pyEQL 1.0.3__tar.gz → 1.1.1__tar.gz

{pyeql-1.0.3 → pyeql-1.1.1}/.github/dependabot.yml

@@ -1,6 +1,11 @@
 version: 2
 updates:
+  # Maintain dependencies for GitHub Actions
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

{pyeql-1.0.3 → pyeql-1.1.1}/.pre-commit-config.yaml

@@ -12,18 +12,18 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.2
+    rev: v0.5.5
     hooks:
       - id: ruff
         args: [--fix, --ignore, "D,E501", "--show-fixes"]
 
-  - repo: https://github.com/psf/black
-    rev: 24.2.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     hooks:
       - id: black
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -31,7 +31,7 @@ repos:
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks

{pyeql-1.0.3 → pyeql-1.1.1}/CHANGELOG.md

@@ -5,6 +5,31 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.1] - 2024-07-27
+
+### Fixed
+
+- `equilibrate`: Fixed a bug that could cause an `AttributeError` when pH was used for charge
+  balancing.
+- Database: `size.radius_ionic` was missing units for `Ni[+2]` and `Cr[+3]`. Correct units have been added.
+
+### Added
+
+- `Solution`: New automatic charge balancing method will automatically identify the majority (highest concentration)
+  cation or anion as appropriate (depending on the charge balance) for charge balancing. To use this mode, set
+  `balance_charge='auto'` when instantiating a `Solution`.
+
+### Changed
+
+- `Solution.add_amount`: This method will now add solutes that are absent from the Solution. Previously, calling, e.g.,
+  `add_amount('Na+', '1 mol')` on a `Solution` that did not contain any sodium would result in an error. A warning
+  is logged if the method has to add a new solute.
+- Units: use the upstream chemistry context from `pint` instead of the custom one from 2013.
+- `pre-commit autoupdate`
+- Misc. linting and code quality improvements.
+- Unit tests: update `tmpdir` to `tmp_path` text fixture.
+- CI: Small updates to pre-commit and GitHub actions per scientific python [repo review](https://scientific-python.github.io/repo-review/?repo=kingsburylab%2FpyEQL&branch=main).
+
 ## [1.0.3] - 2024-07-20
 
 ### Fixed

{pyeql-1.0.3 → pyeql-1.1.1}/MANIFEST.in

@@ -2,6 +2,5 @@ include README COPYING CHANGELOG LICENSE README.md README.rst README.txt CHANGES
 recursive-include src/pyEQL/database/ *
 recursive-include src/pyEQL/presets/ *
 recursive-include docs/ *
-include src/pyEQL/pint_custom_units.txt
 prune docs/build
 global-exclude *.pyc *~ .DS_Store *__pycache__* *.pyo

{pyeql-1.0.3/src/pyEQL.egg-info → pyeql-1.1.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.0.3
-Summary: A python interace for solution chemistry
+Version: 1.1.1
+Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
 Project-URL: Docs, https://pyeql.readthedocs.io/
 Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
@@ -25,7 +25,7 @@ Requires-Dist: numpy<2
 Requires-Dist: scipy
 Requires-Dist: pymatgen==2024.5.1
 Requires-Dist: iapws
-Requires-Dist: monty
+Requires-Dist: monty>=2024.7.12
 Requires-Dist: maggma>=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: testing

{pyeql-1.0.3 → pyeql-1.1.1}/docs/changelog.md

@@ -5,6 +5,31 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.1] - 2024-07-27
+
+### Fixed
+
+- `equilibrate`: Fixed a bug that could cause an `AttributeError` when pH was used for charge
+  balancing.
+- Database: `size.radius_ionic` was missing units for `Ni[+2]` and `Cr[+3]`. Correct units have been added.
+
+### Added
+
+- `Solution`: New automatic charge balancing method will automatically identify the majority (highest concentration)
+  cation or anion as appropriate (depending on the charge balance) for charge balancing. To use this mode, set
+  `balance_charge='auto'` when instantiating a `Solution`.
+
+### Changed
+
+- `Solution.add_amount`: This method will now add solutes that are absent from the Solution. Previously, calling, e.g.,
+  `add_amount('Na+', '1 mol')` on a `Solution` that did not contain any sodium would result in an error. A warning
+  is logged if the method has to add a new solute.
+- Units: use the upstream chemistry context from `pint` instead of the custom one from 2013.
+- `pre-commit autoupdate`
+- Misc. linting and code quality improvements.
+- Unit tests: update `tmpdir` to `tmp_path` text fixture.
+- CI: Small updates to pre-commit and GitHub actions per scientific python [repo review](https://scientific-python.github.io/repo-review/?repo=kingsburylab%2FpyEQL&branch=main).
+
 ## [1.0.3] - 2024-07-20
 
