Fixes with ruff

thermo/bulk.py

@@ -372,8 +372,8 @@ class BulkSettings:
                 'mu_VL', 'mu_VL_power_exponent', 'k_LL', 'k_LL_power_exponent', 'k_VL', 'k_VL_power_exponent',
                 'sigma_LL', 'sigma_LL_power_exponent', 'T_liquid_volume_ref', 'T_normal', 'P_normal', 'T_standard',
                 'P_standard', 'T_gas_ref', 'P_gas_ref', 'speed_of_sound', 'kappa', 'isobaric_expansion',
-                'Joule_Thomson', 'VL_ID', 'VL_ID_settings', 'S_ID', 'S_ID_settings', 'solid_sort_method', 
-                'liquid_sort_method', 'liquid_sort_cmps', 'solid_sort_cmps', 'liquid_sort_cmps_neg', 'solid_sort_cmps_neg', 
+                'Joule_Thomson', 'VL_ID', 'VL_ID_settings', 'S_ID', 'S_ID_settings', 'solid_sort_method',
+                'liquid_sort_method', 'liquid_sort_cmps', 'solid_sort_cmps', 'liquid_sort_cmps_neg', 'solid_sort_cmps_neg',
                 'liquid_sort_prop', 'solid_sort_prop', 'phase_sort_higher_first', 'water_sort', 'equilibrium_perturbation')
 
     def as_json(self):

thermo/chemical_package.py

@@ -462,7 +462,7 @@ def compound_index(self, CAS=None, name=None, smiles=None, InChI=None,
 
     @property
     def CAS_to_index(self):
-        r'''Dictionary of CAS: index, used for efficiently 
+        r'''Dictionary of CAS: index, used for efficiently
         looking up which index a specified CAS number is in.
         This can save a lot of time, but does take a little more memory.
 

thermo/chemical_utils.py

@@ -165,7 +165,7 @@ def S0_basis_converter(c, S0_liq=None, S0_gas=None, T_ref=298.15):
     # 'S': {'Tm': 388.360, 'Tb': 882.117, 'Hfus': 1721, 'Hvap': 53326,  'solid_T_trans': [368.300], 'solid_H_trans': [401]}, # TODO
     # 'Be': {'Tm': 1560.000, 'Tb': 2741.437, 'Hfus': 7895, 'Hvap': 291572, 'solid_T_trans': [1527.000], 'solid_H_trans': [6849]}, # TODO
     # 'Fe': {'Tm': 3133.345, 'Hfus': 349585, 'solid_T_trans': [1184.000, 1665.000], 'solid_H_trans': [900, 837]}, # TODO
-    
+
     }
 
 shomate_gas_elements = ('H', 'O', 'N', 'F', 'P', 'Cl', 'Br', 'I', 'Mg', 'B', 'Pb', 'Li', 'Na', 'Al', 'K', 'V', 'Cr')
@@ -206,12 +206,12 @@ def element_HeatCapacitySolid_cache(CAS):
 def standard_state_ideal_gas_formation(c, T, Hf=None, Sf=None, T_ref=298.15):
     r'''This function calculates the standard state ideal-gas heat of formation
     of a compound at a specified from first principles. The entropy change and
-    Gibbs free energy change of formation are also returned. 
+    Gibbs free energy change of formation are also returned.
     This special condition is usually tabulated in thermodynamic tables, and
     this function is intended to be consistent with the standard conventions.
 
     The values returned depend on:
-    
+
     * The heat of formation as an ideal gas of the compound at 298.15 K (must be measured experimentally)
     * The ideal gas absolute entropy of the compound at 298.15 K (calculated from heat capacity and phase transitions of the compound and its various phases)
     * The chosen reference states of the elements (convention, but hardcoded)
@@ -260,7 +260,7 @@ def standard_state_ideal_gas_formation(c, T, Hf=None, Sf=None, T_ref=298.15):
     Hf_ref = Hf if Hf is not None else c.Hfgm
     Sf_ref = Sf if Sf is not None else c.Sfgm
     atoms = c.atoms
-    return _standard_state_ideal_gas_formation_direct(T=T, Hf_ref=Hf_ref, Sf_ref=Sf_ref, 
+    return _standard_state_ideal_gas_formation_direct(T=T, Hf_ref=Hf_ref, Sf_ref=Sf_ref,
             atoms=atoms, gas_Cp=c.HeatCapacityGas, T_ref=T_ref)
 
