pyEQL 1.0.0__py2.py3-none-any.whl → 1.0.2__py2.py3-none-any.whl

pyEQL/__init__.py

@@ -47,7 +47,7 @@ ureg.default_format = "P~"
 
 # create a Store for the default database
 json_db_file = files("pyEQL") / "database" / "pyeql_db.json"
-IonDB = JSONStore(str(json_db_file), key="formula")
+IonDB = JSONStore(str(json_db_file), key="formula", encoding="utf8")
 # By calling connect on init, we get the expensive JSON reading operation out
 # of the way. Subsequent calls to connect will bypass this and access the already-
 # instantiated Store in memory, which should speed up instantiation of Solution objects.

pyEQL/activity_correction.py

@@ -14,8 +14,8 @@ are called from within the get_activity_coefficient method of the Solution class
 """
 
 import logging
-import math
 
+import numpy as np
 from pint import Quantity
 
 from pyEQL import ureg
@@ -114,8 +114,8 @@ def _debye_parameter_activity(temperature: str = "25 degC") -> "Quantity":
 
     debyeparam = (
         ureg.elementary_charge**3
-        * (2 * math.pi * ureg.N_A * ureg.Quantity(water_substance.rho, "g/L")) ** 0.5
-        / (4 * math.pi * ureg.epsilon_0 * water_substance.epsilon * ureg.boltzmann_constant * T) ** 1.5
+        * (2 * np.pi * ureg.N_A * ureg.Quantity(water_substance.rho, "g/L")) ** 0.5
+        / (4 * np.pi * ureg.epsilon_0 * water_substance.epsilon * ureg.boltzmann_constant * T) ** 1.5
     )
 
     logger.debug(rf"Computed Debye-Huckel Limiting Law Constant A^{{\gamma}} = {debyeparam} at {temperature}")
@@ -248,7 +248,7 @@ def get_activity_coefficient_debyehuckel(ionic_strength, z=1, temperature="25 de
 
     log_f = -_debye_parameter_activity(temperature) * z**2 * ionic_strength**0.5
 
-    return math.exp(log_f) * ureg.Quantity(1, "dimensionless")
+    return np.exp(log_f) * ureg.Quantity(1, "dimensionless")
 
 
 def get_activity_coefficient_guntelberg(ionic_strength, z=1, temperature="25 degC"):
@@ -285,7 +285,7 @@ def get_activity_coefficient_guntelberg(ionic_strength, z=1, temperature="25 deg
 
     log_f = -_debye_parameter_activity(temperature) * z**2 * ionic_strength**0.5 / (1 + ionic_strength.magnitude**0.5)
 
-    return math.exp(log_f) * ureg.Quantity(1, "dimensionless")
+    return np.exp(log_f) * ureg.Quantity(1, "dimensionless")
 
 
 def get_activity_coefficient_davies(ionic_strength, z=1, temperature="25 degC"):
@@ -327,7 +327,7 @@ def get_activity_coefficient_davies(ionic_strength, z=1, temperature="25 degC"):
         * (ionic_strength.magnitude**0.5 / (1 + ionic_strength.magnitude**0.5) - 0.2 * ionic_strength.magnitude)
     )
 
-    return math.exp(log_f) * ureg.Quantity(1, "dimensionless")
+    return np.exp(log_f) * ureg.Quantity(1, "dimensionless")
 
 
 def get_activity_coefficient_pitzer(
@@ -437,7 +437,7 @@ def get_activity_coefficient_pitzer(
         b,
     )
 
-    return math.exp(loggamma) * ureg.Quantity(1, "dimensionless")
+    return np.exp(loggamma) * ureg.Quantity(1, "dimensionless")
 
 
 def get_apparent_volume_pitzer(
@@ -533,7 +533,7 @@ def get_apparent_volume_pitzer(
         (nu_cation + nu_anion)
         * abs(z_cation * z_anion)
         * (_debye_parameter_volume(temperature) / 2 / b)
-        * math.log(1 + b * ionic_strength**0.5)
+        * np.log(1 + b * ionic_strength**0.5)
     )
 
     third_term = (
@@ -566,7 +566,7 @@ def _pitzer_f1(x):
     # return 0 if the input is 0
     if x == 0:
         return 0
-    return 2 * (1 - (1 + x) * math.exp(-x)) / x**2
+    return 2 * (1 - (1 + x) * np.exp(-x)) / x**2
 
