Solution.from_preset: Add representative industrial wastewaters #317

SuixiongTay · 2026-01-20T14:31:30Z

Summary

This PR adds a set of industrial wastewaters to Solution.from_preset. See https://www.researchsquare.com/article/rs-8743330/v2 for the analysis supporting these compositions.

Todos:

Expand test_from_preset

codecov · 2026-01-20T14:45:41Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.43%. Comparing base (07e2d9b) to head (f7d5d3c).
⚠️ Report is 39 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #317      +/-   ##
==========================================
+ Coverage   85.68%   86.43%   +0.75%     
==========================================
  Files          10       14       +4     
  Lines        1607     1851     +244     
  Branches      285      320      +35     
==========================================
+ Hits         1377     1600     +223     
- Misses        194      207      +13     
- Partials       36       44       +8

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rkingsbury · 2026-01-20T16:16:09Z

Very excited to see these, @SuixiongTay ! Before we finalize, please also add the following:

Choose just one representative ion for each preset. (For the paper analysis, it's good that you've evaluated multiple, but for purposes of distributing to the community we need to use our judgment and pick one)
Update the type annotation and docstring of from_preset with the new preset names and descriptions
Expand test_from_preset to test that 1) all newly added presets can successfully create a Solution and 2) pick 1 or two presets and check specific characteristics (e.g., verify correct pH, TDS, or selected ion concentrations)

rkingsbury · 2026-02-06T18:42:45Z

Hi @SuixiongTay , thanks for these updates. It looks like the automatic tests are getting stuck on test_from_preset , specifically the [ash] preset. Is that test working for you locally? I'm wondering if we've accidentally created some kind of race condition or infinite loop.

rkingsbury · 2026-02-06T18:43:18Z

Small edit - in the References in the docstring, please expand the preprint DOI into a full biobliographic reference (authors, title, preprint available on Research Square"

rkingsbury · 2026-02-06T18:43:48Z

Hi @SuixiongTay , thanks for these updates. It looks like the automatic tests are getting stuck on test_from_preset , specifically the [ash] preset. Is that test working for you locally? I'm wondering if we've accidentally created some kind of race condition or infinite loop.

Also, make sure to update your branch with git pull origin main to ensure you're testing against the latest code in all cases.

SuixiongTay · 2026-02-06T19:51:35Z

Hi @SuixiongTay , thanks for these updates. It looks like the automatic tests are getting stuck on test_from_preset , specifically the [ash] preset. Is that test working for you locally? I'm wondering if we've accidentally created some kind of race condition or infinite loop.

Yes, it is running correctly for me locally, although the pytest is relatively slow.

From the Cl log it looks like the Cl ran into a wall-time limit. One other work around would be to reduce the processing time either by 1) using their elemental compositions/proportions or 2) defining a threshold for the fully speciated ions which should help speed up the workflow.

If the first approach makes sense, I can update the yaml file accordingly.

test_solution.py::test_from_preset[ash] PASSED                               [  3%]
test_solution.py::test_from_preset[batt_mfg] PASSED                          [  3%]
test_solution.py::test_from_preset[batt_recycling] PASSED                    [  3%]
test_solution.py::test_from_preset[coal_washing] PASSED                      [  4%]
test_solution.py::test_from_preset[CRL] PASSED                               [  4%]
test_solution.py::test_from_preset[drilling] PASSED                          [  4%]
test_solution.py::test_from_preset[excavation] PASSED                        [  4%]
test_solution.py::test_from_preset[FGD]

rkingsbury

Hi @SuixiongTay see these comments for some ideas about how to streamline the unit testing here

rkingsbury · 2026-02-06T20:21:28Z

tests/test_solution.py

    # test invalid preset
    with pytest.raises(FileNotFoundError):
        Solution.from_preset("nonexistent_preset")
    # test json as preset
    json_preset = tmp_path / "test.json"
    dumpfn(solution, json_preset)
    solution_json = Solution.from_preset(tmp_path / "test")
    assert isinstance(solution_json, Solution)
    assert solution_json.temperature.to("degC") == ureg.Quantity(data["temperature"])
    assert solution_json.pressure == ureg.Quantity(data["pressure"])
    assert np.isclose(solution_json.pH, data["pH"], atol=0.01)


Since you are now parameterizing this entire test to run on multiple presets, this part of the test should be broken into a separate test, because it doesn't need to be run multiple times.

(these lines don't have anything to do with the specific preset file; they are testing behavior with unrecognized file names and custom files)

rkingsbury · 2026-02-06T20:22:46Z

tests/test_solution.py

    for solute in solution._solutes:
        assert solute in data["solutes"]


Instead of iterating, it will probably be much faster to compare the contents of the entire list at once, e.g.

assert set(solution._solutes) == set(data["solutes"]

This should ensure that every solute in the yaml is present in the solution

Note that converting the list to a set is necessary b/c lists comparisons are ordered, but sets are not. An alternative would be to sort the lists first

rkingsbury · 2026-02-06T20:23:14Z

tests/test_solution.py

    assert isinstance(solution, Solution)
    assert solution.temperature.to("degC") == ureg.Quantity(data["temperature"])
    assert solution.pressure == ureg.Quantity(data["pressure"])
    assert np.isclose(solution.pH, data["pH"], atol=0.01)


Please change the atol here to 0.001; I can't think of a reason why we shouldn't be able to achieve that precision

rkingsbury · 2026-02-06T20:24:13Z

tests/test_solution.py

+        "seawater",
+        "ash",
+        "batt_mfg",
+        "batt_recycling",
+        "coal_washing",
+        "CRL",
+        "drilling",
+        "excavation",
+        "FGD",
+        "flotation",
+        "flue_gas",
+        "gasification",
+        "geothermal",
+        "leachate",
+        "mine_drainage",
+        "mine_tailings",
+        "plating",
+        "pw_conv",
+        "pw_unconv",
+        "refining",
+        "semiconductor",
+        "smelting",
+        "tanning",


I don't think it's necessary to test every preset; let's comment out all except for seawater and perhaps 2 others that have different compositions

Sui Xiong Tay and others added 4 commits November 5, 2025 20:46

Add the to_phreeqc() method

b4362ba

Merge branch 'KingsburyLab:main' into main

3f17c7c

Adding ww project YAML to presets

c50c818

minor correction

b1f1b08

Updating ww industry presets

5ea9fcf

rkingsbury changed the title ~~Adding YAML presets from WW project~~ Solution.from_preset: Add representative industrial wastewaters Feb 5, 2026

Sui Xiong Tay added 3 commits February 5, 2026 18:08

Updated Solution.py type annotation

f7d5d3c

adding yaml in test_from_preset

5def2b6

adding all new yaml in test_from_preset

b0fad0b

rkingsbury reviewed Feb 6, 2026

View reviewed changes

rkingsbury mentioned this pull request Feb 9, 2026

Additional Preset: Geothermal Brine #138

Closed

rkingsbury added this to the v1.4.0 release milestone Feb 9, 2026

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Solution.from_preset: Add representative industrial wastewaters #317

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		for solute in solution._solutes:
		assert solute in data["solutes"]

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