allow compatibility with python 3.6

chemicals/__init__.py

@@ -23,8 +23,8 @@
 """
 
 import os
-
 from . import utils
+from .utils import mark_jit_unsafe
 from . import critical
 from . import elements
 from . import reaction

chemicals/acentric.py

@@ -51,7 +51,7 @@
 __all__ = ['omega', 'LK_omega', 'Stiel_polar_factor',
            'omega_methods', 'omega_all_methods', 'omega_definition']
 
-from chemicals.numba import unsafe
+from chemicals import mark_jit_unsafe
 from chemicals.utils import log, log10
 from chemicals import critical
 from chemicals.data_reader import (retrieve_from_df_dict,
@@ -61,7 +61,7 @@
 omega_all_methods = ('PSRK', 'PD', 'YAWS')
 '''Tuple of method name keys. See the `omega` for the actual references'''
 
-@unsafe
+@mark_jit_unsafe
 def omega_methods(CASRN):
     """Return all methods available for obtaining omega for the desired
     chemical.
@@ -82,7 +82,7 @@ def omega_methods(CASRN):
     """
     return list_available_methods_from_df_dict(critical.omega_sources, CASRN, 'omega')
 
-@unsafe
+@mark_jit_unsafe
 def omega(CASRN, method=None):
     r'''Retrieve a chemical's acentric factor, `omega`.
 

chemicals/combustion.py

@@ -54,7 +54,7 @@
 """
 
 from chemicals.elements import mass_fractions, molecular_weight, simple_formula_parser
-from chemicals.utils import property_molar_to_mass, property_mass_to_molar
+from chemicals.utils import property_molar_to_mass, property_mass_to_molar, mark_jit_unsafe
 from fluids.numerics import normalize
 
 __all__ = ('combustion_stoichiometry',
@@ -145,6 +145,7 @@ def as_atoms(formula):
 O2_CAS = '7782-44-7'
 H2O_CAS = '7732-18-5'
 
+@mark_jit_unsafe
 def combustion_stoichiometry(atoms, MW=None, missing_handling='elemental'):
     r"""Return a dictionary of stoichiometric coefficients of chemical
     combustion, given a dictionary of a molecule's constituent atoms and their
@@ -280,7 +281,7 @@ def combustion_stoichiometry(atoms, MW=None, missing_handling='elemental'):
         raise ValueError("Allowed values for `missing_handling` are 'elemental' and 'ash'.")
     return products
 
-
+@mark_jit_unsafe
 def combustion_products_mixture(atoms_list, zs, reactivities=None, CASs=None,
                                 missing_handling='elemental',
                                 combustion_stoichiometries=None):
@@ -373,7 +374,7 @@ def combustion_products_to_list(products, CASs):
     return zs
 
 
-
+@mark_jit_unsafe
 def is_combustible(CAS, atoms, reactive=True):
     if not reactive:
         return False
@@ -386,6 +387,7 @@ def is_combustible(CAS, atoms, reactive=True):
     else:
         return False
 
+@mark_jit_unsafe
 def HHV_stoichiometry(stoichiometry, Hf, Hf_chemicals=None):
     r"""
     Return the higher heating value [HHV; in J/mol] based on the
@@ -430,6 +432,7 @@ def HHV_stoichiometry(stoichiometry, Hf, Hf_chemicals=None):
     Hfs = Hf_chemicals or Hf_combustion_chemicals
     return sum([Hfs[i] * j for i, j in stoichiometry.items()]) - Hf
 
+@mark_jit_unsafe
 def HHV_modified_Dulong(mass_fractions):
     r"""
     Return higher heating value [HHV; in J/g] based on the modified
@@ -518,6 +521,7 @@ def LHV_from_HHV(HHV, N_H2O):
     """
     return HHV + 44011.496 * N_H2O
 
+@mark_jit_unsafe
 def combustion_data(formula=None, stoichiometry=None, Hf=None, MW=None,
                     method=None, missing_handling='ash'):
     r"""
@@ -620,7 +624,6 @@ def combustion_data(formula=None, stoichiometry=None, Hf=None, MW=None,
                          "not %s" %(method))
     return CombustionData(stoichiometry, HHV, Hf, MW)
 
