remove unittest self.fail syntax, fix more tests, remove more dep meths

JacksonBurns · JacksonBurns · commit 9958b799254b · 2023-07-23T16:08:19.000-04:00
diff --git a/examples/arkane/species/Toulene_Hindered_Rotor_SemiClassicalND/toluene_HinderedRotor.py b/examples/arkane/species/Toulene_Hindered_Rotor_SemiClassicalND/toluene_HinderedRotor.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 bonds = {
-    'C-C': 4,
-    'C-H': 8,
-    'C=C': 3,
+    "C-C": 4,
+    "C-H": 8,
+    "C=C": 3,
 }
 
 externalSymmetry = 1
@@ -12,12 +12,10 @@
 
 opticalIsomers = 1
 
-energy = {
-    'CBS-QB3': Log('TolueneEnergy.log')
-}
+energy = {"CBS-QB3": Log("TolueneEnergy.log")}
 
-geometry = Log('TolueneFreq.log')
+geometry = Log("TolueneFreq.log")
 
-frequencies = Log('TolueneFreq.log')
+frequencies = Log("TolueneFreq.log")
 
-rotors = [HinderedRotorClassicalND(calcPath='TolueneRot1.log', pivots=[[3,12]], tops=[[12,13,14,15]], sigmas=[6], semiclassical=True)]
+rotors = [HinderedRotorClassicalND(calcPath="TolueneRot1.log", pivots=[[3, 12]], tops=[[12, 13, 14, 15]], sigmas=[6], semiclassical=True)]
diff --git a/pytest.ini b/pytest.ini
@@ -4,6 +4,6 @@ markers =
     functional: functional tests
     database: database tests
 # need pytest-cov to do --cov=arkane,rmgpy (?)
-addopts = -p julia.pytestplugin --ignore test/regression --last-failed
+addopts = -p julia.pytestplugin --ignore test/regression
 testpaths = test
 python_files = *Test.py
diff --git a/rmgpy/molecule/inchi.pxd b/rmgpy/molecule/inchi.pxd
@@ -45,8 +45,6 @@ cpdef bint _has_unexpected_lone_pairs(Molecule mol)
 
 cpdef list _get_unpaired_electrons(Molecule mol)
 
-cpdef Molecule _generate_minimum_resonance_isomer(Molecule mol)
-
 cpdef list _compute_agglomerate_distance(list agglomerates, Molecule mol)
 
 cpdef bint _is_valid_combo(list combo, Molecule mol, list distances)
diff --git a/scripts/rmg2to3.py b/scripts/rmg2to3.py
diff --git a/test/rmgpy/data/kinetics/kineticsTest.py b/test/rmgpy/data/kinetics/kineticsTest.py
@@ -114,42 +114,42 @@ def test_load_families_correct(self):
         try:
             database.load_families(path, families=[])
         except DatabaseError:
-            self.fail("Unable to load families using list []")
+            assert False, "Unable to load families using list []"
 
         try:
             database.load_families(path, families="none")
         except DatabaseError:
-            self.fail("Unable to load families using keyword 'none'")
+            assert False, "Unable to load families using keyword 'none'"
 
         try:
             database.load_families(path, families="default")
         except DatabaseError:
-            self.fail("Unable to load families using keyword 'default'")
+            assert False, "Unable to load families using keyword 'default'"
 
         try:
             database.load_families(path, families=["default", "pah"])
         except DatabaseError:
-            self.fail("Unable to load families using list ['default', 'pah']")
+            assert False, "Unable to load families using list ['default', 'pah']"
 
         try:
             database.load_families(path, families=["R_Addition_MultipleBond"])
         except DatabaseError:
-            self.fail("Unable to load families using list ['R_Addition_MultipleBond']")
+            assert False, "Unable to load families using list ['R_Addition_MultipleBond']"
 