 
 def _pitzer_f2(x):
@@ -586,7 +586,7 @@ def _pitzer_f2(x):
     # return 0 if the input is 0
     if x == 0:
         return 0
-    return -2 * (1 - (1 + x + x**2 / 2) * math.exp(-x)) / x**2
+    return -2 * (1 - (1 + x + x**2 / 2) * np.exp(-x)) / x**2
 
 
 def _pitzer_B_MX(ionic_strength, alpha1, alpha2, beta0, beta1, beta2):
@@ -692,6 +692,10 @@ def _pitzer_B_phi(ionic_strength, alpha1, alpha2, beta0, beta1, beta2):
         and Representation with an Ion Interaction (Pitzer) Model.
         Journal of Chemical & Engineering Data, 55(2), 830-838. doi:10.1021/je900487a
     """
+    import math
+
+    # TODO - for some reason this specific method requires the use of math.exp rather than np.exp. Using np.exp raises
+    # a dimensionalityerror.
     return beta0 + beta1 * math.exp(-alpha1 * ionic_strength**0.5) + beta2 * math.exp(-alpha2 * ionic_strength**0.5)
 
 
@@ -772,7 +776,7 @@ def _pitzer_log_gamma(
         -1
         * abs(z_cation * z_anion)
         * _debye_parameter_osmotic(temperature)
-        * (ionic_strength**0.5 / (1 + b * ionic_strength**0.5) + 2 / b * math.log(1 + b * ionic_strength**0.5))
+        * (ionic_strength**0.5 / (1 + b * ionic_strength**0.5) + 2 / b * np.log(1 + b * ionic_strength**0.5))
     )
     second_term = 2 * molality * nu_cation * nu_anion / (nu_cation + nu_anion) * (B_MX + B_phi)
     third_term = 3 * molality**2 * (nu_cation * nu_anion) ** 1.5 / (nu_cation + nu_anion) * C_phi

pyEQL/engines.py

@@ -47,7 +47,7 @@ class EOS(ABC):
             solution: pyEQL Solution object
             solute: str identifying the solute of interest
 
-        Returns
+        Returns:
             Quantity: dimensionless quantity object
 
         Raises:
@@ -62,7 +62,7 @@ class EOS(ABC):
         Args:
             solution: pyEQL Solution object
 
-        Returns
+        Returns:
             Quantity: dimensionless molal scale osmotic coefficient
 
         Raises:
@@ -77,7 +77,7 @@ class EOS(ABC):
         Args:
             solution: pyEQL Solution object
 
-        Returns
+        Returns:
             Quantity: solute volume in L
 
         Raises:
@@ -94,7 +94,7 @@ class EOS(ABC):
         Args:
             solution: pyEQL Solution object
 
-        Returns
+        Returns:
             Nothing. The speciation of the Solution is modified in-place.
 
         Raises:
@@ -139,7 +139,7 @@ class NativeEOS(EOS):
     def __init__(
         self,
         phreeqc_db: Literal["vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"] = "llnl.dat",
-    ):
+    ) -> None:
         """
         Args:
             phreeqc_db: Name of the PHREEQC database file to use for solution thermodynamics
@@ -173,9 +173,7 @@ class NativeEOS(EOS):
         self._stored_comp = None
 
     def _setup_ppsol(self, solution):
-        """
-        Helper method to set up a PhreeqPython solution for subsequent analysis.
-        """
+        """Helper method to set up a PhreeqPython solution for subsequent analysis."""
         self._stored_comp = solution.components.copy()
         solv_mass = solution.solvent_mass.to("kg").magnitude
         # inherit bulk solution properties
@@ -197,6 +195,16 @@ class NativeEOS(EOS):
         # add the composition to the dict
         # also, skip H and O
         for el, mol in solution.get_el_amt_dict().items():
+            # CAUTION - care must be taken to avoid unintended behavior here. get_el_amt_dict() will return
+            # all distinct oxi states of each element present. If there are elements present whose oxi states
+            # are NOT recognized by PHREEQC (via SPECIAL_ELEMENTS) then the amount of only 1 oxi state will be
+            # entered into the composition dict. This can especially cause problems after equilibrate() has already
+            # been called once. For example, equilibrating a simple NaCl solution generates Cl species that are assigned
+            # various oxidations states, -1 mostly, but also 1, 2, and 3. Since the concentrations of everything
+            # except the -1 oxi state are tiny, this can result in Cl "disappearing" from the solution if
+            # equlibrate is called again. It also causes non-determinism, because the amount is taken from whatever
+            # oxi state happens to be iterated through last.
+
             # strip off the oxi state
             bare_el = el.split("(")[0]
             if bare_el in SPECIAL_ELEMENTS:
@@ -208,7 +216,12 @@ class NativeEOS(EOS):
             else:
                 key = bare_el
 
