Pyeql

Fixed

- Restored filter that suppresses duplicate log messages

Added

- `format_solutes_dict()` method added into the utils module to help format solutes dictionaries with a unit. (DhruvDuseja)

Changed

- Native property database is now instantiated on `pyEQL.__init__` to speed subsequent access by `Solution`
- Numerous performance optimization increased the speed of many `Solution` property and method calls by 3x-10x

Added

- `Solution.print()` added to take the place of the deprecated `list_xxx` methods.

Changed

- **Breaking** `pyEQL.unit` deprecation machinery has been removed to quiet the warning
messages on import. The `pyEQL` unit registry was renamed to `pyEQL.ureg` in v0.6.1.
- Significant documentation updates.
- `Solution.components` is now automatically sorted in descending order of amount, for
consistency with `anions`, `cations`, and `neutrals`.

Removed

- `Solution.list_solutes()` has been removed. Use `Solution.components.keys()` instead.

Fixed

- Bugfix in `as_dict` to make serialization via `dumpfn` possible. Previously, `Quantity`
were not converted to a serializable form. Now, `Quantity` are converted to `str` in
`as_dict()`.

Removed

- python 3.8 is no longer supported

Changed

- `from_dict` modified to avoid call to `super()`, making for more robust behavior if `Solution` is inherited.

Removed

- `copy()` method was removed for consistency with `python` conventions (it returned a deep rather than a
shallow copy). Use `copy.deepcopy(Solution)` instead.

Fixed

- Bugfix in `as_dict` in which the `solutes` attribute was saved with `Quantity` rather than `float`
- Simplified `Solution.get_conductivity` to avoid errors in selected cases.
- Required `pymatgen` version was incorrectly set at `2022.8.10` when it should be `2023.8.10`
- Bug in `get_osmotic_coefficient` that caused a `ZeroDivisionError` with an empty solution.

Added

- New electrolyte engine `PhreeqcEOS` provides `phreeqpython` activities within `pyEQL`
- `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

- `pH` attribute is now calculated from the H+ concentration rather than its activity. For the old behavior,
use `Solution.p('H+')` which defaults to applying the activity correction.
- 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

- Bug in `get_transport_number` caused by migration to standardized solute formulas
- 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`

Changed

- `Solution` now more robustly converts any user-supplied formulas into unique values using `pymatgen.core.ion.Ion.reduced_formula`. This means that the `.components` or `solvent` attributes may now differ slightly from whatever is entered during `__init__`. For example, `Solution(solvent='H2O').solvent` gives `H2O(aq)`. This behavior resolved a small bug that could occur when mixing solutions. User supplied formulas passed to `get_amount` or `Solution.components[xxx]` can still be any valid formula. E.g., `Solution.components["Na+"]`, `Solution.components["Na+1"]`, and `Solution.components["Na[+]"]` will all return the same thing.