Fix build break

Author: joseph-hellerstein

src/pySubnetSB/network.py

@@ -24,12 +24,12 @@ class StructuralAnalysisResult(object):
     # Auxiliary object returned by isStructurallyIdentical
 
     def __init__(self,
-                 assignment_pairs:list[AssignmentPair],
-                 is_truncated:Optional[bool]=False,
-                 num_species_candidate:int=-1,
-                 num_reaction_candidate:int=-1,
-                 network:Optional['Network']=None,
-                 )->None:
+            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.

src/pySubnetSB/network_base.py

@@ -49,7 +49,7 @@ def __init__(self, reactant_arr:Matrix,
         if not np.all(reactant_arr.shape == product_arr.shape):
             raise ValueError("Reactant and product matrices must have the same shape.")
         try:
-            self.num_species, self.num_reaction = np.shape(reactant_arr)
+            self.num_species, self.num_reaction = np.shape(reactant_arr)  # type: ignore
         except:
             # Empty network
             self.num_species = 0
@@ -65,15 +65,15 @@ def __init__(self, reactant_arr:Matrix,
         self.current_species_names = species_names
         self.current_reaction_names = reaction_names
         #
-        self.reactant_nmat = NamedMatrix(self.reactant_arr,
-              row_names=self.current_species_names, column_names=self.current_reaction_names,
-              row_description="species", column_description="reactions")
+        self.reactant_nmat = NamedMatrix(self.reactant_arr,  # type: ignore
+                row_names=self.current_species_names, column_names=self.current_reaction_names,
+                row_description="species", column_description="reactions")
         self.product_nmat = NamedMatrix(self.product_arr,
-              row_names=self.current_species_names, column_names=self.current_reaction_names,
-              row_description="species", column_description="reactions")
+                row_names=self.current_species_names, column_names=self.current_reaction_names,
+                row_description="species", column_description="reactions")
         self.standard_nmat = NamedMatrix(self.product_arr - self.reactant_arr,
-              row_names=self.current_species_names,
-              column_names=self.current_reaction_names, row_description="species", column_description="reactions")
+                row_names=self.current_species_names,
+                column_names=self.current_reaction_names, row_description="species", column_description="reactions")
         #
         self._species_names = self.current_species_names
         self._reaction_names = self.current_reaction_names
@@ -940,5 +940,5 @@ def makeInducedNetwork(self, assignment_pair:AssignmentPair)->'NetworkBase':
         product_arr = self.product_nmat.values[species_assignment, :]
         reactant_arr = reactant_arr[:, reaction_assignment]
         product_arr = product_arr[:, reaction_assignment]
-        return self.__class__(reactant_arr, product_arr, reaction_names=self.reaction_names[reaction_assignment],
+        return self.__class__(reactant_arr, product_arr, reaction_names=self.reaction_names[reaction_assignment],  # type: ignore
                         species_names=self.species_names[species_assignment])

src/pySubnetSB_tests/test_network_base.py

@@ -6,12 +6,13 @@
 from pySubnetSB.assignment_pair import AssignmentPair # type: ignore
 
 import os
-from pynauty import Graph  # type: ignore
+#from pynauty import Graph  # type: ignore
 import matplotlib.pyplot as plt
 import numpy as np
 import copy
 import tellurium as te  # type: ignore
 import unittest
+from typing import cast
 
 
 IGNORE_TEST = False
@@ -84,7 +85,7 @@
 class TestNetwork(unittest.TestCase):
 
     def setUp(self):
-        self.network = copy.deepcopy(NETWORK)
+        self.network = cast(NetworkBase, copy.deepcopy(NETWORK))
 
