fix(types): resolve typecheck warnings by xraymemory · Pull Request #269 · diff-use/sampleworks

xraymemory · 2026-06-22T16:51:58Z

Summary

tighten MSA typing around string/integer keys and keep deterministic Protenix ordering
normalize Protenix MSA output directory argument type
remove stale ty/type ignore comments that now produce warnings

Fixes #249

Validation

uvx ty check
uvx ruff check src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/sf.py src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/transformer.py src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/unitcell.py src/sampleworks/core/samplers/edm.py src/sampleworks/metrics/lddt.py src/sampleworks/metrics/rmsd.py src/sampleworks/models/boltz/wrapper.py src/sampleworks/models/rf3/wrapper.py src/sampleworks/utils/framework_utils.py src/sampleworks/utils/msa.py tests/conftest.py tests/utils/test_atom_array_utils.py tests/utils/test_framework_utils.py tests/utils/test_msa.py
PYTHONPATH=src uvx --with pytest --with loguru --with requests --with tqdm pytest --noconftest tests/utils/test_msa.py -q

coderabbitai · 2026-06-22T16:52:10Z

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📥 Commits

Reviewing files that changed from the base of the PR and between 72f5118 and 4033e23.

📒 Files selected for processing (14)

src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/sf.py
src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/transformer.py
src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/unitcell.py
src/sampleworks/core/samplers/edm.py
src/sampleworks/metrics/lddt.py
src/sampleworks/metrics/rmsd.py
src/sampleworks/models/boltz/wrapper.py
src/sampleworks/models/rf3/wrapper.py
src/sampleworks/utils/framework_utils.py
src/sampleworks/utils/msa.py
tests/conftest.py
tests/utils/test_atom_array_utils.py
tests/utils/test_framework_utils.py
tests/utils/test_msa.py

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Commit unit tests in branch michaelanzuoni/issue-249-typecheck-warnings

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Copilot

Pull request overview

This PR focuses on eliminating ty typecheck warnings across the codebase by tightening MSA-related typing (including deterministic ordering for Protenix), normalizing a Protenix MSA output-dir argument type, and removing now-stale ty: ignore[...] comments that were producing warnings.

Changes:

Refine MSA typing/ordering: introduce a deterministic key sort helper for mixed int/str keys and add coverage for it.
Normalize Protenix MSA search invocation (cast output directory to str) and clean up related typing.
Remove unnecessary ty: ignore[...] suppressions across tests and runtime code where types are now accepted or warnings are gone.

Confidence: ~80% (reviewed all provided diff hunks; one typing semantic issue flagged via PR comment).

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/utils/test_msa.py	Adds a regression test for deterministic mixed-key sorting used by Protenix MSA logic.
tests/utils/test_framework_utils.py	Removes now-stale `ty: ignore` suppressions for negative/error-path tests.
tests/utils/test_atom_array_utils.py	Removes stale `ty: ignore` suppressions in error-path tests.
tests/conftest.py	Removes type-ignore suppressions for tensor ops/return typing in a fixture.
src/sampleworks/utils/msa.py	Introduces `MSAData` alias + deterministic Protenix key ordering; normalizes Protenix out-dir argument type.
src/sampleworks/utils/framework_utils.py	Removes no-longer-needed `ty: ignore` suppressions around broadcast/tile operations.
src/sampleworks/models/rf3/wrapper.py	Removes `ty: ignore` for a pipeline call now expected to typecheck cleanly.
src/sampleworks/models/boltz/wrapper.py	Removes `ty: ignore` suppressions by relying on updated MSA/GenerativeModelInput typing.
src/sampleworks/metrics/rmsd.py	Removes stale ignores around `add_global_token_id_annotation` usage.
src/sampleworks/metrics/lddt.py	Removes stale ignores around `add_global_token_id_annotation` usage.
src/sampleworks/core/samplers/edm.py	Removes a stale ignore for scalar–tensor multiplication.
src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/unitcell.py	Removes unused file-level typecheck suppression directives.
src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/transformer.py	Removes unused file-level `ty` suppression directive.
src/sampleworks/core/forward_models/xray/real_space_density_deps/qfit/sf.py	Removes unused file-level `ty` suppression directive (keeps ruff ignore).