 _standard_formation_reaction_cache = {}
@@ -282,14 +282,14 @@ def _standard_state_ideal_gas_formation_direct(T, Hf_ref, Sf_ref, atoms, gas_Cp,
 
     dH_compound = gas_Cp.T_dependent_property_integral(T_ref, T)
     dS_compound = gas_Cp.T_dependent_property_integral_over_T(T_ref, T)
-    
+
     H_calc = reactant_coeff*Hf_ref + reactant_coeff*dH_compound
     S_calc = reactant_coeff*Sf_ref + reactant_coeff*dS_compound
     # if the compound is an element it will need special handling to go from solid liquid to gas if needed
 
     solid_ele = set(['C'])
     liquid_ele = set([''])
-    
+
     for coeff, ele_data in zip(elemental_counts, elemental_composition):
         ele = list(ele_data.keys())[0]
         element_obj = periodic_table[ele]
@@ -334,7 +334,7 @@ def _standard_state_ideal_gas_formation_direct(T, Hf_ref, Sf_ref, atoms, gas_Cp,
         elif ele == 'P':
             # White phosphorus is the basis here
             T_alpha_beta_P = 195.400
-            Htrans_alpha_beta_P = 521.0 # 525.5104 reported in 
+            Htrans_alpha_beta_P = 521.0 # 525.5104 reported in
             # The thermodynamic properties of elementary phosphorus The heat capacities of two crystalline modifications of red phosphorus, of α and β white phosphorus, and of black phosphorus from 15 to 300 K
             Tm_P = 317.300
             Hfus_P = 659
@@ -389,7 +389,7 @@ def _standard_state_ideal_gas_formation_direct(T, Hf_ref, Sf_ref, atoms, gas_Cp,
         H_calc -= coeff*dH_ele
         S_calc -= coeff*dS_ele
     G_calc = H_calc - T*S_calc
-    
+
     H_calc, S_calc, G_calc = H_calc/reactant_coeff, S_calc/reactant_coeff, G_calc/reactant_coeff
-    
+
     return H_calc, S_calc, G_calc

thermo/equilibrium.py

@@ -3395,7 +3395,7 @@ def get_bulk_property(self):
                'Gs_ideal_gas_standard_state', 'S_ideal_gas_standard_state', 'Ss_ideal_gas_standard_state',
 
                 'concentrations_mass_gas', 'concentrations_mass_gas_normal', 'concentrations_mass_gas_standard',
-                'concentrations_gas_standard', 'concentrations_gas_normal', 'concentrations_gas'              
+                'concentrations_gas_standard', 'concentrations_gas_normal', 'concentrations_gas'
  ]
 
 

thermo/fitting.py

@@ -68,17 +68,17 @@ def split_data(x, y, folds=5, seed=42):
     if pts != len(y):
         raise ValueError("Wrong size")
     z = list(range(pts))
-    
+
     Random(seed).shuffle(z)
     # go one by one and assign data to each group
-    
+
     fold_xs = [[] for _ in range(folds)]
     fold_ys = [[] for _ in range(folds)]
     for i in range(pts):
         l = i%folds
         fold_xs[l].append(x[i])
         fold_ys[l].append(y[i])
-    
+
     return fold_xs, fold_ys
 
 def assemble_fit_test_groups(x_groups, y_groups):
@@ -98,7 +98,7 @@ def assemble_fit_test_groups(x_groups, y_groups):
             if j != i:
                 x_train.extend(x_groups[j])
                 y_train.extend(y_groups[j])
-        
+
         train_x_groups.append(x_train)
         train_y_groups.append(y_train)
     return (train_x_groups, test_x_groups, train_y_groups, test_y_groups)
@@ -851,7 +851,7 @@ def jac_wrapped_for_leastsq(params):
         statistics['min_ratio'] = float(stats[2])
         statistics['max_ratio'] = float(stats[3])
         try:
-            pcov = float(pcov) 
+            pcov = float(pcov)
         except:
             # ndarray or None
             pass

thermo/flash/flash_base.py

@@ -832,7 +832,7 @@ def _finish_initialization_base(self):
         self.scalar = scalar_statuses.pop()
 
         self.supports_lnphis_args = all(p.supports_lnphis_args for p in self.phases)
-        
+
         # Make the phases aware of the constants and properties
         constants = self.constants
         correlations = self.correlations

thermo/flash/flash_utils.py

@@ -70,7 +70,7 @@
     'generate_phase_boundaries_naive',
     'water_wet_bulb_temperature',
     'water_dew_point_from_humidity',
-    'solve_water_wet_bulb_temperature_nested', 
+    'solve_water_wet_bulb_temperature_nested',
     'solve_water_wet_bulb_temperature_direct',
 ]
 
@@ -5280,13 +5280,13 @@ def water_dew_point_from_humidity(flasher, T, P, humidity, zs_air, zs_added):
     except:
         return None
     N = flasher.N
-    ratio = sat.flash_convergence['mixing_factor'] 
+    ratio = sat.flash_convergence['mixing_factor']
     feed_ns = zs_air
     zs_for_factor = flash_mixing_remove_overlap(zs_air, zs_added)
     n_factor = sum([feed_ns[i] if zs_for_factor[i] > 0 else 0 for i in range(N)])
     ns_out = [n_factor*(zs_for_factor[i] + zs_added[i]*ratio*humidity) for i in range(N)]
     zs_my_flash = normalize(ns_out)
-    
+
     return water_wet_bulb_temperature(flasher, zs=zs_my_flash, T=T, P=P)
 