 ### Fixed

{pyeql-1.0.3 → pyeql-1.1.1}/pyproject.toml

@@ -2,7 +2,7 @@
 name = "pyEQL"
 readme = "README.md"
 dynamic = ["version"]
-description="A python interace for solution chemistry"
+description="A python interface for solution chemistry"
 authors =[
     {name = "Ryan Kingsbury", email = "kingsbury@princeton.edu"}
 ]
@@ -25,7 +25,7 @@ dependencies = [
         "scipy",
         "pymatgen==2024.5.1",
         "iapws",
-        "monty",
+        "monty>=2024.7.12",
         "maggma>=0.67.0",
         "phreeqpython",
     ]
@@ -72,7 +72,6 @@ version_scheme = "no-guess-dev"
 line-length = 120
 
 [tool.ruff]
-target-version = "py39"
 line-length = 120
 exclude = [".dat"]
 src = ["src"]

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL/__init__.py

@@ -37,11 +37,8 @@ ureg = UnitRegistry(cache_folder=":auto:")
 # convert "offset units" so that, e.g. Quantity('25 degC') works without error
 # see https://pint.readthedocs.io/en/0.22/user/nonmult.html?highlight=offset#temperature-conversion
 ureg.autoconvert_offset_to_baseunit = True
-# append custom unit definitions and contexts
-fname = files("pyEQL") / "pint_custom_units.txt"
-ureg.load_definitions(fname)
 # activate the "chemistry" context globally
-ureg.enable_contexts("chem")
+ureg.enable_contexts("chemistry")
 # set the default string formatting for pint quantities
 ureg.default_format = "P~"
 

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL/database/pyeql_db.json

@@ -6698,7 +6698,7 @@
         "n_elements": 1,
         "size": {
             "radius_ionic": {
-                "value": "0.755",
+                "value": "0.755 Å",
                 "reference": "pymatgen",
                 "data_type": "experimental"
             },
@@ -24663,7 +24663,7 @@
         "n_elements": 1,
         "size": {
             "radius_ionic": {
-                "value": "0.83",
+                "value": "0.83 Å",
                 "reference": "pymatgen",
                 "data_type": "experimental"
             },

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL/engines.py

@@ -11,7 +11,7 @@ import os
 import warnings
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Literal
+from typing import TYPE_CHECKING, Literal
 
 from phreeqpython import PhreeqPython
 
@@ -26,6 +26,9 @@ SPECIAL_ELEMENTS = ["S", "C", "N", "Cu", "Fe", "Mn"]
 
 logger = logging.getLogger(__name__)
 
+if TYPE_CHECKING:
+    from pyEQL import Solution
+
 
 class EOS(ABC):
     """
@@ -38,7 +41,7 @@ class EOS(ABC):
     """
 
     @abstractmethod
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
@@ -55,7 +58,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of a Solution.
 
@@ -70,7 +73,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def get_solute_volume(self):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the volume of only the solutes.
 
@@ -85,7 +88,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """
         Adjust the speciation and pH of a Solution object to achieve chemical equilibrium.
 
@@ -105,25 +108,25 @@ class EOS(ABC):
 class IdealEOS(EOS):
     """Ideal solution equation of state engine."""
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
         """
         return ureg.Quantity(1, "dimensionless")
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
         """
         return ureg.Quantity(1, "dimensionless")
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         return ureg.Quantity(0, "L")
 
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """Adjust the speciation of a Solution object to achieve chemical equilibrium."""
         warnings.warn("equilibrate() has no effect in IdealEOS!")
         return
@@ -138,7 +141,9 @@ class NativeEOS(EOS):
 
     def __init__(
         self,
-        phreeqc_db: Literal["vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"] = "llnl.dat",
+        phreeqc_db: Literal[
+            "phreeqc.dat", "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
+        ] = "llnl.dat",
     ) -> None:
         """
         Args:
@@ -172,7 +177,7 @@ class NativeEOS(EOS):
         # store the solution composition to see whether we need to re-instantiate the solution
         self._stored_comp = None
 
