Speciation support via phreeqpython

CHANGELOG.md

@@ -9,11 +9,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- `Solution`: use total element concentrations when performing salt matching (can be disabled via kwarg)
+- `Solution`: add speciation support to the native engine via `phreeqpython`
+- `Solution`: add keyword argument to enable automatic charge balancing
+- `Salt`: class is now MSONable (i.e., serializable via `as_dict` / `from_dict`)
+- `Solution`: new properties `anions`, `cations`, `neutrals` provide easy access to subsets `components`.
+- `Solution`: improvements to `get_total_amount`.
+- `Solution`: new function `get_components_by_element` that lists all species associated with elements in specific
+  oxidation states.
 - `Solution`: new properties `elements` and `chemical_system`, new function `get_el_amt_dict` to compute the total
   number of moles of each element present in the Solution.
 
+### Changed
+
+- Update `test_salt_ion_match` to `pytest` format and add additional tests
+- Update `test_bulk_properties` to `pytest` format
+
+### Removed
+
+- `Solution.list_salts()` has been removed. See `Solution.get_salt_dict()` for equivalent functionality
+- `salt_ion_match.generate_salt_list` and `identify_salt` have been removed. See `Solution.get_salt_dict()` and `Solution.get_salt()` for equivalent functionality.
+
 ### Fixed
 
+- Scaling of salt concentrations in `get_salt_dict` was incorrect in some edge cases
+- Disable hydrate notation in `standardize_formula`, which caused hydroxides such as 'Ca(OH)3' to be written 'CaO2H.H2O'
+- Inconsistent formatting of oxidation states in `get_total_amount` and `Solute`
+- Inconsistent return type from `get_property` when `molar_volume` and `diffusion_coefficient` were missing
 - Two issues with the formatting of the `H2O(aq)` entry in the database, `pyeql_db.json`
 
 ## [0.7.0] - 2023-08-22

pyproject.toml

@@ -11,8 +11,10 @@ version_scheme = "no-guess-dev"
 line-length = 120
 
 [tool.ruff]
-target-version = "py37"
+target-version = "py38"
 line-length = 120
+exclude = [".dat"]
+src = ["src"]
 select = [
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
@@ -65,7 +67,6 @@ ignore = [
 ]
 pydocstyle.convention = "google"
 isort.split-on-trailing-comma = false
-src = ["src"]
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401"]
@@ -85,5 +86,4 @@ no_implicit_optional = false
 
 [tool.codespell]
 ignore-words-list = "nd"
-skip = 'tests/test_files/*'
-exclude = 'src/pyEQL/database/pyeql_db.json'
+skip = "tests/test_files/*,src/pyEQL/database/*"

setup.cfg

@@ -49,7 +49,6 @@ python_requires = >=3.8
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
-    importlib-metadata; python_version<"3.8"
     pint>=0.19
     numpy
     scipy
@@ -58,6 +57,7 @@ install_requires =
     iapws
     monty
     maggma
+    phreeqpython
 
 [options.packages.find]
 where = src