[dnncha]

Summary

• Add a typed Python surface: py.typed, MatchStatus IntEnum, Literal policies, TypedDict summaries, TargetRow, strict mypy + pyright gates, and 3.9-safe public type shapes.
• Add a static/example test flow: assert_type API contracts, doctests, expect-style snapshots, typed quickstart, and make quality.
• Speed up the Python binding path with NamedTuple results, a status lookup, str/bytes marshalling fast path, and 256-read stream batches.

Verification

• make typecheck (mypy strict + pyright): clean
• make lint: clean
• pytest python/tests: 532 passed
• make examples-test: 16 passed
• python scripts/check_python_wheel.py: wheel and sdist include py.typed
• Local median-of-31 benchmark (Apple M5, 40k reads / 4,096 targets): Hamming +59.5%, Levenshtein +17.1%, exact +64.2%, stream +71.9%. Raw data in benchmarks/raw/python_api_binding_20261027.json.

Note: result records are now NamedTuples (field access and keyword construction unchanged; tuple-compatible equality).

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-27T19:59:29.856335Z	a537166	PR opened

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review" or "@codex security review".

Codex reacts with 👀 while any review is running, comments if it has suggestions, and reacts with 👍 once all reviews finish with no findings.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: a53716648b

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Report the actual 0.1.9 release on the homepage

The homepage tells users that v0.2.2 is available from PyPI and Bioconda, and repeats that version in the release trust fact, but this commit declares and documents 0.1.9 in pyproject.toml, package.json, and docs/distribution-release.json. Anyone following the package links will find a different release than advertised, so these claims should use the recorded 0.1.9 version.

Useful? React with 👍 / 👎.

[chatgpt-codex-connector]

Describe best-policy assignments accurately

For an AssaySpec using ambiguity_policy = "best", the generated methods.md still says that reads were assigned only when exactly one target was compatible. Under the best policy, a read can be assigned uniquely when several targets lie within k as long as only one has the best distance, so this statement makes the generated methods and handoff artifacts misdescribe the actual selection rule. Generate policy-specific wording instead.

Useful? React with 👍 / 👎.