-    def _setup_ppsol(self, solution):
+    def _setup_ppsol(self, solution: "Solution") -> None:
         """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
@@ -244,13 +249,13 @@ class NativeEOS(EOS):
 
         self.ppsol = ppsol
 
-    def _destroy_ppsol(self):
-        """Remove the PhreeqPython solution from memory"""
+    def _destroy_ppsol(self) -> None:
+        """Remove the PhreeqPython solution from memory."""
         if self.ppsol is not None:
             self.ppsol.forget()
             self.ppsol = None
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str):
         r"""
         Whenever the appropriate parameters are available, the Pitzer model [may]_ is used.
         If no Pitzer parameters are available, then the appropriate equations are selected
@@ -329,7 +334,7 @@ class NativeEOS(EOS):
 
         # show an error if no salt can be found that contains the solute
         if salt is None:
-            logger.error("No salts found that contain solute %s. Returning unit activity coefficient." % solute)
+            logger.error(f"No salts found that contain solute {solute}. Returning unit activity coefficient.")
             return ureg.Quantity(1, "dimensionless")
 
         # use the Pitzer model for higher ionic strength, if the parameters are available
@@ -344,14 +349,14 @@ class NativeEOS(EOS):
             # alpha1 and alpha2 based on charge
             if salt.nu_cation >= 2 and salt.nu_anion <= -2:
                 if salt.nu_cation >= 3 or salt.nu_anion <= -3:
-                    alpha1 = 2
-                    alpha2 = 50
+                    alpha1 = 2.0
+                    alpha2 = 50.0
                 else:
                     alpha1 = 1.4
                     alpha2 = 12
             else:
-                alpha1 = 2
-                alpha2 = 0
+                alpha1 = 2.0
+                alpha2 = 0.0
 
             # determine the average molality of the salt
             # this is necessary for solutions inside e.g. an ion exchange
@@ -427,7 +432,7 @@ class NativeEOS(EOS):
 
         return molal
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         r"""
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
@@ -574,7 +579,7 @@ class NativeEOS(EOS):
             # this means the solution is empty
             return 1
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         # identify the predominant salt in the solution
         salt = solution.get_salt()
@@ -596,14 +601,14 @@ class NativeEOS(EOS):
             # alpha1 and alpha2 based on charge
             if salt.nu_cation >= 2 and salt.nu_anion >= 2:
                 if salt.nu_cation >= 3 or salt.nu_anion >= 3:
-                    alpha1 = 2
-                    alpha2 = 50
+                    alpha1 = 2.0
+                    alpha2 = 50.0
                 else:
                     alpha1 = 1.4
                     alpha2 = 12
             else:
-                alpha1 = 2
-                alpha2 = 0
+                alpha1 = 2.0
+                alpha2 = 0.0
 
             apparent_vol = ac.get_apparent_volume_pitzer(
                 solution.ionic_strength,
@@ -633,7 +638,7 @@ class NativeEOS(EOS):
 
             pitzer_calc = True
 
-            logger.debug("Updated solution volume using Pitzer model for solute %s" % salt.formula)
+            logger.debug(f"Updated solution volume using Pitzer model for solute {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
@@ -649,7 +654,7 @@ class NativeEOS(EOS):
             part_vol = solution.get_property(solute, "size.molar_volume")
             if part_vol is not None:
                 solute_vol += part_vol * ureg.Quantity(mol, "mol")
-                logger.debug("Updated solution volume using direct partial molar volume for solute %s" % solute)
+                logger.debug(f"Updated solution volume using direct partial molar volume for solute {solute}")
 
             else:
                 logger.warning(
@@ -658,7 +663,7 @@ class NativeEOS(EOS):
 
         return solute_vol.to("L")
 
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """Adjust the speciation of a Solution object to achieve chemical equilibrium."""
         if self.ppsol is not None:
             self.ppsol.forget()
@@ -699,7 +704,7 @@ class NativeEOS(EOS):
             if solution.balance_charge is None:
                 pass
             elif solution.balance_charge == "pH":
-                solution.components["H+"] += charge_adjust.magnitude
+                solution.components["H+"] += charge_adjust
             elif solution.balance_charge == "pE":
                 raise NotImplementedError
             else:
@@ -734,7 +739,7 @@ class PhreeqcEOS(NativeEOS):
     def __init__(
         self,
         phreeqc_db: Literal[
-            "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
+            "phreeqc.dat", "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
         ] = "phreeqc.dat",
     ) -> None:
         """
@@ -751,12 +756,12 @@ class PhreeqcEOS(NativeEOS):
         """
         super().__init__(phreeqc_db=phreeqc_db)
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
         """
-        if self.ppsol is None or solution.components != self._stored_comp:
+        if (self.ppsol is None) or (solution.components != self._stored_comp):
             self._destroy_ppsol()
             self._setup_ppsol(solution)
 