-            d[key] = str(mol / solv_mass)
+            if key in d:
+                # when multiple oxi states for the same (non-SPECIAL) element are present, make sure to
+                # add all their amounts together
+                d[key] += str(mol / solv_mass)
+            else:
+                d[key] = str(mol / solv_mass)
 
             # tell PHREEQC which species to use for charge balance
             if (
@@ -660,7 +673,6 @@ class NativeEOS(EOS):
             solution.components[s] = mol
 
         # make sure all species are accounted for
-        charge_adjust = 0
         assert set(self._stored_comp.keys()) - set(solution.components.keys()) == set()
 
         # log a message if any components were not touched by PHREEQC
@@ -671,6 +683,11 @@ class NativeEOS(EOS):
                 f"After equilibration, the amounts of species {missing_species} were not modified "
                 "by PHREEQC. These species are likely absent from its database."
             )
+
+        # re-adjust charge balance for any missing species
+        # note that if balance_charge is set, it will have been passed to PHREEQC, so we only need to adjust
+        # for any missing species here.
+        charge_adjust = 0
         for s in missing_species:
             charge_adjust += -1 * solution.get_amount(s, "eq").magnitude
         if charge_adjust != 0:
@@ -679,11 +696,10 @@ class NativeEOS(EOS):
                 f" {charge_adjust} eq of charge were added via {solution.balance_charge}"
             )
 
-            # re-adjust charge balance
             if solution.balance_charge is None:
                 pass
             elif solution.balance_charge == "pH":
-                solution.components["H+"] += charge_adjust
+                solution.components["H+"] += charge_adjust.magnitude
             elif solution.balance_charge == "pE":
                 raise NotImplementedError
             else:
@@ -696,7 +712,7 @@ class NativeEOS(EOS):
         # call to equilibrate can thus result in a slight change in the Solution mass.
         solution.components[solution.solvent] = orig_solvent_moles
 
-    def __deepcopy__(self, memo):
+    def __deepcopy__(self, memo) -> "NativeEOS":
         # custom deepcopy required because the PhreeqPython instance used by the Native and Phreeqc engines
         # is not pickle-able.
         import copy
@@ -720,7 +736,7 @@ class PhreeqcEOS(NativeEOS):
         phreeqc_db: Literal[
             "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
         ] = "phreeqc.dat",
-    ):
+    ) -> None:
         """
         Args:
         phreeqc_db: Name of the PHREEQC database file to use for solution thermodynamics

pyEQL/equilibrium.py

@@ -11,7 +11,8 @@ NOTE: these methods are not currently used but are here for the future.
 
 # import libraries for scientific functions
 import logging
-import math
+
+import numpy as np
 
 from pyEQL import ureg
 
@@ -51,7 +52,7 @@ def adjust_temp_pitzer(c1, c2, c3, c4, c5, temp, temp_ref=ureg.Quantity("298.15
     return (
         c1
         + c2 * (1 / temp + 1 / temp_ref)
-        + c2 * math.log(temp / temp_ref)
+        + c2 * np.log(temp / temp_ref)
         + c3 * (temp - temp_ref)
         + c4 * (temp**2 - temp_ref**2)
         + c5 * (temp**-2 - temp_ref**-2)
@@ -91,7 +92,7 @@ def adjust_temp_vanthoff(equilibrium_constant, enthalpy, temperature, reference_
         >>> adjust_temp_vanthoff(0.15,ureg.Quantity('-197.6 kJ/mol'),ureg.Quantity('42 degC')) #doctest: +ELLIPSIS
         0.00203566...
     """
-    output = equilibrium_constant * math.exp(
+    output = equilibrium_constant * np.exp(
         enthalpy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
     )
 
@@ -128,7 +129,7 @@ def adjust_temp_arrhenius(
         TODO - add better reference
 
         .. math::
-            ln(\frac{K2}{K1} = \frac{E_a}{R} ( \frac{1}{T_{1}} - {\frac{1}{T_2}} )
+            ln(\frac{K2}{K1}) = \frac{E_a}{R} ( \frac{1}{T_{1}} - {\frac{1}{T_2}} )
 