         try:
             database.load_families(path, families=["!H_Abstraction", "!Disproportionation"])
         except DatabaseError:
-            self.fail("Unable to load families using list ['!H_Abstraction', '!Disproportionation']")
+            assert False, "Unable to load families using list ['!H_Abstraction', '!Disproportionation']"
 
         try:
             database.load_families(path, families="!pah")
         except DatabaseError:
-            self.fail("Unable to load families using keyword '!pah'")
+            assert False, "Unable to load families using keyword '!pah'"
 
         try:
             database.load_families(path, families=["H_Abstraction", "pah"])
         except DatabaseError:
-            self.fail("Unable to load families using list ['H_Abstraction', 'pah']")
+            assert False, "Unable to load families using list ['H_Abstraction', 'pah']"
 
 
 class TestReactionDegeneracy:
diff --git a/test/rmgpy/molecule/adjlistTest.py b/test/rmgpy/molecule/adjlistTest.py
@@ -898,7 +898,7 @@ def test_check_hund_rule_success(self):
                 saturate_h=True,
             )
         except InvalidAdjacencyListError:
-            self.fail("InvalidAdjacencyListError thrown unexpectedly!")
+            assert False, "InvalidAdjacencyListError thrown unexpectedly!"
 
     def test_check_multiplicity(self):
         """
@@ -911,7 +911,7 @@ def test_check_multiplicity(self):
                                             1 N u3 p1 c0"""
             )
         except InvalidAdjacencyListError:
-            self.fail("InvalidAdjacencyListError thrown unexpectedly for N tri-rad!")
+            assert False, "InvalidAdjacencyListError thrown unexpectedly for N tri-rad!"
 
         # A general molecule with 4 radicals, multiplicity 5:
         try:
@@ -924,7 +924,7 @@ def test_check_multiplicity(self):
                                             5 O u1 p2 c0 {4,S}"""
             )
         except InvalidAdjacencyListError:
-            self.fail("InvalidAdjacencyListError thrown unexpectedly for a molecule with 4 radicals, multiplicity 5")
+            assert False, "InvalidAdjacencyListError thrown unexpectedly for a molecule with 4 radicals, multiplicity 5"
 
         # A general molecule with 4 radicals, multiplicity 3:
         try:
@@ -937,7 +937,7 @@ def test_check_multiplicity(self):
                                             5 O u1 p2 c0 {4,S}"""
             )
         except InvalidAdjacencyListError:
-            self.fail("InvalidAdjacencyListError thrown unexpectedly for a molecule with 4 radicals, multiplicity 3")
+            assert False, "InvalidAdjacencyListError thrown unexpectedly for a molecule with 4 radicals, multiplicity 3"
 
         # [N]=C=[N] singlet:
         try:
@@ -948,4 +948,4 @@ def test_check_multiplicity(self):
                                             3 N u1 p1 c0 {2,D}"""
             )
         except InvalidAdjacencyListError:
-            self.fail("InvalidAdjacencyListError thrown unexpectedly for singlet [N]=C=[N]!")
+            assert False, "InvalidAdjacencyListError thrown unexpectedly for singlet [N]=C=[N]!"
diff --git a/test/rmgpy/molecule/converterTest.py b/test/rmgpy/molecule/converterTest.py
@@ -120,7 +120,7 @@ def test_atom_mapping_2(self):
                     try:
                         rdkitmol.GetBondBetweenAtoms(rd_atom_indices[at1], rd_atom_indices[at2])
                     except RuntimeError:
-                        self.fail("RDKit failed in finding the bond in the original atom!")
+                        assert False, "RDKit failed in finding the bond in the original atom!"
 
