Add Needleman-Wunsch distance as a faster alignment metric - #725

Draft

felixpetschko wants to merge 29 commits into

scverse:mainfrom

felixpetschko:performance/needleman-wunsch-cpu

Commits on Aug 6, 2026

Add needleman-wunsch implementation
felixpetschko
committed
ecd271c
Add length diff prefilter
felixpetschko
committed
a775d84
Change diagonal handling
felixpetschko
committed
a572341
Add block-wise progress bar
felixpetschko
committed
e8df9c9
Add bandwidth restriction
felixpetschko
committed
ced1ad6
Extend blosum 62 alphabet
felixpetschko
committed
9f51d8f
Avoid negative distance values
felixpetschko
committed
37f48c2
Adapt param docstrings
felixpetschko
committed
ab90910
Adapt docstring
felixpetschko
committed
2ed19a2
Move scoring matrices to module constants
felixpetschko
committed
a7df67b
Add tests
felixpetschko
committed
c8c888f
Adapt ambiguous X score test
felixpetschko
committed
65a3f61
Add test case comments
felixpetschko
committed
ce52e01
Increase n_jobs for test_needleman_wunsch_reference() to make it faster
felixpetschko
committed
a7623a8
Do not allow cutoff=None anymore
felixpetschko
committed
878fa5f
Validate Needleman-Wunsch cutoff and clarify banding logic
felixpetschko
committed
b2a817f
Update changelog
felixpetschko
committed
0fb1841
Lower n_jobs for test_needleman_wunsch_reference()
felixpetschko
committed
dd10e5b
Change gap_penalty default value
felixpetschko
committed
4174d06
Deprecate alignment distance metrics in favor of Needleman-Wunsch
felixpetschko
committed
98ec934
Correct typo in MetricType Literal
felixpetschko
committed
484524a
Add Needleman-Wunsch calculator to API docs
felixpetschko
committed
7d0e6c1
Use joblib helper for block-wise progress
felixpetschko
committed
089920d
Refactor substitution matrix organization
felixpetschko
committed
44d3b00
Centralize substitution matrix preparation
felixpetschko
committed
3cf47f7
Document substitution matrix alphabets
felixpetschko
committed
187231a
Test substitution matrix alphabet mapping
felixpetschko
committed
76ce28b
Clarify alignment metric deprecations
felixpetschko
committed
6ef18c0
Fix alignment deprecation warning test
felixpetschko
committed
c1f2f33

Navigation Menu

Uh oh!

Add Needleman-Wunsch distance as a faster alignment metric - #725

Add Needleman-Wunsch distance as a faster alignment metric#725
felixpetschko wants to merge 29 commits into
scverse:mainfrom
felixpetschko:performance/needleman-wunsch-cpu

Commits on Aug 6, 2026

Add needleman-wunsch implementation

Add length diff prefilter

Change diagonal handling

Add block-wise progress bar

Add bandwidth restriction

Extend blosum 62 alphabet

Avoid negative distance values

Adapt param docstrings

Adapt docstring

Move scoring matrices to module constants

Add tests

Adapt ambiguous X score test

Add test case comments

Increase n_jobs for test_needleman_wunsch_reference() to make it faster

Do not allow cutoff=None anymore

Validate Needleman-Wunsch cutoff and clarify banding logic

Update changelog

Lower n_jobs for test_needleman_wunsch_reference()

Change gap_penalty default value

Deprecate alignment distance metrics in favor of Needleman-Wunsch

Correct typo in MetricType Literal

Add Needleman-Wunsch calculator to API docs

Use joblib helper for block-wise progress

Refactor substitution matrix organization

Centralize substitution matrix preparation

Document substitution matrix alphabets

Test substitution matrix alphabet mapping

Clarify alignment metric deprecations

Fix alignment deprecation warning test