enable solid-liquid and gas-liquid equilibrium calculations in equilibrate()

[vineetbansal]

Code and tests for PHREEQC's phase equilibrium calculations.

This PR supersedes PR 286

Not done yet - @SuixiongTay was planning to add some tests, and I will as well.

Checklist

• Google format doc strings added.
• Code linted with ruff. (For guidance in fixing rule violates, see rule list)
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• I have run the tests locally and they passed.

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[codecov]

Codecov Report

❌ Patch coverage is 92.30769% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.77%. Comparing base (c630c50) to head (e357b71).
⚠️ Report is 29 commits behind head on main.

Files with missing lines	Patch %	Lines
src/pyEQL/engines.py	91.30%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #292      +/-   ##
==========================================
+ Coverage   84.21%   84.77%   +0.55%     
==========================================
  Files          10       10              
  Lines        1495     1517      +22     
  Branches      261      263       +2     
==========================================
+ Hits         1259     1286      +27     
+ Misses        203      199       -4     
+ Partials       33       32       -1     

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[vineetbansal]

Removed all tests. @SuixiongTay - please add tests as you see fit. As we discussed earlier, the codecov/patch action will tell you if all the newly introduced code lines have been covered.

[vineetbansal]

Thanks @SuixiongTay. @rkingsbury - can you wait till Friday (12/12) before you look at this? I'm meeting with @SuixiongTay tomorrow and we may add one more commit with some minor tweaks.

[rkingsbury]

Thanks everyone! Great work overall. I've requested a series of minor changes (mostly docstrings, comments, and small tweaks) mostly to support future maintain-ability and clarity. I'll merge as soon as addressed.

[vineetbansal]

@SuixiongTay, @YitongPan1 - I've added a commit addressing all conversations above, except these 3:

Please add N2 here. I know it doesn't really dissolve to any appreciable extent in most cases, but we should have it here to avoid unexpected behavior

Also, being picky here, is -3.5 the most up to date partial pressure of CO2? It has changed in our lifetimes, I believe the current atmospheric conc. is close to 400 ppm? Please include a reference for the values you used in the comments.

Please add one more test test_equilbrate_with_atm that includes only atmosphere=True (no other gases). Then check that the concentrations of all three - CO2, O2, and N2 are as expected. (Currently the O2 concentration is not tested anywhere).

Addressing the first may change some test values - I think we should be okay adding a commit with the changed atmospheric composition, then another commit that fixes failing tests (if any) because of that change.

[vineetbansal]

Thanks @SuixiongTay - your final edits make sense. I've added one more commit, mostly with a wording change that Ryan wanted, and some additional comments on atmospheric composition.

Regarding the differences between Phreeqc UI and Phreeqc Wrapper, I suspect we can make them match exactly by passing in some kind of precision setting, but I'm not sure. I'll make a note of this (if it works, it will be a useful debugging feature in the new wrappers anyway).