     References:
         http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics/Reaction_Rates/Temperature_Dependence_of_Reaction_Rates/Arrhenius_Equation
@@ -137,7 +138,7 @@ def adjust_temp_arrhenius(
         >>> adjust_temp_arrhenius(7,900*ureg.Quantity('kJ/mol'),37*ureg.Quantity('degC'),97*ureg.Quantity('degC')) #doctest: +ELLIPSIS
         1.8867225...e-24
     """
-    output = rate_constant * math.exp(
+    output = rate_constant * np.exp(
         activation_energy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
     )
 

pyEQL/functions.py

@@ -7,7 +7,8 @@ pyEQL functions that take Solution objects as inputs or return Solution objects.
 """
 
 import logging
-import math
+
+import numpy as np
 
 from pyEQL import Solution, ureg
 
@@ -55,7 +56,7 @@ def gibbs_mix(solution1: Solution, solution2: Solution):
     for solution in term_list:
         for solute in solution.components:
             if solution.get_amount(solute, "fraction") != 0:
-                term_list[solution] += solution.get_amount(solute, "mol") * math.log(solution.get_activity(solute))
+                term_list[solution] += solution.get_amount(solute, "mol") * np.log(solution.get_activity(solute))
 
     return (ureg.R * blend.temperature.to("K") * (term_list[blend] - term_list[concentrate] - term_list[dilute])).to(
         "J"
@@ -102,7 +103,7 @@ def entropy_mix(solution1: Solution, solution2: Solution):
     for solution in term_list:
         for solute in solution.components:
             if solution.get_amount(solute, "fraction") != 0:
-                term_list[solution] += solution.get_amount(solute, "mol") * math.log(
+                term_list[solution] += solution.get_amount(solute, "mol") * np.log(
                     solution.get_amount(solute, "fraction")
                 )
 
@@ -242,7 +243,7 @@ def donnan_eql(solution: Solution, fixed_charge: str):
 
         return (act_cation_mem / act_cation_soln) ** (1 / z_cation) * (act_anion_soln / act_anion_mem) ** (
             1 / z_anion
-        ) - math.exp(delta_pi * exp_term)
+        ) - np.exp(delta_pi * exp_term)
 
     # solve the function above using one of scipy's nonlinear solvers
 

pyEQL/salt_ion_match.py

@@ -21,7 +21,7 @@ from pyEQL.utils import standardize_formula
 class Salt(MSONable):
     """Class to represent a salt."""
 
-    def __init__(self, cation, anion):
+    def __init__(self, cation, anion) -> None:
         """
         Create a Salt object based on its component ions.
 

pyEQL/solute.py

@@ -150,7 +150,7 @@ class Solute:
         return dict(asdict(self).items())
 
     # set output of the print() statement
-    def __str__(self):
+    def __str__(self) -> str:
         return (
             "Species "
             + str(self.formula)

pyEQL/solution.py

@@ -9,7 +9,6 @@ pyEQL Solution Class.
 from __future__ import annotations
 
 import logging
-import math
 import os
 import warnings
 from functools import lru_cache
@@ -58,7 +57,7 @@ class Solution(MSONable):
         database: str | Path | Store | None = None,
         default_diffusion_coeff: float = 1.6106e-9,
         log_level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] | None = "ERROR",
-    ):
+    ) -> None:
         """
         Instantiate a Solution from a composition.
 
@@ -433,6 +432,10 @@ class Solution(MSONable):
                 activity = False) of the solute.
         """
         try:
+            # TODO - for some reason this specific method requires the use of math.log10 rather than np.log10.
+            # Using np.exp raises ZeroDivisionError
+            import math
+
             if activity is True:
                 return -1 * math.log10(self.get_activity(solute))
             return -1 * math.log10(self.get_amount(solute, "mol/L").magnitude)
@@ -647,7 +650,7 @@ class Solution(MSONable):
         x_cat = self.get_amount(salt.cation, "fraction").magnitude
 
         # calculate the kinematic viscosity
-        nu = math.log(nu_w * MW_w / MW) + 15 * x_cat**2 + x_cat**3 * G_123 + 3 * x_cat * G_23 * (1 - 0.05 * x_cat)
+        nu = np.log(nu_w * MW_w / MW) + 15 * x_cat**2 + x_cat**3 * G_123 + 3 * x_cat * G_23 * (1 - 0.05 * x_cat)
 
         return ureg.Quantity(np.exp(nu), "m**2 / s")
 
