Apply ruff formatting and safe lint fixes by kroenlein · Pull Request #1061 · CitrineInformatics/citrine-python

kroenlein · 2026-08-07T02:32:02Z

The only purpose of the PR is running all package lines through ruff so that future formatting issues do not distract from code changes.

PR Type:

Breaking change (fix or feature that would cause existing functionality to change)
Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Maintenance (non-breaking change to assist developers)

Adherence to team decisions

I have added tests for 100% coverage
I have written Numpy-style docstrings for every method and class.
I have communicated the downstream consequences of the PR to others.
I have bumped the version in __version__.py

…igial-test-fields [v5.0] Remove vestigial experimental fields from test fixture

Ran `ruff format` and `ruff check --fix` (safe fixes only, line-length 99) over all Python files in src/ and tests/. Resolved conflicts with the project's flake8 configuration: - Disabled RUF100 during the fix so noqa comments flake8 relies on (D-codes, E501, W505) are preserved. - Hand-wrapped 8 f-strings that exceeded 99 chars after .format() -> f-string conversion. - Added E203 to the flake8 ignore list (standard ruff/black slice-spacing exception). Fixed two autofixes that would have broken the test suite: - Restored the load-bearing import order in tests/utils/fakes/__init__.py (marked # isort: skip_file) to avoid a circular import. - Restored the pytest fixture import in tests/serialization/test_scorers.py (marked # noqa: F401). flake8 is clean and all 1237 tests pass. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

anoto-moniz · 2026-08-19T13:51:05Z

+        self.attribute_constraints = (
+            None
+            if attribute_constraints is None
            else [(_make_link_by_uid(x[0]), x[1]) for x in attribute_constraints]
+        )


I'm not a fan of this. I never like splitting ternary operators across multiple lines, but blowing it up like this means it's longer than the equivalent traditional if-statement.

I'd love if for ternaries that are too long, we could explode them into if statements. Or maybe just have ruff allow them to be two lines, like this one initially was?

I abstracted this into an explicit if clause, and then noticed we repeated that code 6 times, so I created a static method to consolidate.

anoto-moniz · 2026-08-19T13:56:47Z

+                "{} is not a valid design subspace type. Must be in {}.".format(
+                    data["type"], type_dict.keys()
+                )


Wait, why didn't it convert this formatted string into an f-string? Did I misinterpret the previous conversions?

Because we support 3.10, but nested double quotes isn't supported until 5.12. Manually addressed by swapping to single quotes.

I just find it odd the formatter didn't realize that simple fix on its own. ¯_(ツ)_/¯

anoto-moniz · 2026-08-19T14:10:16Z

        self.mean = mean
        self.std = std
-        pass  # pragma: no cover
+        # pragma: no cover


This should be removed now.

anoto-moniz · 2026-08-19T14:10:28Z

    def __init__(self, *, probabilities: dict):
        self.probabilities = probabilities
-        pass  # pragma: no cover
+        # pragma: no cover


anoto-moniz · 2026-08-19T14:10:35Z

        self.quantities = quantities
        self.labels = labels or {}
-        pass  # pragma: no cover
+        # pragma: no cover


Drop.

This file has a bunch of #pragma: no cover statements on blank lines following the removal of unnecessary pass statements. They should all be dropped.

anoto-moniz · 2026-08-19T14:16:47Z

-        pass  # pragma: no cover
+        # pragma: no cover


This one I get, because having a method with no body in Python feels weird. But a docstring makes it legal, so we can drop the pragma.

anoto-moniz · 2026-08-19T14:40:27Z

+                errors=[
+                    IngestionErrorTrace.from_validation_error(x) for x in source.validation_errors
+                ]


I've never been a fan of splitting for-comprehensions across lines. But at least the original form of this line makes it a bit clearer, since the for begins the second line, before closing the list. This new form obfuscates it in the middle of the line, surrounded by other stuff.

I'd prefer if we could get ruff to use the two-line version.

Couldn't find a direct fix, so I reverted and used # fmt: skip. The only "solution" was extending max line length, which would just trigger more problems.

anoto-moniz · 2026-08-19T14:41:44Z

+            return IngestionStatus.build(
+                {
+                    "status": IngestionStatusType.INGESTION_CREATED,
+                    "errors": self.errors,
+                }
+            )


Hmmmmmmmmmm...not the most egregious, but feels needlessly verbose. Personally, I don't think we gain any clarity by having the braces on their own lines.

Fixed in pyproject.toml via skip-magic-trailing-comma.

anoto-moniz · 2026-08-19T14:53:05Z

+    properties = Optional(
+        List(
+            Union(
+                [
+                    LinkOrElse(GEMDPropertyTemplate),
+                    SpecifiedMixedList(
+                        [LinkOrElse(GEMDPropertyTemplate), Optional(Object(BaseBounds))]
+                    ),
+                ]
+            )
+        ),
+        "properties",
+        override=True,
+    )


Oof. I hate this. However, it's more an expression of how messy the definition of the serde stuff is generally, laid bare by the complication of the type itself. So not sure there's anything to be done. Ugh.

I created an alias for LinkOrElse(GEMDPropertyTemplate) and swapped the Union to a |. I think it's more legible.

anoto-moniz · 2026-08-19T14:54:48Z

+            | LinkByUID
+            | Sequence[PropertyTemplate | LinkByUID | BaseBounds | None]
+        ]
+        | None = None,


I continue to think multi-line type definitions in the middle of a function definition are the work of the devil. But I'm not sure a super long line is much better...

anoto-moniz · 2026-08-24T14:34:41Z

-    serialized = [(key_serialized, value_serialized),]
+    serialized = [
+        (key_serialized, value_serialized),
+    ]


It would be great if there was some rule that if ruff finds a collection on a single line with a trailing comma, it removed the comma instead of inserting newlines. That is, I'd want this to be turned into

serialized = [(key_serialized, value_serialized)]

anoto-moniz · 2026-08-24T14:37:17Z

+    assert (
+        query.criteria[0].property_templates_filter
+        == query_copy.criteria[0].property_templates_filter
+    )


I don't know the best option for something like this, but I do know I dislike this method of splitting the assert.