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marcuscollins · 2026-06-23T20:26:31Z

 MAX_PAIRED_SEQS = 8192
 MAX_MSA_SEQS = 16384
+MSAData = Mapping[str, str] | Mapping[int, str] | Mapping[str | int, str]
+


@xraymemory I think I agree with copilot here, and would use dict explicitly. Does that not get rid of the warnings for _compute_msa?

manzuoni-astera · 2026-06-22T18:34:48Z

Validation update after the latest fix:

Local validation passed:
- uvx ty check
- ruff on the touched files
- PYTHONPATH=src uvx --with pytest --with loguru --with requests --with tqdm pytest --noconftest tests/utils/test_msa.py -q → 8 passed
GitHub CI run 27974194229 is green for lint, tests, and typecheck across boltz-dev/protenix-dev/rf3-dev.
Remaining non-code status: GPU Tests run 27974191560 is still WAITING on its boltz-dev/protenix-dev/rf3-dev jobs, with no failure logs available yet.

marcuscollins

Left a few comments but nothing blocking. Approved.

marcuscollins · 2026-06-23T20:23:14Z

        # AtomArrayStack at runtime
-        predicted_atom_array_stack = add_global_token_id_annotation(
-            predicted_atom_array_stack  # ty: ignore[invalid-argument-type]
+        predicted_atom_array_stack = cast(


This seems like something we should fix in AtomWorks or push into our own macromolecular-observables package. The AtomWorks problem is that they don't properly annotate the input/output types. Probably we should just put it in our own package and move away from AtomWorks.

In any event, I dislike cast because of the visual distraction, so we should fix the underlying problem, but for this PR I don't think anything needs to be done except to create an issue.

marcuscollins · 2026-06-23T20:26:31Z

 MAX_PAIRED_SEQS = 8192
 MAX_MSA_SEQS = 16384
+MSAData = Mapping[str, str] | Mapping[int, str] | Mapping[str | int, str]
+


@xraymemory I think I agree with copilot here, and would use dict explicitly. Does that not get rid of the warnings for _compute_msa?

marcuscollins · 2026-06-23T20:31:45Z


        with pytest.raises(TypeError, match="can only accept AtomArray or AtomArrayStack"):
-            select_altloc(invalid_input, "A")  # ty: ignore[invalid-argument-type]
+            select_altloc(cast(Any, invalid_input), "A")


I'm surprised this doesn't still flag it as an invalid argument type. Can you explain?

marcuscollins · 2026-06-23T20:34:20Z

            # make sure sort order stays the same:
-            data_keys = sorted(data.keys())
-            sequences = [data[key] for key in data_keys]
+            data_items = sorted(data.items(), key=lambda item: _msa_data_key_sort_key(item[0]))


Maybe add a comment what _msa_data_key_sort_key does (and maybe give it a better name?)

marcuscollins · 2026-06-23T20:34:58Z

    assert base != MSAManager._hash_arguments({"B": "GGGAA", "A": "MKTAY"}, "greedy")


+def test_msa_data_key_sort_preserves_numeric_order_and_handles_mixed_keys():


IMO, this is a perfect unit test in that it explains why the function is needed in the first place.

fix(types): resolve typecheck warnings

eec8f38

Copilot AI review requested due to automatic review settings June 22, 2026 16:51

xraymemory had a problem deploying to gpu-testing June 22, 2026 16:52 — with GitHub Actions Error

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manzuoni-astera mentioned this pull request Jun 22, 2026

Typecheck warning #249

Open

Copilot AI reviewed Jun 22, 2026

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fix(types): avoid environment-specific diagnostics

4033e23

xraymemory requested a deployment to gpu-testing June 22, 2026 18:15 — with GitHub Actions Waiting

marcuscollins requested a review from DorisMai June 23, 2026 20:13

marcuscollins approved these changes Jun 23, 2026

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fix(types): resolve typecheck warnings#269

fix(types): resolve typecheck warnings#269
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		assert base != MSAManager._hash_arguments({"B": "GGGAA", "A": "MKTAY"}, "greedy")


		def test_msa_data_key_sort_preserves_numeric_order_and_handles_mixed_keys():

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