@@ -930,9 +933,7 @@ class Solution(MSONable):
             :attr:`dielectric_constant`
 
         """
-        bjerrum_length = ureg.e**2 / (
-            4 * math.pi * self.dielectric_constant * ureg.epsilon_0 * ureg.k * self.temperature
-        )
+        bjerrum_length = ureg.e**2 / (4 * np.pi * self.dielectric_constant * ureg.epsilon_0 * ureg.k * self.temperature)
         return bjerrum_length.to("nm")
 
     @property
@@ -975,7 +976,7 @@ class Solution(MSONable):
         partial_molar_volume_water = self.get_property(self.solvent, "size.molar_volume")
 
         osmotic_pressure = (
-            -1 * ureg.R * self.temperature / partial_molar_volume_water * math.log(self.get_water_activity())
+            -1 * ureg.R * self.temperature / partial_molar_volume_water * np.log(self.get_water_activity())
         )
         self.logger.debug(
             f"Calculated osmotic pressure of solution as {osmotic_pressure} Pa at T= {self.temperature} degrees C"
@@ -1835,12 +1836,12 @@ class Solution(MSONable):
                 * ureg.Quantity(0.018015, "kg/mol")
                 * self.get_total_moles_solute()
                 / self.solvent_mass
-                / math.log(self.get_amount(self.solvent, "fraction"))
+                / np.log(self.get_amount(self.solvent, "fraction"))
             )
         if scale == "fugacity":
             return np.exp(
                 -molal_phi * ureg.Quantity(0.018015, "kg/mol") * self.get_total_moles_solute() / self.solvent_mass
-                - math.log(self.get_amount(self.solvent, "fraction"))
+                - np.log(self.get_amount(self.solvent, "fraction"))
             ) * ureg.Quantity(1, "dimensionless")
 
         raise ValueError("Invalid scale argument. Pass 'molal', 'rational', or 'fugacity'.")
@@ -1939,14 +1940,14 @@ class Solution(MSONable):
                         ureg.R
                         * self.temperature.to("K")
                         * self.get_amount(item, "mol")
-                        * math.log(self.get_activity(item))
+                        * np.log(self.get_activity(item))
                     )
                 else:
                     E += (
                         ureg.R
                         * self.temperature.to("K")
                         * self.get_amount(item, "mol")
-                        * math.log(self.get_amount(item, "fraction"))
+                        * np.log(self.get_amount(item, "fraction"))
                     )
             # If we have a solute with zero concentration, we will get a ValueError
             except ValueError:
@@ -2511,7 +2512,7 @@ class Solution(MSONable):
         return loadfn(filename)
 
     # arithmetic operations
-    def __add__(self, other: Solution):
+    def __add__(self, other: Solution) -> Solution:
         """
         Solution addition: mix two solutions together.
 
@@ -2582,12 +2583,12 @@ class Solution(MSONable):
             "this property is planned for a future release."
         )
         # calculate the new pH and pE (before reactions) by mixing
-        mix_pH = -math.log10(float(mix_species["H+"].split(" ")[0]) / mix_vol.to("L").magnitude)
+        mix_pH = -np.log10(float(mix_species["H+"].split(" ")[0]) / mix_vol.to("L").magnitude)
 
         # pE = -log[e-], so calculate the moles of e- in each solution and mix them
         mol_e_self = 10 ** (-1 * self.pE) * self.volume.to("L").magnitude
         mol_e_other = 10 ** (-1 * other.pE) * other.volume.to("L").magnitude
-        mix_pE = -math.log10((mol_e_self + mol_e_other) / mix_vol.to("L").magnitude)
+        mix_pE = -np.log10((mol_e_self + mol_e_other) / mix_vol.to("L").magnitude)
 
         # create a new solution
         return Solution(
@@ -2599,10 +2600,10 @@ class Solution(MSONable):
             pE=mix_pE,
         )
 
-    def __sub__(self, other: Solution):
+    def __sub__(self, other: Solution) -> None:
         raise NotImplementedError("Subtraction of solutions is not implemented.")
 