     @util.timeit
     def testConstrutor(self):
@@ -107,7 +108,7 @@ def testCopyEqual(self):
     def testIsMatrixEqual(self):
         if IGNORE_TEST:
             return
-        network = NetworkBase.makeFromAntimonyStr(NETWORK1, network_name=NETWORK_NAME)
+        network = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK1, network_name=NETWORK_NAME))
         network3 = NetworkBase.makeFromAntimonyStr(NETWORK3, network_name=NETWORK_NAME)
         self.assertTrue(network.isMatrixEqual(network3, identity=cn.ID_WEAK))
         self.assertFalse(network.isMatrixEqual(network3, identity=cn.ID_STRONG))
@@ -121,7 +122,7 @@ def testRandomlyPermuteTrue(self):
         def test(size, num_iteration=500):
             reactant_arr = np.random.randint(0, 3, (size, size))
             product_arr = np.random.randint(0, 3, (size, size))
-            network = NetworkBase(reactant_arr, product_arr)
+            network = NetworkBase(reactant_arr, product_arr)  # type: ignore
             for _ in range(num_iteration):
                 new_network, assignment_pair = network.permute()
                 if network == new_network:
@@ -157,10 +158,10 @@ def test(size, num_iteration=500):
     def testIsStructurallyCompatible(self):
         if IGNORE_TEST:
             return
-        network1 = NetworkBase.makeFromAntimonyStr(NETWORK1, network_name=NETWORK_NAME)
-        network2 = NetworkBase.makeFromAntimonyStr(NETWORK2, network_name=NETWORK_NAME)
-        network3 = NetworkBase.makeFromAntimonyStr(NETWORK3, network_name=NETWORK_NAME)
-        network4 = NetworkBase.makeFromAntimonyStr(NETWORK4, network_name=NETWORK_NAME)
+        network1 = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK1, network_name=NETWORK_NAME))
+        network2 = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK2, network_name=NETWORK_NAME))
+        network3 = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK3, network_name=NETWORK_NAME))
+        network4 = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK4, network_name=NETWORK_NAME))
         self.assertFalse(network1.isStructurallyCompatible(network4))
         self.assertTrue(network1.isStructurallyCompatible(network2))
         self.assertTrue(network1.isStructurallyCompatible(network3, identity=cn.ID_WEAK))
@@ -169,7 +170,7 @@ def testIsStructurallyCompatible(self):
     def testPrettyPrintReaction(self):
         if IGNORE_TEST:
             return
-        network = NetworkBase.makeFromAntimonyStr(NETWORK3, network_name="Network3")
+        network = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(NETWORK3, network_name="Network3"))
         stg = network.prettyPrintReaction(0)
         self.assertTrue("2.0 S1 -> 2.0 S1 + S2" in stg)
 
@@ -193,8 +194,8 @@ def testMakeRandomNetworkFromReactionType2(self):
         size = 3
         species_names = ["S1", "S5", "S10"]
         reaction_names = ['JJ1', 'JJ2', 'JJ3']
-        network = NetworkBase.makeRandomNetworkByReactionType(size, species_names=species_names,
-              reaction_names=reaction_names, is_exact=True)
+        network = NetworkBase.makeRandomNetworkByReactionType(size, species_names=species_names,  # type: ignore
+                reaction_names=reaction_names, is_exact=True)  # type: ignore
         self.assertEqual(len(species_names), network.num_species)
         for species_name in species_names:
             self.assertTrue(species_name in network.species_names)
@@ -283,6 +284,7 @@ def testFill(self):
             self.assertLessEqual(filled_network.num_species, network.num_species + fill_size)
             self.assertEqual(filled_network.num_reaction, network.num_reaction + fill_size)
         #
+        network = NetworkBase.makeRandomNetworkByReactionType(5, 5)
         with self.assertRaises(ValueError):
             network.fill(num_fill_reaction=0, num_fill_species=0)
 
@@ -297,7 +299,7 @@ def testIsBoundaryNetwork(self):
             k1 = 0.1; k2 = 0.2
             A = 0; B = 0
         """
-        network = NetworkBase.makeFromAntimonyStr(boundary_network)
+        network = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(boundary_network))
         self.assertTrue(network.isBoundaryNetwork())
         #
         boundary_network = """
@@ -307,21 +309,21 @@ def testIsBoundaryNetwork(self):
             k1 = 0.1; k2 = 0.2
             A = 0; B = 0
         """
-        network = NetworkBase.makeFromAntimonyStr(boundary_network)
+        network = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(boundary_network))
         self.assertFalse(network.isBoundaryNetwork())
 
     def testMakeFromAntimonyStrRoadrunner(self):
         if IGNORE_TEST:
             return
         roadrunner = te.loada(BIG_NETWORK)
-        network = NetworkBase.makeFromAntimonyStr(None, roadrunner=roadrunner)
+        network = cast(NetworkBase, NetworkBase.makeFromAntimonyStr(None, roadrunner=roadrunner))  # type: ignore
         self.assertGreater(network.num_species, 0)
 
     def testMakeFromSBMLFile(self):
         if IGNORE_TEST:
             return
         PATH = os.path.join(cn.TEST_DIR, "xml_files/BIOMD0000000033.xml")
-        network = NetworkBase.makeFromSBMLFile(PATH)
+        network = cast(NetworkBase, NetworkBase.makeFromSBMLFile(PATH))
         self.assertGreater(network.num_species, 0)
 
     def testMakeInducedNetwork(self):