 
@@ -5413,10 +5413,10 @@ def solve_water_wet_bulb_temperature_direct(flasher, zs, T, P, T_wet_bulb):
     H_water_product = water_product.H()
     flashes2 = []
 
-    '''Known: T_wet_bulb. Product T. Product P.
+    """Known: T_wet_bulb. Product T. Product P.
 
     Unknown: x_w out, how many moles water to add to cause saturation of water, the temperature of the end flash
-    '''
+    """
     def wet_bulb_T_error_direct(guess):
         # TODO make a standalone function for this
         moles_water_1, moles_water_2 = guess
@@ -5439,7 +5439,7 @@ def wet_bulb_T_error_direct(guess):
         zs_out = normalize(ns_out_2)
 
         # As best as I can tell, the VF=1 flash is required otherwise the newton solver will
-        # go nuts with no jacobian. 
+        # go nuts with no jacobian.
         flash_out = flasher.flash(VF=1, P=P, zs=zs_out)
         flashes2[:] = [flash_out]
         energy_err = H_out_balanced - flash_out.H()

thermo/functional_groups.py

@@ -2829,7 +2829,7 @@ def count_rings_attatched_to_rings(mol, allow_neighbors=True, atom_rings=None):
 benzene_smarts = 'c1ccccc1'
 
 def benene_rings(mol):
-    r'''Given a `rdkit.Chem.rdchem.Mol` object, returns the number of benzene rings 
+    r'''Given a `rdkit.Chem.rdchem.Mol` object, returns the number of benzene rings
     in the molecule.
 
     Parameters
@@ -2914,9 +2914,9 @@ def is_radionuclide(mol):
 
     References
     ----------
-    .. [1] Kondev, F. G., M. Wang, W. J. Huang, S. Naimi, and G. Audi. 
-       "The NUBASE2020 Evaluation of Nuclear Physics Properties *." 
-       Chinese Physics C 45, no. 3 (March 2021): 030001. 
+    .. [1] Kondev, F. G., M. Wang, W. J. Huang, S. Naimi, and G. Audi.
+       "The NUBASE2020 Evaluation of Nuclear Physics Properties *."
+       Chinese Physics C 45, no. 3 (March 2021): 030001.
        https://doi.org/10.1088/1674-1137/abddae.
     '''
     for atom in mol.GetAtoms():

thermo/heat_capacity.py

@@ -1551,7 +1551,7 @@ class HeatCapacityLiquidMixture(MixtureProperty):
     ranked_methods = [LALIBERTE, LINEAR]
     pure_references = ('HeatCapacityLiquids',)
     pure_reference_types = (HeatCapacityLiquid,)
-    
+
     pure_constants = ('MWs', )
     custom_args = pure_constants
 

thermo/phases/gibbs_eos.py

@@ -27,7 +27,7 @@
 
 class GibbsEOS(Phase):
     # http://www.iapws.org/relguide/Advise3.pdf is useful
-    def V(self):    
+    def V(self):
         return self.dG_dP()
         # return self._V
 
@@ -41,7 +41,7 @@ def dV_dP(self):
         return self.d2G_dP2()
 
     dV_dP_T = dV_dP
-    
+
     def dP_dV(self):
         return 1.0/self.d2G_dP2()
 
@@ -55,12 +55,12 @@ def dV_dT(self):
 
     def dT_dV(self):
         return 1.0/self.d2G_dTdP()
-    
+
     dT_dV_P = dT_dV
 
     def d2V_dT2(self):
         return self.d3G_dT2dP()
-    
+
     def d2V_dTdP(self):
         return self.d3G_dTdP2()
 
@@ -72,7 +72,7 @@ def dP_dT(self):
 
     def dT_dP(self):
         return 1.0/self.dP_dT()
-    
+
     dT_dP_V = dT_dP
 
 
@@ -81,10 +81,10 @@ def H(self):
 
     def S(self):
         return -self.dG_dT()
-    
+
     def Cp(self):
         return -self.T*self.d2G_dT2()
-    
+
     def U(self):
         return self.G() - self.T*self.dG_dT() - self.P*self.dG_dP()
 