     def test_atom_mapping_3(self):
         """Test that to_rdkit_mol with save_order=True retains the atom order and create the correct RDKit Molecule"""
diff --git a/test/rmgpy/molecule/graphTest.py b/test/rmgpy/molecule/graphTest.py
@@ -83,7 +83,7 @@ def test_add_edge(self):
         edge = Edge(vertex1, vertex2)
         try:
             self.graph.add_edge(edge)
-            self.fail("Added edge between vertices not in graph to graph.")
+            assert False, "Added edge between vertices not in graph to graph."
         except ValueError:
             pass
         self.graph.add_vertex(vertex1)
@@ -104,7 +104,7 @@ def test_get_edge(self):
         vertex2 = self.graph.vertices[4]
         try:
             self.graph.get_edge(vertex1, vertex2)
-            self.fail("Returned an edge between vertices that should not be connected in graph.")
+            assert False, "Returned an edge between vertices that should not be connected in graph."
         except ValueError:
             pass
         vertex1 = self.graph.vertices[2]
diff --git a/test/rmgpy/molecule/groupTest.py b/test/rmgpy/molecule/groupTest.py
@@ -591,7 +591,7 @@ def test_apply_action_break_bond(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("GroupBond.apply_action() unexpectedly processed a BREAK_BOND action.")
+                assert False, "GroupBond.apply_action() unexpectedly processed a BREAK_BOND action."
             except ActionError:
                 pass
 
@@ -608,7 +608,7 @@ def test_apply_action_form_bond(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("GroupBond.apply_action() unexpectedly processed a FORM_BOND action.")
+                assert False, "GroupBond.apply_action() unexpectedly processed a FORM_BOND action."
             except ActionError:
                 pass
 
@@ -648,7 +648,7 @@ def test_apply_action_gain_radical(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("GroupBond.apply_action() unexpectedly processed a GAIN_RADICAL action.")
+                assert False, "GroupBond.apply_action() unexpectedly processed a GAIN_RADICAL action."
             except ActionError:
                 pass
 
@@ -662,7 +662,7 @@ def test_apply_action_lose_radical(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("GroupBond.apply_action() unexpectedly processed a LOSE_RADICAL action.")
+                assert False, "GroupBond.apply_action() unexpectedly processed a LOSE_RADICAL action."
             except ActionError:
                 pass
 
@@ -784,7 +784,7 @@ def test_get_labeled_atom(self):
                 assert atom == self.group.get_labeled_atoms(atom.label)[0]
         try:
             self.group.get_labeled_atoms("*3")[0]
-            self.fail("Unexpected successful return from Group.get_labeled_atoms() with invalid atom label.")
+            assert False, "Unexpected successful return from Group.get_labeled_atoms() with invalid atom label."
         except ValueError:
             pass
 
diff --git a/test/rmgpy/molecule/moleculeTest.py b/test/rmgpy/molecule/moleculeTest.py
@@ -689,7 +689,7 @@ def test_apply_action_break_bond(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("Bond.apply_action() unexpectedly processed a BREAK_BOND action " "with order {0}.".format(order0))
+                assert False, "Bond.apply_action() unexpectedly processed a BREAK_BOND action " "with order {0}.".format(order0)
             except ActionError:
                 pass
 
@@ -703,7 +703,7 @@ def test_apply_action_form_bond(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("Bond.apply_action() unexpectedly processed a FORM_BOND action " "with order {0}.".format(order0))
+                assert False, "Bond.apply_action() unexpectedly processed a FORM_BOND action " "with order {0}.".format(order0)
             except ActionError:
                 pass
 
@@ -743,7 +743,7 @@ def test_apply_action_gain_radical(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("Bond.apply_action() unexpectedly processed a GAIN_RADICAL action " "with order {0}.".format(order0))
+                assert False, "Bond.apply_action() unexpectedly processed a GAIN_RADICAL action " "with order {0}.".format(order0)
             except ActionError:
                 pass
 
@@ -757,7 +757,7 @@ def test_apply_action_lose_radical(self):
             bond = bond0.copy()
             try:
                 bond.apply_action(action)
-                self.fail("Bond.apply_action() unexpectedly processed a LOSE_RADICAL action " "with order {0}.".format(order0))
+                assert False, "Bond.apply_action() unexpectedly processed a LOSE_RADICAL action " "with order {0}.".format(order0)
             except ActionError:
                 pass
 
