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Fix typed-release gates and tighten typed tests #167

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dnncha merged 1 commit into from
Oct 27, 2026
Merged

Fix typed-release gates and tighten typed tests #167

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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,14 @@ All notable user-facing changes are tracked here. Public statements in release n
## Unreleased

### Added
- Strict typed Python surface: `py.typed`, `MatchStatus`, `Literal` policies, `TypedDict` summaries, a typed `TargetRow`, and strict mypy/pyright gates (`make typecheck`).
- Strict typed Python surface: `py.typed`, `MatchStatus`, `Literal` policies, `TypedDict` summaries, a typed `TargetRow`, and mypy strict and pyright gates (`make typecheck`).
- Example and snapshot testing flow: executable doctests, Rust `expect-test`-style snapshots, static API contract tests, and a typed quickstart (`make examples-test`).

### Changed
- Assignment result records (`MatchResult`, `AssignmentStats`, `PosteriorAssignment`, `FastqRecord`, `StreamAssignment`) are immutable `NamedTuple`s. Field access and keyword construction are unchanged. They are now tuple-compatible, so equality with a plain tuple is true; `dataclasses.asdict`, `fields`, and `replace` no longer apply.

### Performance
- Python binding path: immutable result records moved to `NamedTuple`, status conversion uses a lookup table, read marshalling has a `str`/`bytes` fast path, and `stream_assign` uses 256-read batches. Local median-of-31 developer measurement against main 91e162b (Apple M5, CPython 3.12, 40k reads/4,096 targets): Hamming 1,273,487 -> 1,683,587 reads/s (+32.2%), Levenshtein 596,400 -> 699,997 (+17.4%), exact 1,297,718 -> 1,968,851 (+51.7%), stream Hamming 296,564 -> 395,915 (+33.5%). See `docs/benchmarks/python-api-binding.md`; local measurement, not a public cross-machine claim.
- Python binding path: immutable result records moved to `NamedTuple`, status conversion uses a lookup table, read marshalling has a `str`/`bytes` fast path, and `stream_assign` uses 256-read batches. Local median-of-31 developer measurement against 91e162b (Apple M5, CPython 3.12, 40k reads/4,096 targets): Hamming 1,300,623 -> 1,823,206 reads/s (+40.2%), Levenshtein 605,585 -> 699,968 (+15.6%), exact 1,341,603 -> 1,967,205 (+46.6%), stream Hamming 304,908 -> 398,864 (+30.8%). See `docs/benchmarks/python-api-binding.md`; local measurement, not a public cross-machine claim.

### Fixed

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5 changes: 3 additions & 2 deletions Makefile
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@@ -1,6 +1,7 @@
PYTHON ?= python3
TYPED_PYTHON_SOURCES ?= \
python/dotmatch/_optional.py \
python/dotmatch/fastq_io.py \
python/dotmatch/_types.py \
python/dotmatch/_validation.py \
python/dotmatch/assayspec.py \
Expand Down Expand Up @@ -534,10 +535,10 @@ repository-ready:
python3 scripts/check_reviewer_readiness_assets.py
$(MAKE) docs-ready

release-ready: typecheck lint examples-test python-test python-package-test docs-ready scientific-readiness-ready assay-evidence-ready alphabet-policy-ready citation-metadata-ready native-comparator-scope-ready workflow-examples-ready evidence-gallery-ready distribution-record-ready bioconda-recipe-ready gpu-evidence-gate native-exact-gate hamming-seed-layout-gate guide-counter-gate public-crispr-evidence-gate crispr-comparison-gate barcode-comparison-gate feature-barcode-public-gate perturb-seq-public-gate perturb-seq-case-study-fixture-gate perturb-seq-case-study-public-gate amplicon-panel-public-gate bcl-tiny-public-gate oligo-adapter-public-gate reviewer-readiness-ready assaycode-readiness-ready agent-tools-ready agent-skill-ready agent-reference-workflows-ready
release-ready: examples-test python-test python-package-test docs-ready scientific-readiness-ready assay-evidence-ready alphabet-policy-ready citation-metadata-ready native-comparator-scope-ready workflow-examples-ready evidence-gallery-ready distribution-record-ready bioconda-recipe-ready gpu-evidence-gate native-exact-gate hamming-seed-layout-gate guide-counter-gate public-crispr-evidence-gate crispr-comparison-gate barcode-comparison-gate feature-barcode-public-gate perturb-seq-public-gate perturb-seq-case-study-fixture-gate perturb-seq-case-study-public-gate amplicon-panel-public-gate bcl-tiny-public-gate oligo-adapter-public-gate reviewer-readiness-ready assaycode-readiness-ready agent-tools-ready agent-skill-ready agent-reference-workflows-ready
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python3 scripts/check_release_readiness.py

pretag-ready: typecheck lint examples-test
pretag-ready: examples-test
$(MAKE) test
$(MAKE) cli-test
$(MAKE) asan
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