@@ -109,6 +109,6 @@ def d2S_dP2(self):
 
     def d2S_dTdP(self):
         return -self.d3G_dT2dP()
-
 
-
+
+

thermo/phases/iapws_phase.py

@@ -47,7 +47,7 @@ class IAPWS95(HelmholtzEOS):
     Hfs = [-241822.0]
     Sfs = [-44.5]
     Gfs = [-228554.325]
-    
+
     N = 1
     rhoc_inv = rho_to_Vm(rhoc_mass, _MW)
     rhoc = 1.0/rhoc_inv
@@ -756,35 +756,35 @@ def _set_core(self):
 
         tau2 = tau*tau
         v0 = pi - pi0
-        r2 = (v0*(v0*(2.34801409215913e-11 - 2.85651142904972e-11j) 
+        r2 = (v0*(v0*(2.34801409215913e-11 - 2.85651142904972e-11j)
                      + (-5.57107698030123e-5 + 4.64578634580806e-5j))
                      + (-72.597457432922 - 78.100842711287j))
 
-        r2p = (v0*(7.677551608692879e-14-9.340239477516712e-14j) 
+        r2p = (v0*(7.677551608692879e-14-9.340239477516712e-14j)
                + (-9.108171704568459e-08+7.595411065038183e-08j))
-        g0 = (v0*(v0*(v0*(-5.56464869058991e-22*v0 + 3.39746123271053e-15) 
+        g0 = (v0*(v0*(v0*(-5.56464869058991e-22*v0 + 3.39746123271053e-15)
                - 1.89369929326131e-8) + 0.655022213658955) - 632020.233335886)
         g0p = (v0*(v0*(-3.6390648292032365e-24*v0 + 1.666356094695489e-17)
                 - 6.192030151739651e-11) + 0.0010708979275295713)
-        g0pp = ((-1.7848556441943294e-26*v0 + 5.44866189611331e-20)*v0 
+        g0pp = ((-1.7848556441943294e-26*v0 + 5.44866189611331e-20)*v0
                 - 1.0123370045204503e-13)
 
 
         log_t1_tau = logc(t1 + tau)
         log_t1_n_tau = logc(t1 - tau)
         log_t2_tau = logc(t2 + tau)
         log_t2_n_tau = logc(t2 - tau)
-        
+
         log_t1 = logc(t1)
         log_t2 = logc(t2)
-        
+
         t2_inv = 1.0/t2
         t1_inv = 1.0/t1
-        
+
         tau_t2inv = tau*t2_inv
         t2_log_t2 = t2*log_t2
         t2_log_t2_2 = t2_log_t2 + t2_log_t2
-        
+
         g_real_sum = (r1*((t1-tau)*log_t1_n_tau + (t1+tau)*log_t1_tau - 2.0*t1*log_t1 - tau2*t1_inv)
                    + (r2*((t2-tau)*log_t2_n_tau + (t2+tau)*log_t2_tau - t2_log_t2_2 - tau2*t2_inv))).real
         g = g0 - s0*Tt*tau + Tt*g_real_sum
@@ -798,7 +798,7 @@ def _set_core(self):
         g_TT = 0.0036608581051398447*g_TT_real_sum #1.0/Tt*g_TT_real_sum
 
         x0 = (t2-tau)*log_t2_n_tau + (t2+tau)*log_t2_tau - t2_log_t2_2 - tau2*t2_inv
-        
+
         g_P_real_sum = (r2p*(x0)).real
         g_P = g0p + Tt*g_P_real_sum
         g_PP_real_sum = (self.r2pp*(x0)).real
@@ -828,19 +828,19 @@ def G(self):
 
     def dG_dT(self):
         return self._dG_dT
-    
+
     def d2G_dT2(self):
         return self._d2G_dT2
 
     def dG_dP(self):
         return self._dG_dP
-    
+
     def d2G_dP2(self):
         return self._d2G_dP2
-    
+
     def d2G_dTdP(self):
         return self._d2G_dTdP
-        
+
     d2G_dPdT = d2G_dTdP
 
     def P_sub(self):

thermo/phases/phase.py

@@ -358,12 +358,12 @@ def is_same_model(self, other_phase, ignore_phase=False):
         if identical_model_attribute_ids:
             if ignore_phase:
                 return True
-            return self.__class__.__name__ == other_phase.__class__.__name__ 
+            return self.__class__.__name__ == other_phase.__class__.__name__
 
         # Using identities only we could not confirm if the phase was the same or not.
         # The values may still be the same if the identities are not.
         return self.model_hash(ignore_phase) == other_phase.model_hash(ignore_phase)
-    
+
     def model_hash(self, ignore_phase=False):
         r'''Method to compute a hash of a phase.
 
@@ -6363,7 +6363,7 @@ def _der(self, property=a, differentiate_by=b, at_constant=c):
              # These will probably need their doc fixed
              'd2G_dP2', 'd2G_dT2',
              'd2G_dPdT', 'd2G_dTdP',
-             
+
              ]
 derivatives_thermodynamic_mass = []