Merge pull request #151 from CalebBell/caleb/ruff_2024_07_26

Caleb/ruff 2024 07 26

.ruff.toml

@@ -10,13 +10,28 @@ exclude = [
 #   "UP031",
 #   "UP032",
 # ]
+
+
+
+[lint]
 select = ["ALL"]
+
 extend-ignore = [
+    "FIX002", # TODO are OK
+    "FIX004", # HACK is OK
+
     "D415", # First docstring line should end with a period, question mark, or exclamation point
     "DTZ004", # utcfromtimestamp makes sense for atmosphere model
     "PGH003", # type ignoring makes sense for numba-related things
     "S102", # Yes, exec is dangerous but it can be quite useful as well
 
+    "PYI056", # changing __all__
+
+    "RUF012", # not using typing today
+    "PERF403", # obvious, use an autofix if one becomes available
+    "PERF203", # `try`-`except` within a loop incurs performance overhead
+    "PERF401", # PERF401 Use a list comprehension to create a transformed list
+
     # chemicals specific
     "E701", # lots of this here
 
@@ -139,13 +154,15 @@ extend-ignore = [
     "TRY002",  
     "TRY003",  
     "TRY004",  
-    "TRY200",  
+    "B904",  
     "TRY201",  
     "TRY300",  
     "TRY301",  
     "TRY400",  
     "Q000",  
     "Q002",  
+
+    "PYI024", # PYI024 Use `typing.NamedTuple` instead of `collections.namedtuple
 ]
-[mccabe]
+[lint.mccabe]
 max-complexity = 10

thermo/__init__.py

@@ -97,6 +97,7 @@
         phase_identification,
         phases,
         property_package,
+        redlich_kister,
         regular_solution,
         stream,
         thermal_conductivity,
@@ -107,7 +108,6 @@
         viscosity,
         volume,
         wilson,
-        redlich_kister,
     )
     from .activity import *  # noqa: F403
     from .bulk import *  # noqa: F403
@@ -138,6 +138,7 @@
     from .phase_identification import *  # noqa: F403
     from .phases import *  # noqa: F403
     from .property_package import *  # noqa: F403
+    from .redlich_kister import *  # noqa: F403
     from .regular_solution import *  # noqa: F403
     from .stream import *  # noqa: F403
     from .thermal_conductivity import *  # noqa: F403
@@ -148,7 +149,6 @@
     from .viscosity import *  # noqa: F403
     from .volume import *  # noqa: F403
     from .wilson import *  # noqa: F403
-    from .redlich_kister import * # noqa: F403
 
     #from chemicals import *
 
@@ -271,7 +271,6 @@ def complete_lazy_loading():
         # pytest timings are hard to measure with lazy loading
         complete_lazy_loading()
 
-    global vectorized, numba, units, numba_vectorized
     if numerics.PY37:
         def __getattr__(name):
             global vectorized, numba, units, numba_vectorized

thermo/activity.py

@@ -69,10 +69,9 @@
 __all__ = ['GibbsExcess', 'IdealSolution']
 from chemicals.utils import d2xs_to_dxdn_partials, dns_to_dn_partials, dxs_to_dn_partials, dxs_to_dns, hash_any_primitive, normalize, object_data
 from fluids.constants import R, R_inv
-from fluids.numerics import exp, log, trunc_exp, derivative, jacobian, hessian
+from fluids.numerics import derivative, exp, hessian, jacobian, log, trunc_exp
 from fluids.numerics import numpy as np
 
-from thermo import serialize
 from thermo.fitting import fit_customized
 from thermo.serialize import JsonOptEncodable
 
@@ -328,7 +327,7 @@ def __repr__(self):
         IdealSolution(T=300.0, xs=[.1, .2, .3, .4])
         '''
         # Other classes with different parameters should expose them here too
-        s = f'{self.__class__.__name__}(T={repr(self.T)}, xs={repr(self.xs)})'
+        s = f'{self.__class__.__name__}(T={self.T!r}, xs={self.xs!r})'
         return s
 
