Remove N2 from ATMOSPHERE

[SuixiongTay]

Summary

• Removed N2 from ATMOSPHERE in presets/__init__.py.
• Fixes Incorrect pH from using Solution.equilibrate(atmosphere=True) #336

[rkingsbury]

Thank you Shaun!

[rkingsbury]

I see you've got a lot of merge conflicts. One way to solve that, if your local branch has gotten out of sync with main, is to

git rebase -i origin main

which will interactively "replay" your commits on top of an up to date copy of main.

[rkingsbury]

Regarding the two test failures here:

_____________________________ test_equilibrate_2L ______________________________
[gw3] linux -- Python 3.13.11 /opt/hostedtoolcache/Python/3.13.11/x64/bin/python

    def test_equilibrate_2L():
        solution = Solution({"Cu+2": "1 umol/L", "O-2": "1 umol/L"}, volume="2 L", engine="phreeqc2026")
        solution.equilibrate(atmosphere=True)
>       assert np.isclose(solution.get_total_amount("Cu", "umol").magnitude, 1.9999998687384424)
E       AssertionError: assert np.False_
E        +  where np.False_ = <function isclose at 0x7f408cd303f0>(1.9899095628456385, 1.9999998687384424)
E        +    where <function isclose at 0x7f408cd303f0> = np.isclose
E        +    and   1.9899095628456385 = <Quantity(1.9899095628456385, 'micromole')>.magnitude
E        +      where <Quantity(1.9899095628456385, 'micromole')> = get_total_amount('Cu', 'umol')
E        +        where get_total_amount = <pyEQL.solution.Solution object at 0x7f406582f9b0>.get_total_amount

solution   = <pyEQL.solution.Solution object at 0x7f406582f9b0>

tests/test_engine_phreeqc2026.py:395: AssertionError
__________________________ test_equilibrate_with_atm ___________________________
[gw3] linux -- Python 3.13.11 /opt/hostedtoolcache/Python/3.13.11/x64/bin/python

    def test_equilibrate_with_atm():
        s1 = Solution({}, pH=7.0, volume="1 L", engine="phreeqc2026")
        s1.equilibrate(atmosphere=True)
        # PHREEQCUI final CO2, O2, and N2 concentrations were slightly adjusted for consistency with wrapper outputs
>       assert np.isclose(s1.get_amount("CO2(aq)", "mol/L").magnitude, 1.397209520185121e-05)  # PHREQCUI - 1.389e-05
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E       AssertionError: assert np.False_
E        +  where np.False_ = <function isclose at 0x7f408cd303f0>(1.424944456303147e-05, 1.397209520185121e-05)
E        +    where <function isclose at 0x7f408cd303f0> = np.isclose
E        +    and   1.424944456303147e-05 = <Quantity(1.424944456303147e-05, 'mole / liter')>.magnitude
E        +      where <Quantity(1.424944456303147e-05, 'mole / liter')> = get_amount('CO2(aq)', 'mol/L')
E        +        where get_amount = <pyEQL.solution.Solution object at 0x7f4065048490>.get_amount

s1         = <pyEQL.solution.Solution object at 0x7f4065048490>

tests/test_engine_phreeqc2026.py:427: AssertionError

For the first one, since you are comparing the Cu concentration in micromolar, a much higher tolerance is OK (e.g., atol=0.1). Alternatively, do the comparison in mol and leave the default tolerances.

For the second, make sure you've adjusted the expected (PHREEQCUI) value.

[rkingsbury]

Fixes #336

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.31%. Comparing base (23fc5fe) to head (5ba25e8).
⚠️ Report is 32 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #339   +/-   ##
=======================================
  Coverage   86.31%   86.31%           
=======================================
  Files          14       14           
  Lines        1856     1856           
  Branches      322      322           
=======================================
  Hits         1602     1602           
  Misses        208      208           
  Partials       46       46           

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