(self)->List[str]:
         results:list = []
         for i, key in enumerate(self.option_names):
             if self.__dict__[key]:
@@ -122,7 +123,7 @@ def iterator(self):
         Iteratively returns an OptionCollection of the same type with all combinations of
         values for the boolean attributes.
         """
-        name_collections = util.getAllSubsets(self.short_names)
+        name_collections = util.getAllSubsets(self.short_names) # type: ignore
         for name_collection in name_collections:
             yield self.makeOptionFromShortNames(name_collection)
 

src/pySubnetSB/network.py

@@ -23,15 +23,15 @@ class StructuralAnalysisResult(object):
     # Auxiliary object returned by isStructurallyIdentical
 
     def __init__(self,
-            assignment_pairs:list[AssignmentPair],
+            assignment_pairs:List[AssignmentPair],
             is_truncated:Optional[bool]=False,
             num_species_candidate:int=-1,
             num_reaction_candidate:int=-1,
             network:Optional['Network']=None,
             )->None:
         """
         Args:
-            assignment_pairs (list[AssignmentPair]): List of assignment pairs.
+            assignment_pairs (List[AssignmentPair]): List of assignment pairs.
             is_trucnated (bool): True if the number of assignments exceeds the maximum number of assignments.
             num_species_candidate (int): Number of species candidates assignments
             num_reaction_candidate (int): Number of reaction candidates assignments.