     def __eq__(self, other):
@@ -391,7 +390,7 @@ def exact_hash(self):
         d = object_data(self)
         ans = hash_any_primitive((self.__class__.__name__, d))
         return ans
-    
+
     def as_json(self, cache=None, option=0):
         r'''Method to create a JSON-friendly representation of the Gibbs Excess
         model which can be stored, and reloaded later.
@@ -448,9 +447,9 @@ def from_json(cls, json_repr, cache=None):
     def _custom_from_json(self, *args):
         vectorized = self.vectorized
         if vectorized and hasattr(self, 'cmp_group_idx'):
-            setattr(self, 'cmp_group_idx', tuple(array(v) for v in getattr(self, 'cmp_group_idx')))
+            self.cmp_group_idx = tuple(array(v) for v in self.cmp_group_idx)
         if vectorized and hasattr(self, 'group_cmp_idx'):
-            setattr(self, 'group_cmp_idx', tuple(array(v) for v in getattr(self, 'group_cmp_idx')))
+            self.group_cmp_idx = tuple(array(v) for v in self.group_cmp_idx)
 
     def HE(self):
         r'''Calculate and return the excess entropy of a liquid phase using an
@@ -1028,7 +1027,7 @@ def _regress_binary_parameters(cls, gammas, xs, fitting_func, fit_parameters,
                     **fit_kwargs)
         return res
 
-        
+
 derivatives_added = [('dGE_dT', 'GE', 1),
  ('d2GE_dT2', 'GE', 2),
  ('d3GE_dT3', 'GE', 3),

thermo/bulk.py

@@ -73,13 +73,14 @@
 
 __all__ = ['Bulk', 'BulkSettings', 'default_settings']
 
-from chemicals.utils import Joule_Thomson, isobaric_expansion, isothermal_compressibility, object_data, speed_of_sound, hash_any_primitive
+from chemicals.utils import Joule_Thomson, hash_any_primitive, isobaric_expansion, isothermal_compressibility, object_data, speed_of_sound
 from fluids.constants import R, atm
 from fluids.numerics import exp, log, sqrt
 from fluids.two_phase_voidage import gas_liquid_viscosity
-from thermo.serialize import arrays_to_lists, JsonOptEncodable, object_lookups
+
 from thermo.phase_identification import DENSITY_MASS, PROP_SORT, S_ID_D2P_DVDT, VL_ID_PIP, WATER_NOT_SPECIAL
 from thermo.phases import Phase
+from thermo.serialize import JsonOptEncodable, object_lookups
 
 """Class designed to have multiple phases.
 
@@ -1715,4 +1716,4 @@ def G_min_criteria(self):
 
 
 object_lookups[Bulk.__full_path__] = Bulk
-object_lookups[BulkSettings.__full_path__] = BulkSettings
+object_lookups[BulkSettings.__full_path__] = BulkSettings

thermo/chemical.py

@@ -71,7 +71,7 @@
 from chemicals.volume import ideal_gas
 from fluids.constants import epsilon_0
 from fluids.core import Bond, Capillary, Grashof, Jakob, Peclet_heat, Prandtl, Reynolds, Weber, nu_mu_converter, thermal_diffusivity
-from fluids.numerics import exp, log, newton, secant
+from fluids.numerics import exp, log, secant
 
 from thermo import functional_groups
 from thermo.electrochem import conductivity, conductivity_methods
@@ -99,7 +99,7 @@
 CHEMSEP = (298., 101325, 'g', 0, 0, True) # It has an option to add Hf to the reference
 PRO_II = (298.15, 101325, 'gas', 0, 0, True)
 HYSYS = (298.15, 101325, 'calc', 'Hf', 0, True)
-UNISIM = HYSYS #
+UNISIM = HYSYS
 SUPERPRO = (298.15, 101325, 'calc', 0, 0, True) # No support for entropy found, 0 assumed
 # note soecifying a phase works for chemicals but not mixtures.
 
@@ -755,11 +755,11 @@ def __init__(self, ID, T=298.15, P=101325, autocalc=True):
             self.formula = ID['formula']
             # DO NOT REMOVE molecular_weight until the database gets updated with consistent MWs
             self.MW = ID['MW'] if 'MW' in ID else molecular_weight(simple_formula_parser(self.formula))
-            self.PubChem = ID['PubChem'] if 'PubChem' in ID else None
-            self.smiles = ID['smiles'] if 'smiles' in ID else None
-            self.InChI = ID['InChI'] if 'InChI' in ID else None
-            self.InChI_Key = ID['InChI_Key'] if 'InChI_Key' in ID else None
-            self.synonyms = ID['synonyms'] if 'synonyms' in ID else None
+            self.PubChem = ID.get('PubChem', None)
+            self.smiles = ID.get('smiles', None)
+            self.InChI = ID.get('InChI', None)
+            self.InChI_Key = ID.get('InChI_Key', None)
+            self.synonyms = ID.get('synonyms', None)
         else:
             self.ID = ID
             # Identification
@@ -3249,15 +3249,15 @@ def Peclet_heat(self, V=None, D=None):
 # Add the functional groups
 def _make_getter_group(name):
     def get(self):
-        base_name = 'is_%s' %(name)
+        base_name = f'is_{name}'
         ref = getattr(functional_groups, base_name)
         return ref(self.rdkitmol)
 