@@ -999,7 +999,7 @@ def test_get_labeled_atom(self):
                 assert atom == self.molecule[0].get_labeled_atoms(atom.label)[0]
         try:
             self.molecule[0].get_labeled_atoms("*3")[0]
-            self.fail("Unexpected successful return from Molecule.get_labeled_atoms() with invalid atom label.")
+            assert False, "Unexpected successful return from Molecule.get_labeled_atoms() with invalid atom label."
         except ValueError:
             pass
 
@@ -2190,7 +2190,7 @@ def test_large_mol_update(self):
         try:
             mol.update_connectivity_values()
         except OverflowError:
-            self.fail("update_connectivity_values() raised OverflowError unexpectedly!")
+            assert False, "update_connectivity_values() raised OverflowError unexpectedly!"
 
     def test_large_mol_creation(self):
         """
@@ -2202,7 +2202,7 @@ def test_large_mol_creation(self):
             try:
                 Molecule(smiles=smi)
             except OverflowError:
-                self.fail("Creation of C{} failed!".format(i))
+                assert False, "Creation of C{} failed!".format(i)
 
     def test_get_polycyclic_rings(self):
         """
diff --git a/test/rmgpy/molecule/resonanceTest.py b/test/rmgpy/molecule/resonanceTest.py
@@ -477,7 +477,7 @@ def test_fused_aromatic1(self):
             if perylene.is_isomorphic(isomer):
                 break
         else:  # didn't break
-            self.fail("{} isn't isomorphic with any aromatic forms of {}".format(perylene.to_smiles(), perylene2.to_smiles()))
+            assert False, "{} isn't isomorphic with any aromatic forms of {}".format(perylene.to_smiles(), perylene2.to_smiles())
 
     def test_fused_aromatic2(self):
         """Test we can make aromatic naphthalene from both adjlist and SMILES"""
@@ -508,7 +508,7 @@ def test_fused_aromatic2(self):
             if naphthalene.is_isomorphic(isomer):
                 break
         else:  # didn't break
-            self.fail("{} isn't isomorphic with any aromatic forms of {}".format(naphthalene.to_smiles(), naphthalene2.to_smiles()))
+            assert False, "{} isn't isomorphic with any aromatic forms of {}".format(naphthalene.to_smiles(), naphthalene2.to_smiles())
 
     def test_aromatic_resonance_structures(self):
         """Test that generate_optimal_aromatic_resonance_structures gives consistent output
diff --git a/test/rmgpy/qm/qmMainTest.py b/test/rmgpy/qm/qmMainTest.py
@@ -72,7 +72,7 @@ def test_check_all_set(self):
         try:
             self.settings1.check_all_set()
         except AssertionError:
-            self.fail("check_all_set() raised unexpected AssertionError.")
+            assert False, "check_all_set() raised unexpected AssertionError."
 
         with pytest.raises(AssertionError):
             self.settings2.check_all_set()
@@ -177,9 +177,9 @@ def test_initialize(self):
             self.gauss1.initialize()
             self.gauss2.initialize()
         except AssertionError:
-            self.fail("initialize() raised unexpected AssertionError.")
+            assert False, "initialize() raised unexpected AssertionError."
         except Exception:
-            self.fail("initialize() raised Exception. Output file paths not correctly set.")
+            assert False, "initialize() raised Exception. Output file paths not correctly set."
 
     def test_get_thermo_data(self):
         """
diff --git a/test/rmgpy/quantityTest.py b/test/rmgpy/quantityTest.py
diff --git a/test/rmgpy/rmg/mainTest.py b/test/rmgpy/rmg/mainTest.py
diff --git a/test/rmgpy/statmech/rotationTest.py b/test/rmgpy/statmech/rotationTest.py
diff --git a/test/rmgpy/statmech/torsionTest.py b/test/rmgpy/statmech/torsionTest.py
