Pyeql

Added

- `Solution`: enable passing an `EOS` instance to the `engine` kwarg.
- `Solution`: new properties `total_dissolved_solids` and alias `TDS`
- `Solution`: support new units in `get_amount` - ppm, ppb, eq/L, etc.
- `Solution`: implemented arithmetic operations `+` (for mixing two solutions), `*` and `\` for scaling their amounts

Changed

- `pyEQL.unit` was renamed to `pyEQL.ureg` (short for `UnitRegistry`) for consistency with the `pint` documentation and tutorials.

Added

- `Solution`: add tests to confirm that solution density changes with temperature and pressure
- `Solution`: add tests for `charge_balance`, `alkalinity`, `hardness`, `osmotic_pressure`, `p()`, and `conductivity`
- `Solution`: `pE` attribute and kwarg
- `Solution`: add support for passing solutes as a `dict`
- Implement extensible system for connecting `Solution` to various activity and speciation
models. Models can be integrated into pyEQL by implementing an `EOS` class. The desired
activity model is selected on init. Currently available models are `native` (for pyEQL's
implementation of Pitzer, which decays gracefully into Debye-Huckel and other models if
parameters are not available) or `ideal` for a dummy engine that returns unit activity
coefficients. Support for additional external engines such as [`phreeqpython`](https://github.com/Vitens/phreeqpython) is planned.
- Add `pymatgen`, `monty`, and `maggma` as dependencies
- Add `pre-commit` configuration
- Add pull request template, new GitHub actions, and `tox -e autodocs` environment to serve and update docs in real time
- Add pre-commit configuration and lint with `ruff` using rulesets mostly borrowed from `pymatgen`
- Add more comprehensive platform testing via `tox`

Changed

- Complete overhaul of the property database. The database is now distributed in a .json file containing serialize `Solute` objects. `Solution` can now be connected to this database (by default) or to any other `maggma` `Store` containing properly formatted data. `database.py`, `parameter.py`, and all the `.tsv` data files have been removed and replaced with `pyeql_db.json`.
- Docs: update, change theme, convert to .md format, and adopt Keep a Changelog format
- Replace `water_properties.py` with [iapws](https://github.com/jjgomera/iapws) package
- Replace `elements.py`` with `pymatgen.core.periodic_table`
- `Solution.charge_balance` now returns in equivalents instead of Coulombs
- Migrate all tests to `pytest`
- Update packaging format to use [pyscaffold](https://pyscaffold.org/en/stable/index.html)

Deprecated

- `Solution`: new properties `pressure`, `temperature`, `volume`, `pH`, `mass`, `density`, `viscosity_dynamic`, `viscosity_kinematic`, `ionic_strength`, `conductivity`, `debye_length`, `bjerrum_length`, `alkalinity`, `hardness`, `dielectric_constant`, `osmotic_pressure`, `solvent_mass`, `charge_balance` have replaced the corresponding get_XXX and set_XXX (for temperature and pressure) methods, which will be removed in a future release. `get_viscosity_relative` will be removed entirely.
- `Solute`: methods `get_formal_charge()`, `get_name()`, and `get_molecular_weight()` have been
replaced by direct access to the attributes `charge`, `formula`, and `mw`, respectively.

Removed

- disable 'verbose' kwarg in `get_activity` and `get_activity_coefficient`

Fixed

- Fixed various documentation rendering issues
- bug in `alkalinity`

- Fix breaking bug introduced by upstream pint change to avogadro_number
- Format project with black
- Misc. linting and docstring changes

- Implement the effective Pitzer model for improved activity calculations in multicomponent solutions
- Add support for calculation of activity and osmotic coefficients on different scales
- Add support for calculating % by weight to get_amount()
- Added methods for calculating the osmolarity or osmolality of a Solution
- Add the ability to filter list_concentrations() to show only cations or anions
- Add two medical solutions - normal saline and Ringer's lacate -to the autogenerate method
- Add shorthand abbreviations for 'seawater' and 'wastewater' in the autogenerate method
- Enhance automatic test suite to compare results with experimental data based on relative error
- Add test suites for the effective Pitzer model and a multicomponent salt solution
- DEPRECATED get_mole_fraction. Use get_amount() instead
- Fix bug causing get_activity_coefficient to fail if the solute concentration was zero

- Add ability to calculate dielectric constant based on solution composition for salts
- Add database entries for the viscosity 'B' parameter for 63 more inorganic ions
- Add domestic wastewater and human urine to the autogenerate()method
- Improve entry point for running automated tests (16, thanks Hernan Grecco)
- Significantly expand documentation of activity correction methods
- Make output of get_osmotic_coefficient more verbose when Pitzer parameters are not found
- Fix bug causing activity corrections for non 1:1 salts to be calculated incorrectly (15)
- Fix bug causing 'bad operand type' error when calculating osmotic pressure on some systems
- Fix bug causing ValueError exceptions when a solute has zero concentration
- Numerous fixes and corrections in the documentation

- Fix packaging problems preventing installation from PyPi
- Fix character encoding issue in Erying_viscosity database file