     return get
 for _name in group_names:
     getter = property(_make_getter_group(_name))
-    name = 'is_%s' %(_name)
-    _add_attrs_doc =  r"""Method to return whether or not this chemical is in the category %s, [-]
-            """ %(_name)
+    name = f'is_{_name}'
+    _add_attrs_doc =  rf"""Method to return whether or not this chemical is in the category {_name}, [-]
+            """
     getter.__doc__ = _add_attrs_doc
     setattr(Chemical, name, getter)

thermo/chemical_package.py

@@ -84,7 +84,7 @@
 from chemicals.safety import LFL, STEL, TWA, UFL, Carcinogen, Ceiling, Skin, T_autoignition, T_flash
 from chemicals.solubility import solubility_parameter
 from chemicals.triple import Pt, Tt
-from chemicals.utils import Parachor, hash_any_primitive, property_molar_to_mass
+from chemicals.utils import Parachor, hash_any_primitive
 from fluids.constants import R
 
 from thermo.chemical import user_chemical_property_lookup
@@ -101,14 +101,21 @@
 from thermo.interface import SurfaceTension, SurfaceTensionMixture
 from thermo.permittivity import PermittivityLiquid
 from thermo.phase_change import EnthalpySublimation, EnthalpyVaporization
-from thermo.thermal_conductivity import ThermalConductivityGas, ThermalConductivityGasMixture, ThermalConductivityLiquid, ThermalConductivityLiquidMixture, ThermalConductivitySolid
+from thermo.serialize import JsonOptEncodable
+from thermo.thermal_conductivity import (
+    ThermalConductivityGas,
+    ThermalConductivityGasMixture,
+    ThermalConductivityLiquid,
+    ThermalConductivityLiquidMixture,
+    ThermalConductivitySolid,
+)
 from thermo.unifac import UNIFAC_RQ, UNIFAC_group_assignment_DDBST, Van_der_Waals_area, Van_der_Waals_volume
 from thermo.utils import identify_phase
+from thermo.utils.mixture_property import MixtureProperty
 from thermo.vapor_pressure import SublimationPressure, VaporPressure
 from thermo.viscosity import ViscosityGas, ViscosityGasMixture, ViscosityLiquid, ViscosityLiquidMixture
 from thermo.volume import VolumeGas, VolumeGasMixture, VolumeLiquid, VolumeLiquidMixture, VolumeSolid, VolumeSolidMixture
-from thermo.utils.mixture_property import MixtureProperty
-from thermo.serialize import JsonOptEncodable
+
 CAS_H2O = '7732-18-5'
 
 
@@ -128,7 +135,7 @@
             fairly easily once the data entry is complete."""
 
 
-class ChemicalConstantsPackage():
+class ChemicalConstantsPackage:
     non_vector_properties = ('atomss', 'Carcinogens', 'CASs', 'Ceilings', 'charges',
                  'conductivities', 'dipoles', 'economic_statuses', 'formulas', 'Gfgs',
                  'Gfgs_mass', 'GWPs', 'Hcs', 'Hcs_lower', 'Hcs_lower_mass', 'Hcs_mass',
@@ -186,7 +193,7 @@ def _custom_as_json(self, d, cache):
         for k in ('PSRK_groups', 'UNIFAC_Dortmund_groups', 'UNIFAC_groups'):
             # keys are stored as strings and not ints
             d[k] = [{str(k): v for k, v in r.items()} if r is not None else r for r in d[k]]
-        
+
 
         # This is not so much a performance optimization as an improvement on file size
         # and readability. Do not remove it! Comparing against an empty list is the
@@ -1374,9 +1381,9 @@ def __init__(self, CASs=None, names=None, MWs=None, Tms=None, Tbs=None,
 """
 for name, (var_type, desc, units, return_desc) in constants_docstrings.items():
     type_name = var_type if type(var_type) is str else var_type.__name__
-    new = """{} : {}
-    {}, {}.
-""".format(name, type_name, desc, units)
+    new = f"""{name} : {type_name}
+    {desc}, {units}.
+"""
     constants_doc += new
 
 try:
@@ -1868,7 +1875,7 @@ def as_poly_fit(self, props=None):
             else:
                 iter_props = self.pure_correlations
 