-    def __mul__(self, factor: float):
+    def __mul__(self, factor: float) -> None:
         """
         Solution multiplication: scale all components by a factor. For example, Solution * 2 will double the moles of
         every component (including solvent). No other properties will change.
@@ -2610,7 +2611,7 @@ class Solution(MSONable):
         self.volume *= factor
         return self
 
-    def __truediv__(self, factor: float):
+    def __truediv__(self, factor: float) -> None:
         """
         Solution division: scale all components by a factor. For example, Solution / 2 will remove half of the moles
         of every compoonents (including solvent). No other properties will change.
@@ -2656,7 +2657,7 @@ class Solution(MSONable):
 
             print(f"{i}:\t {amt:0.{places}f}")
 
-    def __str__(self):
+    def __str__(self) -> str:
         # set output of the print() statement for the solution
         l1 = f"Volume: {self.volume:.3f~}"
         l2 = f"Temperature: {self.temperature:.3f~}"

pyEQL/utils.py

@@ -9,6 +9,7 @@ pyEQL utilities
 import logging
 from collections import UserDict
 from functools import lru_cache
+from typing import Any
 
 from iapws import IAPWS95, IAPWS97
 from pymatgen.core.ion import Ion
@@ -59,7 +60,39 @@ def standardize_formula(formula: str):
         be enclosed in square brackets to remove any ambiguity in the meaning of the formula. For example, 'Na+',
         'Na+1', and 'Na[+]' will all standardize to "Na[+1]"
     """
-    return Ion.from_formula(formula).reduced_formula
+    sform = Ion.from_formula(formula).reduced_formula
+
+    # TODO - manual formula adjustments. May be implemented upstream in pymatgen in the future
+    # thanks to @xiaoxiaozhu123 for pointing out these issues in
+    # https://github.com/KingsburyLab/pyEQL/issues/136
+
+    # ammonia
+    if sform == "H4N[+1]":
+        sform = "NH4[+1]"
+    elif sform == "H3N(aq)":
+        sform = "NH3(aq)"
+    # phosphoric acid system
+    elif sform == "PH3O4(aq)":
+        sform = "H3PO4(aq)"
+    elif sform == "PHO4[-2]":
+        sform = "HPO4[-2]"
+    elif sform == "P(HO2)2[-1]":
+        sform = "H2PO4[-1]"
+    # thiocyanate
+    elif sform == "CSN[-1]":
+        sform = "SCN[-1]"
+    # triiodide
+    elif sform == "I[-0.33333333]":
+        sform = "I3[-1]"
+    # formate
+    elif sform == "HCOO[-1]":
+        sform = "HCO2[-1]"
+    # oxalate
+    elif sform == "CO2[-1]":
+        sform = "C2O4[-2]"
+
+    # TODO - consider adding recognition of special formulas like MeOH for methanol or Cit for citrate
+    return sform
 
 
 def format_solutes_dict(solute_dict: dict, units: str):
@@ -115,18 +148,18 @@ class FormulaDict(UserDict):
     formula notation (e.g., "Na+", "Na+1", "Na[+]" all have the same effect)
     """
 
-    def __getitem__(self, key):
+    def __getitem__(self, key) -> Any:
         return super().__getitem__(standardize_formula(key))
 
-    def __setitem__(self, key, value):
+    def __setitem__(self, key, value) -> None:
         super().__setitem__(standardize_formula(key), value)
         # sort contents anytime an item is set
         self.data = dict(sorted(self.items(), key=lambda x: x[1], reverse=True))
 
     # Necessary to define this so that .get() works properly in python 3.12+
     # see https://github.com/python/cpython/issues/105524
-    def __contains__(self, key):
+    def __contains__(self, key) -> bool:
         return standardize_formula(key) in self.data
 
-    def __delitem__(self, key):
+    def __delitem__(self, key) -> None:
         super().__delitem__(standardize_formula(key))

{pyEQL-1.0.0.dist-info → pyEQL-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.0.0
+Version: 1.0.2
 Summary: Python tools for solution chemistry
 Home-page: https://github.com/KingsburyLab/pyEQL
 Author: Ryan Kingsbury
@@ -19,12 +19,12 @@ License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
 Requires-Dist: pint >=0.19
-Requires-Dist: numpy
+Requires-Dist: numpy <2
 Requires-Dist: scipy
-Requires-Dist: pymatgen >=2023.10.11
+Requires-Dist: pymatgen ==2024.5.1
 Requires-Dist: iapws
 Requires-Dist: monty
-Requires-Dist: maggma >=0.57.5
+Requires-Dist: maggma >=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: docs
 Requires-Dist: sphinx >=3.2.1 ; extra == 'docs'
@@ -37,6 +37,7 @@ Requires-Dist: setuptools ; extra == 'testing'
 Requires-Dist: pre-commit ; extra == 'testing'
 Requires-Dist: pytest ; extra == 'testing'
 Requires-Dist: pytest-cov ; extra == 'testing'
+Requires-Dist: pytest-xdist ; extra == 'testing'
 Requires-Dist: black ; extra == 'testing'
 Requires-Dist: mypy ; extra == 'testing'
 Requires-Dist: ruff ; extra == 'testing'

pyEQL-1.0.2.dist-info/RECORD

@@ -0,0 +1,27 @@
+pyEQL/__init__.py,sha256=JErflmaJVP373dm3-YGHUomFu05dgX0iXWS-Z5AgSTU,2118
+pyEQL/activity_correction.py,sha256=eOixjgTd5hTrTRD5s6aPCCG12lAIH7-lRN0Z1qHu678,37151
+pyEQL/engines.py,sha256=b9ay7FYqmnINmhSMyNpVmENAtZVW-gyBfXUPf1PEUoY,34946
+pyEQL/equilibrium.py,sha256=YCtoAJSgn1WC9NJnc3H4FTJdKQvogsvCuj7HqlKMtww,8307
+pyEQL/functions.py,sha256=nc-Hc61MmW-ELBR1PByJvQnELxM7PZexMHbU_O5-Bnw,10584
+pyEQL/pint_custom_units.txt,sha256=XHmcMlwVvqF9nEW7_e9Xgyq-xWEr-cDYqieas11T3eY,2882
+pyEQL/salt_ion_match.py,sha256=0nCZXmeo67VqcyYWQpPx-81hjSvnsg8HFB3fIyfjW_k,4070
+pyEQL/solute.py,sha256=no00Rc3tRfHmyht4wm2UXA1KZhKC45tWMO5QEkZY6yg,5140
+pyEQL/solution.py,sha256=XwtQmll3gPwdnnkXpQsnO7QebwTjplmlfhbEIU8rHDo,115940
+pyEQL/utils.py,sha256=unsY7zrrhl_1mOmt9_kumSKmLE5N5Hvh4bOErfS3nws,5168
+pyEQL/database/geothermal.dat,sha256=kksnfcBtWdOTpNn4CLXU1Mz16cwas2WuVKpuMU8CaVI,234230
+pyEQL/database/llnl.dat,sha256=jN-a0kfUFbQlYMn2shTVRg1JX_ZhLa-tJ0lLw2YSpLU,751462
+pyEQL/database/phreeqc_license.txt,sha256=8W1r8VxC2kVptIMSU9sDFNASYqN7MdwKEtIWWfjTQuM,2906
+pyEQL/database/pyeql_db.json,sha256=TQKKofds7QBNd-Hw5QQuPwP6rQ8YWh_hHlRAtoQX0m8,1080793
+pyEQL/presets/Ringers lactate.yaml,sha256=vtSnuvgALHR27XEjpDzC0xyw5-E6b2FSsF1EUEBiWpw,413
+pyEQL/presets/normal saline.yaml,sha256=i2znhnIeXfNx1iMFFSif7crMRCFRP6xN1m7Wp7USduM,318
+pyEQL/presets/rainwater.yaml,sha256=S0WHZNDfCJyjSSFxNFdkypjn2s3P0jJGCiYIxvi1ibA,337
+pyEQL/presets/seawater.yaml,sha256=oryc1CkhRz20RpWE6uiGiT93HoZnqlB0s-0PmBWr3-U,843
+pyEQL/presets/urine.yaml,sha256=0Njtc-H1fFRo7UhquHdiSTT4z-8VZJ1utDCk02qk28M,679
+pyEQL/presets/wastewater.yaml,sha256=jTTFBpmKxczaEtkCZb0xUULIPZt7wfC8eAJ6rthGnmw,502
+pyEQL-1.0.2.dist-info/AUTHORS.md,sha256=K9ZLhKFwZ2zLlFXwN62VuUYCpr5T6n4mOUCUHlytTUs,415
+pyEQL-1.0.2.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
+pyEQL-1.0.2.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
+pyEQL-1.0.2.dist-info/METADATA,sha256=YwIdTX8P0sFSCsTf65iFdxGZtQR_W_SdgfFEZy7RM0M,5889
+pyEQL-1.0.2.dist-info/WHEEL,sha256=0XQbNV6JE5ziJsWjIU8TRRv0N6SohNonLWgP86g5fiI,109
+pyEQL-1.0.2.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
+pyEQL-1.0.2.dist-info/RECORD,,