-
 class CombustionData(object):
     r"""
     Return a CombustionData object (a named tuple) that contains the stoichiometry
@@ -757,7 +760,7 @@ def air_fuel_ratio_solver(ratio, Vm_air, Vm_fuel, MW_air, MW_fuel,
     mass_ratio, volume_ratio = MW_air/MW_fuel*mole_ratio, Vm_air/Vm_fuel*mole_ratio
     return n_air, n_fuel, mole_ratio, mass_ratio, volume_ratio
 
-
+@mark_jit_unsafe
 def fuel_air_spec_solver(zs_air, zs_fuel, CASs, atomss, n_fuel=None,
                          n_air=None, n_out=None,
                          O2_excess=None, frac_out_O2=None,
@@ -1092,7 +1095,7 @@ def fuel_air_spec_solver(zs_air, zs_fuel, CASs, atomss, n_fuel=None,
 
     return results
 
-
+@mark_jit_unsafe
 def fuel_air_third_spec_solver(zs_air, zs_fuel, zs_third, CASs, atomss, n_third,
                            n_fuel=None, n_air=None, n_out=None,
                            O2_excess=None, frac_out_O2=None,
@@ -1242,7 +1245,7 @@ def fix_ratios(results):
 
         return ans
 
-
+@mark_jit_unsafe
 def combustion_spec_solver(zs_air, zs_fuel, zs_third, CASs, atomss, n_third,
                            n_fuel=None, n_air=None, n_out=None,
                            O2_excess=None, frac_out_O2=None,

chemicals/critical.py

@@ -96,7 +96,7 @@
            'critical_surface_all_methods']
 
 import os
-from chemicals.numba import unsafe
+from chemicals import mark_jit_unsafe
 from fluids.constants import R, R_inv, N_A
 from chemicals.utils import log, PY37, source_path, os_path_join, can_load_data
 from chemicals.data_reader import (register_df_source,
@@ -189,7 +189,7 @@ def __getattr__(name):
 Tc_all_methods = (IUPAC, MATTHEWS, CRC, PSRK, PD, YAWS)
 '''Tuple of method name keys. See the `Tc` for the actual references'''
 
-@unsafe
+@mark_jit_unsafe
 def Tc_methods(CASRN):
     """Return all methods available to obtain Tc for the desired chemical.
 
@@ -210,7 +210,7 @@ def Tc_methods(CASRN):
     if not _critical_data_loaded: _load_critical_data()
     return list_available_methods_from_df_dict(Tc_sources, CASRN, 'Tc')
 
-@unsafe
+@mark_jit_unsafe
 def Tc(CASRN, method=None):
     r'''This function handles the retrieval of a chemical's critical
     temperature. Lookup is based on CASRNs. Will automatically select a data
@@ -347,7 +347,7 @@ def Tc(CASRN, method=None):
 Pc_all_methods = (IUPAC, MATTHEWS, CRC, PSRK, PD, YAWS)
 '''Tuple of method name keys. See the `Pc` for the actual references'''
 
-@unsafe
+@mark_jit_unsafe
 def Pc_methods(CASRN):
     """Return all methods available to obtain Pc for the desired chemical.
 
@@ -367,7 +367,7 @@ def Pc_methods(CASRN):
     """
     return list_available_methods_from_df_dict(Pc_sources, CASRN, 'Pc')
 
-@unsafe
+@mark_jit_unsafe
 def Pc(CASRN, method=None):
     r'''This function handles the retrieval of a chemical's critical
     pressure. Lookup is based on CASRNs. Will automatically select a data
@@ -503,7 +503,7 @@ def Pc(CASRN, method=None):
 Vc_all_methods = (IUPAC, MATTHEWS, CRC, PSRK, YAWS)
 '''Tuple of method name keys. See the `Vc` for the actual references'''
 
-@unsafe
+@mark_jit_unsafe
 def Vc_methods(CASRN):
     """Return all methods available to obtain Vc for the desired chemical.
 
