Pyeql

Fixed

- `Solute.from_formula`: Fix bug in which an uncaught exception could occur when
if `pymatgen` failed to guess the oxidation state of a solute. (Issue 103 - thanks to xiaoxiaozhu123 for reporting).
- `Solution.get_total_amount`: Fix bug that would cause the method to fail if
mass-based units such as mg/L or ppm were requested.

Added

- `Solution`: new kwarg `default_diffusion_coeff` which allows the user to specify a value to use
when a species diffusion coefficient is missing from the database. By default, the value for NaCl
salt (1.61e-9 m2/s) is used. This is important for conductivity and transport number calculations,
which perform weighted summations of diffusion coefficients over every species in the solution.
Previously, species with missing diffusion coefficients would be excluded from such calculations,
possibly resulting in inaccuracies, particularly after calling `equilibrate()`, which often
generates charged complexes such as NaSO4- or MgCl+.

Fixed

- `Solution.__add__`: Bugfix in the addition operation `+` that could cause problems with
child classes (i.e., classes that inherit from `Solution`) to work improperly

Changed

- Removed deprecated `pkg_resources` import in favor of `importlib.resources`

Added

- Add tests for `gibbs_mix` and `entropy_mix` functions. Format docstrings in Google style.

Fixed

- `Solution.from_preset`: Fixed a packaging error that made this method fail with a `FileNotFoundError`.

Removed

- `functions.py` is no longer imported into the root namespace. You'll now need to say `from pyEQL.functions import gibbs_mix`
instead of `from pyEQL import gibbs_mix`

Changed

- `PhreeqcEOS`: performance improvements for the `phreeqc` engine. The `EOS` instance now retains
the `phreeqpython` solution object in between calls, only re-initializing it if the composition
of the `Solution` has changed since the previous call.

Fixed

- `equilibrate`: Fixed several bugs affecting `NativeEOS` and `PhreeqcEOS` in which calling `equilibrate()`
would mess up the charge balance. This was especially an issue if `balance_charge` was set to something
other than `pH`.

Removed

- `equilibrium.equilibrate_phreeqc()` has been removed to reduce redundant code. All its
was absorbed into `NativeEOS` and `PhreeqcEOS`

Added

- utility function `create_water_substance` with caching to speed up access to IAPWS instances

Changed

- `Solution.get_diffusion_coefficient`: the default diffusion coefficient (returned when D for a solute is not found in
the database) is now adjusted for temperature and ionic strength.
- `Solution.water_substance` - use the IAPWS97 model instead of IAPWS95 whenever possible, for a substantial speedup.

Added

- `Solution`: Revamped docstrings for `conductivity`, `get_transport_number`, `get_molar_conductivity`, and
`get_diffusion_coefficient`.
- `Solution`: new method `get_diffusion_coefficient` for dedicated retrieval of diffusion coefficients. This method
implements an improved algorithm for temperature adjustment and a new algorithm for adjusting infinite dilution D values
for ionic strengthe effects. The algorithm is identical to that implemented in PHREEQC >= 3.4.
- Database: empirical parameters for temperature and ionic strength adjustment of diffusion coefficients for 15 solutes
- Added tests for temperature and ionic strength adjustment and conductivity
- Docs: new tutorial notebooks
- Docs: remove duplicate contributing pages (Closes [68](https://github.com/KingsburyLab/pyEQL/issues/68))
- `Solution`: new method `to_file()` for more convenient saving Solution object to json or yaml files. (kirill-push)
- `Solution`: new method `from_file()` for more convenient loading Solution object from json or yaml files. (kirill-push)
- `Solution`: new classmethod `from_preset()` to `replace pyEQL.functions.autogenerate()` and instantiate a solution from a preset composition. (kirill-push)

Changed

- `Solution`: method af adjusting diffusion coefficients for temperature was updated (same as used in PHREEQC >= 3.4)
- `Solution.conductvity`: improved equation (same as used in PHREEQC >= 3.4) which is more accurate at higher concentrations

Fixed

- Database errors with `Cs[+1]` diffusion coefficient and `KBr` Pitzer parameters
- Restored filter that suppresses duplicate log messages

Deprecated

- `replace pyEQL.functions.autogenerate()` is now deprecated. Use `from_preset` instead.

Removed

- The `activity_correction` kwarg in `get_transport_number` has been removed, because this now occurs by default and is
handled in `get_diffusion_coefficient`.