overhaul logging system; adjust message levels

src/pyEQL/activity_correction.py

@@ -12,14 +12,17 @@
 :license: LGPL, see LICENSE for more details.
 
 """
+
+import logging
 import math
 
 from pint import Quantity
 
 from pyEQL import ureg
-from pyEQL.logging_system import logger
 from pyEQL.utils import create_water_substance
 
+logger = logging.getLogger(__name__)
+
 
 def _debye_parameter_B(temperature: str = "25 degC") -> Quantity:
     r"""
@@ -115,7 +118,7 @@ def _debye_parameter_activity(temperature: str = "25 degC") -> "Quantity":
         / (4 * math.pi * ureg.epsilon_0 * water_substance.epsilon * ureg.boltzmann_constant * T) ** 1.5
     )
 
-    logger.info(rf"Computed Debye-Huckel Limiting Law Constant A^{{\gamma}} = {debyeparam} at {temperature}")
+    logger.debug(rf"Computed Debye-Huckel Limiting Law Constant A^{{\gamma}} = {debyeparam} at {temperature}")
     return debyeparam.to("kg ** 0.5 / mol ** 0.5")
 
 
@@ -149,7 +152,7 @@ def _debye_parameter_osmotic(temperature="25 degC"):
 
     """
     output = 1 / 3 * _debye_parameter_activity(temperature)
-    logger.info(f"Computed Debye-Huckel Limiting slope for osmotic coefficient A^phi = {output} at {temperature}")
+    logger.debug(f"Computed Debye-Huckel Limiting slope for osmotic coefficient A^phi = {output} at {temperature}")
     return output.to("kg ** 0.5 /mol ** 0.5")
 
 
@@ -206,7 +209,7 @@ def _debye_parameter_volume(temperature="25 degC"):
     if T.to("degC").magnitude != 25:
         logger.warning("Debye-Huckel limiting slope for volume is approximate when T is not equal to 25 degC")
 
-    logger.info(f"Computed Debye-Huckel Limiting Slope for volume A^V = {result} at {temperature}")
+    logger.debug(f"Computed Debye-Huckel Limiting Slope for volume A^V = {result} at {temperature}")
 
     return result.to("cm ** 3 * kg ** 0.5 /  mol ** 1.5")
 
@@ -280,9 +283,7 @@ def get_activity_coefficient_guntelberg(ionic_strength, z=1, temperature="25 deg
     if not ionic_strength.magnitude <= 0.1:
         logger.warning("Ionic strength exceeds valid range of the Guntelberg approximation")
 
-    log_f = (
-        -_debye_parameter_activity(temperature) * z**2 * ionic_strength**0.5 / (1 + ionic_strength.magnitude**0.5)
-    )
+    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")
 
@@ -615,9 +616,7 @@ def _pitzer_B_MX(ionic_strength, alpha1, alpha2, beta0, beta1, beta2):
         :func:`_pitzer_f1`
 
     """
-    coeff = (
-        beta0 + beta1 * _pitzer_f1(alpha1 * ionic_strength**0.5) + beta2 * _pitzer_f1(alpha2 * ionic_strength**0.5)
-    )
+    coeff = beta0 + beta1 * _pitzer_f1(alpha1 * ionic_strength**0.5) + beta2 * _pitzer_f1(alpha2 * ionic_strength**0.5)
     return coeff.magnitude
 
 

src/pyEQL/engines.py

@@ -6,6 +6,7 @@
 
 """
 
+import logging
 import os
 import warnings
 from abc import ABC, abstractmethod
@@ -14,20 +15,17 @@
 
 from phreeqpython import PhreeqPython
 
-# internal pyEQL imports
 import pyEQL.activity_correction as ac
-
-# import the parameters database
-# the pint unit registry
 from pyEQL import ureg
-from pyEQL.logging_system import logger
 from pyEQL.salt_ion_match import Salt
 from pyEQL.utils import standardize_formula
 
 # These are the only elements that are allowed to have parenthetical oxidation states
 # PHREEQC will ignore others (e.g., 'Na(1)')
 SPECIAL_ELEMENTS = ["S", "C", "N", "Cu", "Fe", "Mn"]
 
+logger = logging.getLogger(__name__)
+
 
 class EOS(ABC):
     """
@@ -367,14 +365,14 @@ def get_activity_coefficient(self, solution, solute):
                 str(solution.temperature),
             )
 
-            logger.info(
+            logger.debug(
                 f"Calculated activity coefficient of species {solute} as {activity_coefficient} based on salt {salt} using Pitzer model"
             )
             molal = activity_coefficient
 
         # for very low ionic strength, use the Debye-Huckel limiting law
         elif solution.ionic_strength.magnitude <= 0.005:
-            logger.info(
+            logger.debug(
                 "Ionic strength = %s. Using Debye-Huckel to calculate activity coefficient." % solution.ionic_strength
             )
             molal = ac.get_activity_coefficient_debyehuckel(
@@ -385,7 +383,7 @@ def get_activity_coefficient(self, solution, solute):
 