{pyEQL-1.0.0.dist-info → pyEQL-1.0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

pyEQL-1.0.0.dist-info/RECORD

@@ -1,27 +0,0 @@
-pyEQL/__init__.py,sha256=IebzxPm-7Kz9cG2bl4anfo8NxOOKZj_ggkxBYyySvWE,2101
-pyEQL/activity_correction.py,sha256=mtpHdrjyrqkwWGUKh-91lH10HLOTTw3dQUqA10hMgms,36999
-pyEQL/engines.py,sha256=xpKlnAhdOXX25fM9EUzHMmYkJgaPX1FKqJ0ldMvFMKY,33539
-pyEQL/equilibrium.py,sha256=Y_jFqsPW-mcfqC524zV4dvMzWr4uwP7ZjGv8Kgkx5G0,8304
-pyEQL/functions.py,sha256=qsFXOs1BTQ6TB1DH_oD9WhX78DyaYHOjKKVZkaPW6Ew,10582
-pyEQL/pint_custom_units.txt,sha256=XHmcMlwVvqF9nEW7_e9Xgyq-xWEr-cDYqieas11T3eY,2882
-pyEQL/salt_ion_match.py,sha256=D4HJdV7iVsBEW5bW9tWpvc6pK-jrexTlvJV80YabHo4,4062
-pyEQL/solute.py,sha256=R4XjPiAZP2787ImIo072CWD1vjIYjGPt6zvxCrVO1pA,5133
-pyEQL/solution.py,sha256=nMbR1qprVag5UkIJFzLwkzDHJfpLyIdTgOzFzZdyHd8,115753
-pyEQL/utils.py,sha256=2VLl_sqcKcqBrVdP0ogtIYsOlc-wl4repi43Jqr-8yg,4156
-pyEQL/database/geothermal.dat,sha256=kksnfcBtWdOTpNn4CLXU1Mz16cwas2WuVKpuMU8CaVI,234230
-pyEQL/database/llnl.dat,sha256=jN-a0kfUFbQlYMn2shTVRg1JX_ZhLa-tJ0lLw2YSpLU,751462
-pyEQL/database/phreeqc_license.txt,sha256=8W1r8VxC2kVptIMSU9sDFNASYqN7MdwKEtIWWfjTQuM,2906
-pyEQL/database/pyeql_db.json,sha256=TQKKofds7QBNd-Hw5QQuPwP6rQ8YWh_hHlRAtoQX0m8,1080793
-pyEQL/presets/Ringers lactate.yaml,sha256=vtSnuvgALHR27XEjpDzC0xyw5-E6b2FSsF1EUEBiWpw,413
-pyEQL/presets/normal saline.yaml,sha256=i2znhnIeXfNx1iMFFSif7crMRCFRP6xN1m7Wp7USduM,318
-pyEQL/presets/rainwater.yaml,sha256=S0WHZNDfCJyjSSFxNFdkypjn2s3P0jJGCiYIxvi1ibA,337
-pyEQL/presets/seawater.yaml,sha256=oryc1CkhRz20RpWE6uiGiT93HoZnqlB0s-0PmBWr3-U,843
-pyEQL/presets/urine.yaml,sha256=0Njtc-H1fFRo7UhquHdiSTT4z-8VZJ1utDCk02qk28M,679
-pyEQL/presets/wastewater.yaml,sha256=jTTFBpmKxczaEtkCZb0xUULIPZt7wfC8eAJ6rthGnmw,502
-pyEQL-1.0.0.dist-info/AUTHORS.md,sha256=K9ZLhKFwZ2zLlFXwN62VuUYCpr5T6n4mOUCUHlytTUs,415
-pyEQL-1.0.0.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
-pyEQL-1.0.0.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
-pyEQL-1.0.0.dist-info/METADATA,sha256=5y38qhav2GITqPJ1yYXjBuMu_DZYKBvAkVpoodWcP4A,5839
-pyEQL-1.0.0.dist-info/WHEEL,sha256=DZajD4pwLWue70CAfc7YaxT1wLUciNBvN_TTcvXpltE,110
-pyEQL-1.0.0.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
-pyEQL-1.0.0.dist-info/RECORD,,