I reworked this as looping over lambdas, since it there were honestly a lot of characters to track on that line.

anoto-moniz · 2026-08-24T14:46:36Z

+    assert expected_data_updates["predictors"][0]["predictor_id"] == str(
+        actual_data_updates.predictors[0].uid
+    )


This is even worse. If it must split them across lines, at least keep the left- and right-hand operands together.

anoto-moniz · 2026-08-24T14:53:55Z

+            session.set_response(
+                obj.dump()
+            )  # Delete calls get, must return object data internally


I don't love wrapping due to a comment, even less so in a test. We should just move this comment to the line above.

anoto-moniz · 2026-08-24T14:54:00Z

+            session.set_response(
+                obj.dump()
+            )  # Delete calls get, must return object data internally


anoto-moniz · 2026-08-24T17:09:54Z

+        assert (
+            next(
+                (
+                    var
+                    for var in def1.variables
+                    if name in var.headers and isinstance(var, IngredientLabelsSetByProcessAndName)
+                ),
+                None,
+            )
+            is not None
+        )


This is another example of linting making for terribly unreadable code. Is there some way to tell ruff to not format this line? Or do we just need to refactor it to be shorter?

Honestly, even the original version doesn't spark joy.

anoto-moniz · 2026-08-24T17:10:52Z

+        BadRequest(
+            ""
+        ),  # Attempted POST throws BadRequest because, for example, the template bounds are being narrowed.


We should move the comment to make this more readable.

Maybe if there's some way to automatically do that? Can we get ruff to move comments to the line above if the line is short enough without it?

anoto-moniz · 2026-08-24T17:17:08Z

+        assert (
+            "1234"
+            == Citrine(
+                api_key="1234", scheme="http", host="citrine-testing.fake", port="8080"
+            ).session.refresh_token
+        )


This line is particularly ugly.

anoto-moniz · 2026-08-24T17:17:39Z

+        assert (
+            "1234"
+            == Session(
+                refresh_token="1234", scheme="ftp", host="citrine-testing.fake", port="8080"
+            ).refresh_token
+        )


Follow-up to the ruff-formatting pass, addressing Austin's review feedback and applying the same fixes to unflagged instances of each concern type. - Add [tool.ruff] config: skip-magic-trailing-comma (collapses single-line collections instead of exploding them) with isort.split-on-trailing-comma disabled for compatibility. - Convert .format() calls on string literals to f-strings. - Drop orphaned `# pragma: no cover` comments left after `pass` removal. - Refactor split-operand/wrapped asserts to keep operands together (extract locals, loop over cases, lambda accessors) and move comments that forced line wraps above their expressions. - gemtables/variables.py: extract the repeated ternary into a module-level `_build_attribute_constraints` helper and hoist the duplicated `_AttributeType`/`_ObjectType`/`_ConstraintType` aliases to module scope. - Restore correct (separate) LinkOrElse instances in the template property definitions; shared Property descriptors break serialization-path assignment. - validate_type: raise ValueError instead of bare Exception. - Cover PvA __iter__ explicitly after switching next(iter(...)) reads to []. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

kroenlein · 2026-08-24T21:37:19Z

        if data_dict_copy["type"] != type_name:
-            raise Exception(
-                "Object type must be {}, but was instead {}.".format(type_name, data_dict["type"])
+            raise ValueError(


I chose to change the type here because we really shouldn't have been throwing an Exception,

kroenlein · 2026-08-24T21:40:47Z

+        assert any(
+            var
+            for var in def1.variables
+            if name in var.headers and isinstance(var, IngredientQuantityByProcessAndName)


Not formally the same but close enough and much more legible.

kroenlein · 2026-08-24T21:41:41Z

+    cast = str(team_member)
+    assert user.screen_name in cast
+    assert all(a in cast for a in team_member.actions)
+    assert team.name in cast


Seemed like it was actually testing what we cared about plus dropped the operator-split.

kroenlein · 2026-08-24T21:42:57Z

+    return {
+        "type": "ContinuousDimension",
+        "descriptor": {
+            "type": "Real",
+            "descriptor_key": "alpha",
+            "units": "",
+            "lower_bound": 5.0,
+            "upper_bound": 10.0,
+        },
+        "lower_bound": 6.0,
+        "upper_bound": 7.0,
+    }


Showed up as a non-binding warning.

kroenlein and others added 2 commits August 6, 2026 09:09

Merge pull request #1059 from CitrineInformatics/maintain/remove-vest…

b267e8f

…igial-test-fields [v5.0] Remove vestigial experimental fields from test fixture

kroenlein marked this pull request as ready for review August 7, 2026 02:36

kroenlein requested a review from a team as a code owner August 7, 2026 02:36

anoto-moniz force-pushed the release/5.0 branch from b267e8f to 7bcc6e3 Compare August 7, 2026 15:16

Base automatically changed from release/5.0 to main August 7, 2026 15:19

Merge branch 'main' into maintain/ruff-formatting

6b3633f

github-advanced-security Bot found potential problems Aug 17, 2026

View reviewed changes

Comment thread tests/_util/test_functions.py Fixed

Satisfying profound overreaction by CodeQL sanitization false positive

e5d016b

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anoto-moniz reviewed Aug 19, 2026

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anoto-moniz reviewed Aug 24, 2026

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kroenlein commented Aug 24, 2026

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