         # use the Guntelberg approximation for 0.005 < I < 0.1
         elif solution.ionic_strength.magnitude <= 0.1:
-            logger.info(
+            logger.debug(
                 "Ionic strength = %s. Using Guntelberg to calculate activity coefficient." % solution.ionic_strength
             )
             molal = ac.get_activity_coefficient_guntelberg(
@@ -396,7 +394,7 @@ def get_activity_coefficient(self, solution, solute):
 
         # use the Davies equation for 0.1 < I < 0.5
         elif solution.ionic_strength.magnitude <= 0.5:
-            logger.info(
+            logger.debug(
                 "Ionic strength = %s. Using Davies equation to calculate activity coefficient."
                 % solution.ionic_strength
             )
@@ -544,7 +542,7 @@ def get_osmotic_coefficient(self, solution):
                     str(solution.temperature),
                 )
 
-                logger.info(
+                logger.debug(
                     f"Calculated osmotic coefficient of water as {osmotic_coefficient} based on salt {item.formula} using Pitzer model"
                 )
                 effective_osmotic_sum += concentration * osmotic_coefficient
@@ -554,7 +552,7 @@ def get_osmotic_coefficient(self, solution):
                     "Cannot calculate osmotic coefficient because Pitzer parameters for salt %s are not specified. Returning unit osmotic coefficient"
                     % item.formula
                 )
-                effective_osmotic_sum += concentration * osmotic_coefficient
+                return 1
 
         try:
             return effective_osmotic_sum / molality_sum
@@ -621,7 +619,7 @@ def get_solute_volume(self, solution):
 
             pitzer_calc = True
 
-            logger.info("Updated solution volume using Pitzer model for solute %s" % salt.formula)
+            logger.debug("Updated solution volume using Pitzer model for solute %s" % salt.formula)
 
         # add the partial molar volume of any other solutes, except for water
         # or the parent salt, which is already accounted for by the Pitzer parameters
@@ -637,7 +635,7 @@ def get_solute_volume(self, solution):
             part_vol = solution.get_property(solute, "size.molar_volume")
             if part_vol is not None:
                 solute_vol += part_vol * ureg.Quantity(mol, "mol")
-                logger.info("Updated solution volume using direct partial molar volume for solute %s" % solute)
+                logger.debug("Updated solution volume using direct partial molar volume for solute %s" % solute)
 
             else:
                 logger.warning(

src/pyEQL/equilibrium.py

@@ -8,12 +8,14 @@
 :license: LGPL, see LICENSE for more details.
 
 """
+
 # import libraries for scientific functions
+import logging
 import math
 
-# the pint unit registry
 from pyEQL import ureg
-from pyEQL.logging_system import logger
+
+logger = logging.getLogger(__name__)
 
 # TODO - not used. Remove?
 SPECIES_ALIAISES = {
@@ -93,11 +95,13 @@ def adjust_temp_vanthoff(equilibrium_constant, enthalpy, temperature, reference_
         enthalpy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
     )
 
-    logger.info(
+    logger.debug(
         "Adjusted equilibrium constant K=%s from %s to %s degrees Celsius with Delta H = %s. Adjusted K = %s % equilibrium_constant,reference_temperature,temperature,enthalpy,output"
     )
 
-    logger.warning("Van't Hoff equation assumes enthalpy is independent of temperature over the range of interest")
+    logger.info(
+        "Note that the Van't Hoff equation assumes enthalpy is independent of temperature over the range of interest"
+    )
     return output
 
 
@@ -137,7 +141,7 @@ def adjust_temp_arrhenius(
         activation_energy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
     )
 
-    logger.info(
+    logger.debug(
         "Adjusted parameter %s from %s to %s degrees Celsius with Activation Energy = %s kJ/mol. Adjusted value = %s % rate_constant,reference_temperature,temperature,activation_energy,output"
     )
 
@@ -215,7 +219,7 @@ def alpha(n, pH, pKa_list):
 
     # return the desired distribution factor
     alpha = terms_list[n] / sum(terms_list)
-    logger.info(
+    logger.debug(
         "Calculated %s-deprotonated acid distribution coefficient of %s for pKa=%s at pH %s % n,alpha,pKa_list,pH"
     )
     return alpha

src/pyEQL/functions.py

@@ -5,13 +5,16 @@
 :license: LGPL, see LICENSE for more details.
 
 """
+
+import logging
 import math
 from typing import Literal
 
 from monty.dev import deprecated
 
 from pyEQL import Solution, ureg
-from pyEQL.logging_system import logger
+
+logger = logging.getLogger(__name__)
 
 
 def gibbs_mix(solution1: Solution, solution2: Solution):

src/pyEQL/salt_ion_match.py

@@ -11,6 +11,7 @@
 :license: LGPL, see LICENSE for more details.
 
 """
+
 from monty.json import MSONable
 from pymatgen.core.ion import Ion
 

src/pyEQL/solute.py

@@ -14,6 +14,7 @@
 
 from __future__ import annotations
 
+import logging
 import warnings
 from dataclasses import asdict, dataclass, field
 from typing import Literal
@@ -23,6 +24,8 @@
 
 from pyEQL.utils import standardize_formula
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class Datum: