[0.4.0] add support for Needleman-Wunsch with scores; update Python version support#23
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andrew-titus merged 21 commits intomainfrom Apr 13, 2026
Merged
[0.4.0] add support for Needleman-Wunsch with scores; update Python version support#23andrew-titus merged 21 commits intomainfrom
andrew-titus merged 21 commits intomainfrom
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…ersion support Add needleman_wunsch_with_scores() function that accepts a custom pairwise scoring function (score_fn: Callable[[T, T], float]) instead of flat match/mismatch scores, enabling continuous similarity measures for applications like OCR text alignment. Also updates Python version support to 3.10-3.14 (dropping EOL 3.9, adding 3.14), adds CHANGELOG.md with full release history, and updates documentation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Replace black, flake8, isort, pylint, pydocstyle, and bandit with ruff (lint + format) and mypy. All Python lint/format configuration is now consolidated in pyproject.toml. Coverage config also moved from .coveragerc to pyproject.toml. Removed: setup.cfg, .pylintrc, .pydocstyle, .pydocstyle_test, mypy.ini, .coveragerc. CI lint matrix reduced from 5 jobs to 3 (fast-linters, mypy, cargo-clippy). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Two tests had wrong expected alignments: - test_asymmetric_scores: expected alignment scored -3 but algorithm correctly finds alignment scoring 1 - test_scores_prefer_gaps_over_bad_match: expected a different tie-breaking path; updated to match diagonal > left > up priority Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- CHANGELOG: add Removed section for deleted legacy config files - README: replace stale black badge with ruff, add Development section Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…pdate CHANGELOG - Rust edition 2024 not yet supported by Maturin; revert to 2021. - PyO3 0.28 handles extension-module automatically; remove from maturin config. - Update CHANGELOG to reflect actual Cargo changes. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
PyO3 0.28 removed the GIL-dependent &PyModule in favor of &Bound<'_, PyModule> for #[pymodule] init functions. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
abi3-py311 uses PyType_GetName which doesn't exist in Python 3.10, causing ImportError on the lowest supported version. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lint.sh: replace --run-only-fast-linters with individual flags for each linter (copyright-check, ruff-check, ruff-format, cargo-fmt) - lib.rs: extract needleman_wunsch_core helper with closure-based scoring to eliminate duplication between NW and NW-with-score-matrix - CHANGELOG: document both refactors Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
andrew-titus
commented
Apr 7, 2026
| /// A Python module implemented in Rust. | ||
| #[pymodule] | ||
| fn _sequence_align(_py: Python, m: &PyModule) -> PyResult<()> { | ||
| fn _sequence_align(m: &Bound<'_, PyModule>) -> PyResult<()> { |
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Note for reviewer -- this was required from an API change in pyo3
Uses char-overlap scoring function for a realistic continuous-similarity benchmark. Runtime and memory thresholds calibrated on R5.4 instance. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
andrew-titus
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a team,
AmieRamie,
libinliang866 and
rayshard-thompson
AmieRamie
reviewed
Apr 9, 2026
AmieRamie
reviewed
Apr 9, 2026
AmieRamie
previously approved these changes
Apr 9, 2026
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Just had some NIT's, otherwise LGTM
libinliang866
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Hi Drew — sorry for the late review. I just noticed the request in my personal email. I’ve left one small question regarding the default value of gap; otherwise, everything looks good to me. Hope you’re feeling better soon.
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Summary
needleman_wunsch_with_scores()supporting custom pairwise scoring functions (score_fn(a, b) -> float) for alignment with continuous similarity measures (e.g., spatial proximity, text edit distance, character overlap) instead of binary match/mismatch.BoundAPI migration) and stable ABI minimum from Python 3.7 to 3.10. Update Python version support to 3.10-3.14 (drop 3.9, add 3.14).--run-only-*flag inscripts/lint.sh.needleman_wunsch_corehelper parameterized by a scoring closure, eliminating code duplication between standard and score-matrix NW variants (zero runtime cost via monomorphization).needleman_wunsch_with_scoresand performance benchmarks (runtime + memory) using a char-overlap scoring function..pylintrc,.pydocstyle,.pydocstyle_test,.coveragerc,setup.cfg,mypy.ini); all configuration now inpyproject.toml. Add CHANGELOG.md with full version history.Test plan
pytest tests/unit -v)pytest tests/perf -v)./scripts/lint.sh)./scripts/lint.sh --run-only-ruff-check)🤖 Generated with Claude Code