-            s = '%s(' %(self.__class__.__name__)
+            s = f'{self.__class__.__name__}('
             s += 'constants=constants, skip_missing=True,\n'
             for prop in iter_props:
                 prop_attr = getattr(self, prop)

thermo/chemical_utils.py

@@ -23,10 +23,12 @@
 
 __all__ = ['standard_entropy', 'S0_basis_converter', 'standard_state_ideal_gas_formation']
 
-from fluids.numerics import quad
-from chemicals.reaction import standard_formation_reaction
-from thermo.heat_capacity import HeatCapacitySolid, HeatCapacityLiquid, HeatCapacityGas
 from chemicals.elements import periodic_table
+from chemicals.reaction import standard_formation_reaction
+from fluids.numerics import quad
+
+from thermo.heat_capacity import HeatCapacityGas, HeatCapacityLiquid, HeatCapacitySolid
+
 
 def standard_entropy(c=None, dS_trans_s=None, dH_trans_s=None, T_trans_s=None,
                      Cp_s_fun=None,
@@ -287,11 +289,11 @@ def _standard_state_ideal_gas_formation_direct(T, Hf_ref, Sf_ref, atoms, gas_Cp,
     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([''])
+    solid_ele = {'C'}
+    liquid_ele = {''}
 
     for coeff, ele_data in zip(elemental_counts, elemental_composition):
-        ele = list(ele_data.keys())[0]
+        ele = next(iter(ele_data.keys()))
         element_obj = periodic_table[ele]
 #         element = Chemical(element_obj.CAS_standard)
         solid_obj = element_HeatCapacitySolid_cache(element_obj.CAS_standard)

thermo/coolprop.py

@@ -34,7 +34,6 @@
 from math import exp, log
 
 from chemicals.utils import mark_numba_incompatible
-from fluids.numerics import assert_close1d
 from fluids.numerics import numpy as np
 
 from thermo.base import data_dir
@@ -49,9 +48,6 @@
 #has_CoolProp = False # For testing
 
 CPiP_min = 17
-global _PropsSI
-
-global _has_CoolProp
 _has_CoolProp = None
 @mark_numba_incompatible
 def has_CoolProp():
@@ -72,7 +68,6 @@ def PropsSI(*args, **kwargs):
         from CoolProp.CoolProp import PropsSI as _PropsSI
     return _PropsSI(*args, **kwargs)
 
-global _HAPropsSI
 _HAPropsSI = None
 @mark_numba_incompatible
 def HAPropsSI(*args, **kwargs):
@@ -81,7 +76,6 @@ def HAPropsSI(*args, **kwargs):
         from CoolProp.CoolProp import HAPropsSI as _HAPropsSI
     return _HAPropsSI(*args, **kwargs)
 
-global _PhaseSI
 _PhaseSI = None
 @mark_numba_incompatible
 def PhaseSI(*args, **kwargs):
@@ -90,7 +84,6 @@ def PhaseSI(*args, **kwargs):
         from CoolProp.CoolProp import PhaseSI as _PhaseSI
     return _PhaseSI(*args, **kwargs)
 
-global _AbstractState
 _AbstractState = None
 @mark_numba_incompatible
 def AbstractState(*args, **kwargs):
@@ -230,7 +223,7 @@ def store_coolprop_fluids():
 
     data = {CASRN: coolprop_fluids[CASRN].as_json() for CASRN in coolprop_dict}
     ver = CoolProp.__version__
-    file = open(os.path.join(data_dir, 'CoolPropFluids%s.json' %ver), 'w')
+    file = open(os.path.join(data_dir, f'CoolPropFluids{ver}.json'), 'w')
     json.dump(data, file)
     file.close()
 
@@ -240,7 +233,7 @@ def load_coolprop_fluids(depth=0):
 
     import CoolProp
     ver = CoolProp.__version__
-    pth = os.path.join(data_dir, 'CoolPropFluids%s.json' %ver)
+    pth = os.path.join(data_dir, f'CoolPropFluids{ver}.json')
     try:
         file = open(pth)
     except:
@@ -418,7 +411,7 @@ def CoolProp_json_alpha0_to_kwargs(json_data, as_np=False):
             # Not relevant
             continue
         else:
-            raise ValueError("Unrecognized alpha0 type %s" %(d['type']))
+            raise ValueError("Unrecognized alpha0 type {}".format(d['type']))
 
     if as_np:
         for k, v in kwargs.items():