@@ -775,7 +780,7 @@ class PhreeqcEOS(NativeEOS):
 
         return ureg.Quantity(act, "dimensionless")
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
@@ -787,7 +792,7 @@ class PhreeqcEOS(NativeEOS):
         # TODO - find a way to access or calculate osmotic coefficient
         return ureg.Quantity(1, "dimensionless")
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         # TODO - phreeqc seems to have no concept of volume, but it does calculate density
         return ureg.Quantity(0, "L")

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL/solution.py

@@ -92,11 +92,15 @@ class Solution(MSONable):
                 -7 to +14. The default value corresponds to a pE value typical of natural
                 waters in equilibrium with the atmosphere.
             balance_charge: The strategy for balancing charge during init and equilibrium calculations. Valid options
-                are 'pH', which will adjust the solution pH to balance charge, 'pE' which will adjust the
-                redox equilibrium to balance charge, or the name of a dissolved species e.g. 'Ca+2' or 'Cl-'
-                that will be added/subtracted to balance charge. If set to None, no charge balancing will be
-                performed either on init or when equilibrate() is called. Note that in this case, equilibrate()
-                can distort the charge balance!
+                are
+                    - 'pH', which will adjust the solution pH to balance charge,
+                    - 'auto' which will use the majority cation or anion (i.e., that with the largest concentration)
+                    as needed,
+                    - 'pE' (not currently implemented) which will adjust the redox equilibrium to balance charge, or
+                    the name of a dissolved species e.g. 'Ca+2' or 'Cl-' that will be added/subtracted to balance
+                    charge.
+                    - None (default), in which case no charge balancing will be performed either on init or when
+                    equilibrate() is called. Note that in this case, equilibrate() can distort the charge balance!
             solvent: Formula of the solvent. Solvents other than water are not supported at this time.
             engine: Electrolyte modeling engine to use. See documentation for details on the available engines.
             database: path to a .json file (str or Path) or maggma Store instance that
@@ -171,7 +175,7 @@ class Solution(MSONable):
         self._pE = pE
         self._pH = pH
         self.pE = self._pE
-        if isinstance(balance_charge, str) and balance_charge not in ["pH", "pE"]:
+        if isinstance(balance_charge, str) and balance_charge not in ["pH", "pE", "auto"]:
             self.balance_charge = standardize_formula(balance_charge)
         else:
             self.balance_charge = balance_charge  #: Standardized formula of the species used for charge balancing.
@@ -273,13 +277,19 @@ class Solution(MSONable):
                 raise NotImplementedError("Balancing charge via redox (pE) is not yet implemented!")
             else:
                 ions = set().union(*[self.cations, self.anions])  # all ions
+                if self.balance_charge == "auto":
+                    # add the most abundant ion of the opposite charge
+                    if cb <= 0:
+                        self.balance_charge = max(self.cations, key=self.cations.get)
+                    elif cb > 0:
+                        self.balance_charge = max(self.anions, key=self.anions.get)
                 if self.balance_charge not in ions:
                     raise ValueError(
                         f"Charge balancing species {self.balance_charge} was not found in the solution!. "
                         f"Species {ions} were found."
                     )
-                z = self.get_property(balance_charge, "charge")
-                self.components[balance_charge] += -1 * cb / z * self.volume.to("L").magnitude
+                z = self.get_property(self.balance_charge, "charge")
+                self.components[self.balance_charge] += -1 * cb / z * self.volume.to("L").magnitude
                 balanced = True
 