@@ -524,7 +524,7 @@ def Vc_methods(CASRN):
     if not _critical_data_loaded: _load_critical_data()
     return list_available_methods_from_df_dict(Vc_sources, CASRN, 'Vc')
 
-@unsafe
+@mark_jit_unsafe
 def Vc(CASRN, method=None):
     r'''This function handles the retrieval of a chemical's critical
     volume. Lookup is based on CASRNs. Will automatically select a data
@@ -654,7 +654,7 @@ def Vc(CASRN, method=None):
 Zc_all_methods = (IUPAC, MATTHEWS, CRC, PSRK, YAWS)
 '''Tuple of method name keys. See the `Zc` for the actual references'''
 
-@unsafe
+@mark_jit_unsafe
 def Zc_methods(CASRN):
     """Return all methods available to obtain Zc for the desired chemical.
 
@@ -675,7 +675,7 @@ def Zc_methods(CASRN):
     if not _critical_data_loaded: _load_critical_data()
     return list_available_methods_from_df_dict(Zc_sources, CASRN, 'Zc')
 
-@unsafe
+@mark_jit_unsafe
 def Zc(CASRN, method=None):
     r'''This function handles the retrieval of a chemical's critical
     compressibility. Lookup is based on CASRNs. Will automatically select a
@@ -845,7 +845,7 @@ def Zc(CASRN, method=None):
     u'Cs': 3.433699060142929,
     u'Zr': 0.9346554283483623}
 
-@unsafe
+@mark_jit_unsafe
 def Mersmann_Kind_predictor(atoms, coeff=3.645, power=0.5,
                             covalent_radii=rcovs_Mersmann_Kind):
     r'''Predicts the critical molar volume of a chemical based only on its

chemicals/elements.py

@@ -67,7 +67,7 @@
            'serialize_formula', 'mixture_atomic_composition_ordered',
            'periodic_table']
 import re
-from chemicals.numba import unsafe
+from chemicals import mark_jit_unsafe
 
 CAS_by_number_standard = ['1333-74-0', '7440-59-7', '7439-93-2', '7440-41-7', '7440-42-8', '7440-44-0', '7727-37-9', '7782-44-7', '7782-41-4', '7440-01-9', '7440-23-5', '7439-95-4', '7429-90-5', '7440-21-3', '7723-14-0', '7704-34-9', '7782-50-5', '7440-37-1', '7440-09-7', '7440-70-2', '7440-20-2', '7440-32-6', '7440-62-2', '7440-47-3', '7439-96-5', '7439-89-6', '7440-48-4', '7440-02-0', '7440-50-8', '7440-66-6', '7440-55-3', '7440-56-4', '7440-38-2', '7782-49-2', '7726-95-6', '7439-90-9', '7440-17-7', '7440-24-6', '7440-65-5', '7440-67-7', '7440-03-1', '7439-98-7', '7440-26-8', '7440-18-8', '7440-16-6', '7440-05-3', '7440-22-4', '7440-43-9', '7440-74-6', '7440-31-5', '7440-36-0', '13494-80-9', '7553-56-2', '7440-63-3', '7440-46-2', '7440-39-3', '7439-91-0', '7440-45-1', '7440-10-0', '7440-00-8', '7440-12-2', '7440-19-9', '7440-53-1', '7440-54-2', '7440-27-9', '7429-91-6', '7440-60-0', '7440-52-0', '7440-30-4', '7440-64-4', '7439-94-3', '7440-58-6', '7440-25-7', '7440-33-7', '7440-15-5', '7440-04-2', '7439-88-5', '7440-06-4', '7440-57-5', '7439-97-6', '7440-28-0', '7439-92-1', '7440-69-9', '7440-08-6', '7440-68-8', '10043-92-2', '7440-73-5', '7440-14-4', '7440-34-8', '7440-29-1', '7440-13-3', '7440-61-1', '7439-99-8', '7440-07-5', '7440-35-9', '7440-51-9', '7440-40-6', '7440-71-3', '7429-92-7', '7440-72-4', '7440-11-1', '10028-14-5', '22537-19-5', '53850-36-5', '53850-35-4', '54038-81-2', '54037-14-8', '54037-57-9', '54038-01-6', '54083-77-1', '54386-24-2', '54084-26-3', '54084-70-7', '54085-16-4', '54085-64-2', '54100-71-9', '54101-14-3', '54144-19-3']
 '''Standard CAS numbers of the elements, indexed by atomic numbers off-by-one up to 118.'''
@@ -554,7 +554,7 @@ class directly.
 '''
 del openbabel_element_data
 
-@unsafe
+@mark_jit_unsafe
 def molecular_weight(atoms):
     r'''Calculates molecular weight of a molecule given a dictionary of its
     atoms and their counts, in the format {symbol: count}.
@@ -603,7 +603,7 @@ def molecular_weight(atoms):
             raise ValueError('Molecule includes unknown atoms')
     return MW
 
-@unsafe
+@mark_jit_unsafe
 def mass_fractions(atoms, MW=None):
     r'''Calculates the mass fractions of each element in a compound,
     given a dictionary of its atoms and their counts, in the format
@@ -654,7 +654,7 @@ def mass_fractions(atoms, MW=None):
             raise ValueError('Molecule includes unknown atoms')
     return mfracs
 
-@unsafe
+@mark_jit_unsafe
 def atom_fractions(atoms):
     r'''Calculates the atomic fractions of each element in a compound,
     given a dictionary of its atoms and their counts, in the format
@@ -695,7 +695,7 @@ def atom_fractions(atoms):
         afracs[i] = atoms[i]/count
     return afracs
 
-@unsafe
+@mark_jit_unsafe
 def mixture_atomic_composition(atomss, zs):
     r'''Simple function to calculate the atomic average composition of a
     mixture, using the mole fractions of each species and their own atomic
@@ -730,7 +730,7 @@ def mixture_atomic_composition(atomss, zs):
                 ans[key] = val*zs_i
     return ans
 
-@unsafe
+@mark_jit_unsafe
 def mixture_atomic_composition_ordered(atomss, zs):
     r'''Simple function to calculate the atomic average composition of a
     mixture, using the mole fractions of each species and their own atomic
@@ -769,7 +769,7 @@ def mixture_atomic_composition_ordered(atomss, zs):
         eles.append(k)
     return nums, eles
 
-@unsafe
+@mark_jit_unsafe
 def atom_matrix(atomss, atom_IDs=None):
     r'''Simple function to create a matrix of elements in each compound, where
     each row has the same elements.
@@ -817,7 +817,7 @@ def atom_matrix(atomss, atom_IDs=None):
 
     return element_matrix
 
-@unsafe
+@mark_jit_unsafe
 def similarity_variable(atoms, MW=None):
     r'''Calculates the similarity variable of an compound, as defined in [1]_.
     Currently only applied for certain heat capacity estimation routines.
@@ -859,7 +859,7 @@ def similarity_variable(atoms, MW=None):
         MW = molecular_weight(atoms)
     return sum(atoms.values())/MW
 
-@unsafe
+@mark_jit_unsafe
 def atoms_to_Hill(atoms):
     r'''Determine the Hill formula of a compound, given a dictionary of its
     atoms and their counts, in the format {symbol: count}.
@@ -920,7 +920,7 @@ def str_ele_count(ele):
 _simple_formula_parser_re_str = r'([A-Z][a-z]{0,2})([\d\.\d]+)?'
 _simple_formula_parser_re = None # Delay creation to simple_formula_parser to speedup start
 
-@unsafe
+@mark_jit_unsafe
 def simple_formula_parser(formula):
     r'''Basic formula parser, primarily for obtaining element counts from
     formulas as formated in PubChem. Handles formulas with integer or decimal
@@ -976,7 +976,7 @@ def simple_formula_parser(formula):
 formula_token_matcher_rational = bracketed_charge_re = None
 letter_set = set('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ')
 
-@unsafe
+@mark_jit_unsafe
 def nested_formula_parser(formula, check=True):
     r'''Improved formula parser which handles braces and their multipliers,
     as well as rational element counts.
@@ -1064,7 +1064,7 @@ def nested_formula_parser(formula, check=True):
                 ans[ele] = count
     return ans
 
-@unsafe
+@mark_jit_unsafe
 def charge_from_formula(formula):
     r'''Basic formula parser to determine the charge from a formula - given
     that the charge is already specified as one element of the formula.
@@ -1120,7 +1120,7 @@ def charge_from_formula(formula):
     else:
         return multiplier*count
 
-@unsafe
+@mark_jit_unsafe
 def serialize_formula(formula):
     r'''Basic formula serializer to construct a consistently-formatted formula.
     This is necessary for handling user-supplied formulas, which are not always