             if not balanced:
@@ -1282,81 +1292,12 @@ class Solution(MSONable):
         Returns:
             Nothing. The concentration of solute is modified.
         """
-        # if units are given on a per-volume basis,
-        # iteratively solve for the amount of solute that will preserve the
-        # original volume and result in the desired concentration
-        if ureg.Quantity(amount).dimensionality in (
-            "[substance]/[length]**3",
-            "[mass]/[length]**3",
-        ):
-            # store the original volume for later
-            orig_volume = self.volume
-
-            # change the amount of the solute present to match the desired amount
-            self.components[solute] += (
-                ureg.Quantity(amount)
-                .to(
-                    "moles",
-                    "chem",
-                    mw=self.get_property(solute, "molecular_weight"),
-                    volume=self.volume,
-                    solvent_mass=self.solvent_mass,
-                )
-                .magnitude
-            )
-
-            # set the amount to zero and log a warning if the desired amount
-            # change would result in a negative concentration
-            if self.get_amount(solute, "mol").magnitude < 0:
-                self.logger.error(
-                    "Attempted to set a negative concentration for solute %s. Concentration set to 0" % solute
-                )
-                self.set_amount(solute, "0 mol")
-
-            # calculate the volume occupied by all the solutes
-            solute_vol = self._get_solute_volume()
-
-            # determine the volume of solvent that will preserve the original volume
-            target_vol = orig_volume - solute_vol
-
-            # adjust the amount of solvent
-            # volume in L, density in kg/m3 = g/L
-            target_mass = target_vol * ureg.Quantity(self.water_substance.rho, "g/L")
-
-            mw = self.get_property(self.solvent, "molecular_weight")
-            target_mol = target_mass / mw
-            self.components[self.solvent] = target_mol.magnitude
-
-        else:
-            # change the amount of the solute present
-            self.components[solute] += (
-                ureg.Quantity(amount)
-                .to(
-                    "moles",
-                    "chem",
-                    mw=self.get_property(solute, "molecular_weight"),
-                    volume=self.volume,
-                    solvent_mass=self.solvent_mass,
-                )
-                .magnitude
-            )
-
-            # set the amount to zero and log a warning if the desired amount
-            # change would result in a negative concentration
-            if self.get_amount(solute, "mol").magnitude < 0:
-                self.logger.error(
-                    "Attempted to set a negative concentration for solute %s. Concentration set to 0" % solute
-                )
-                self.set_amount(solute, "0 mol")
-
-            # update the volume to account for the space occupied by all the solutes
-            # make sure that there is still solvent present in the first place
-            if self.solvent_mass <= ureg.Quantity(0, "kg"):
-                self.logger.error("All solvent has been depleted from the solution")
-                return
-
-            # set the volume recalculation flag
-            self.volume_update_required = True
+        # Get the current amount of the solute
+        current_amt = self.get_amount(solute, amount.split(" ")[1])
+        if current_amt.magnitude == 0:
+            self.logger.warning(f"Add new solute {solute} to the solution")
+        new_amt = ureg.Quantity(amount) + current_amt
+        self.set_amount(solute, new_amt)
 
     def set_amount(self, solute: str, amount: str):
         """
@@ -2465,7 +2406,7 @@ class Solution(MSONable):
         """
         str_filename = str(filename)
         if not ("yaml" in str_filename.lower() or "json" in str_filename.lower()):
-            self.logger.error("Invalid file extension entered - %s" % str_filename)
+            self.logger.error("Invalid file extension entered - {str_filename}")
             raise ValueError("File extension must be .json or .yaml")
         if "yaml" in str_filename.lower():
             solution_dict = self.as_dict()

{pyeql-1.0.3 → pyeql-1.1.1/src/pyEQL.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.0.3
-Summary: A python interace for solution chemistry
+Version: 1.1.1
+Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
 Project-URL: Docs, https://pyeql.readthedocs.io/
 Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
@@ -25,7 +25,7 @@ Requires-Dist: numpy<2
 Requires-Dist: scipy
 Requires-Dist: pymatgen==2024.5.1
 Requires-Dist: iapws
-Requires-Dist: monty
+Requires-Dist: monty>=2024.7.12
 Requires-Dist: maggma>=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: testing

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL.egg-info/SOURCES.txt

@@ -87,7 +87,6 @@ src/pyEQL/activity_correction.py
 src/pyEQL/engines.py
 src/pyEQL/equilibrium.py
 src/pyEQL/functions.py
-src/pyEQL/pint_custom_units.txt
 src/pyEQL/salt_ion_match.py
 src/pyEQL/solute.py
 src/pyEQL/solution.py

{pyeql-1.0.3 → pyeql-1.1.1}/src/pyEQL.egg-info/requires.txt

@@ -3,7 +3,7 @@ numpy<2
 scipy
 pymatgen==2024.5.1
 iapws
-monty
+monty>=2024.7.12
 maggma>=0.67.0
 phreeqpython