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feat: decompose intervals pipeline into chain/tuple/distribution stages#105

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goruha merged 18 commits into
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002-decompose-intervals-pipeline
Jun 25, 2026
Merged

feat: decompose intervals pipeline into chain/tuple/distribution stages#105
goruha merged 18 commits into
mainfrom
002-decompose-intervals-pipeline

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@goruha goruha commented Mar 28, 2026

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Summary

  • Introduces chain_mode (boundary/cycle) and tuple_mode (lossy/normal/redundant) enums, decomposing the monolithic intervals() into three composable stages: intervals_chain → intervals_tuple → intervals_distribution
  • Adds callable introspection via binding(chain) and chain_mode(chain) — detect metadata from a plain ndarray chain without extra state
  • Adds is_valid_intervals_chain(chain) validator (never raises), foapy.ma variants for masked-array sequences, and four ASV benchmark suites
  • All implementations are fully vectorised (no Python loops); backward-compatible — existing intervals() and mode enum unchanged

Test plan

  • 107 new tests across 10 new test files (442 total, 0 failures)
  • Pipeline consistency tests verify intervals_tuple(intervals_chain(X, b, cm), tm) matches intervals() for all lossy/normal/cycle combinations
  • binding(chain) and chain_mode(chain) round-trip tests against chains produced by intervals_chain
  • foapy.ma variants tested with partially masked sequences
  • pre-commit (black / isort / flake8) passes clean

🤖 Generated with Claude Code

Maximus2012 and others added 9 commits March 13, 2026 18:47
@Maximus2012
feat: extract intervals_chain, intervals_tuple, intervals_distributio…
13e478b 
…n from intervals.py (#83 #84 #85)
@Maximus2012
style: reformat __init__.py
3b26e12
@goruha
Added CLAUDE
9b59336
@goruha
Added speckit
4cfeabe
@goruha
Added speckit
570e81f
@goruha
Added spec
ad430a8
@goruha
Clarify
991fdeb
@goruha
Added tasks
32e4184
@goruha @claude
feat: decompose intervals pipeline into chain/tuple/distribution stages
363e0bf 
Introduces chain_mode, tuple_mode enums and four new pipeline functions:
intervals_chain, intervals_tuple, intervals_distribution,
is_valid_intervals_chain — all vectorised (no Python loops), with
callable binding(chain) and chain_mode(chain) introspection, foapy.ma
variants, ASV benchmarks, and 107 new tests (442 total, 0 failures).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@coveralls

coveralls commented Mar 28, 2026 •
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Coverage Report for CI Build 28146813144

Coverage decreased (-0.3%) to 93.596%

Details

  • Coverage decreased (-0.3%) from the base build.
  • Patch coverage: 1 uncovered change across 1 file (125 of 126 lines covered, 99.21%).
  • No coverage regressions found.

Uncovered Changes

File Changed Covered %
src/foapy/core/_intervals_tuple.py 37 36 97.3%
Total (12 files) 126 125 99.21%

Coverage Regressions

No coverage regressions found.

Coverage Stats

Coverage Status
Relevant Lines: 406
Covered Lines: 380
Line Coverage: 93.6%
Coverage Strength: 2.81 hits per line
💛 - Coveralls

@github-actions

github-actions Bot commented Mar 28, 2026 •
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Change Before [58bd76e] <0.0.22> After [879e227] Ratio Benchmark (Parameter)
- 28.8±0.2μs 23.9±0.5μs 0.83 bench_alphabet.AlphabetSuite.time_alphabet(5000, 'Best')
- 538±1μs 478±2μs 0.89 bench_alphabet.AlphabetSuite.time_alphabet(50000, 'Best')
- 10.9±0.4ms 9.54±0.2ms 0.87 bench_ma_order.MaOrderSuite.time_order(5000, 'Normal')
- 39.1±0.3ms 32.1±0.8ms 0.82 bench_ma_order.MaOrderSuite.time_order(5000, 'Worst')
- 1.63±0.07ms 1.39±0.02ms 0.86 bench_order.OrderSuite.time_order(50000, 'Best')
- 12.0±0.5ms 10.0±0.09ms 0.84 bench_order.OrderSuite.time_order(500000, 'Best')
- 29.7±0.1ms 27.0±0.2ms 0.91 bench_order.OrderSuite.time_order(500000, 'DNA')

goruha and others added 7 commits April 1, 2026 17:00
@goruha
refactoring
ad33698
@goruha
Fix intervals_tuple
ba0adec
@goruha
Added status
9dc1406
@goruha
Commit implementation
7ae5e34
@goruha
Update spec
12f5757
@goruha
Fix specs
37c0c7b
@goruha
Depricate intervals and mode (#106)
56f3b42 
* Depricate intervals and mode

* Apply suggestions from code review

Co-authored-by: Igor Rodionov  <496956+goruha@users.noreply.github.com>

* Fix docs

* Fix benchmarks
@goruha goruha added the documentation Improvements or additions to documentation label Apr 19, 2026
@goruha goruha mentioned this pull request Jun 23, 2026
Closed
Maximus2012
Maximus2012 reviewed Jun 24, 2026
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Comment thread src/foapy/core/_intervals_tuple.py
@goruha @Maximus2012
Update src/foapy/core/_intervals_tuple.py
fb4ef8a 
Co-authored-by: Maximus2012 <107984170+Maximus2012@users.noreply.github.com>
Maximus2012
Maximus2012 previously approved these changes Jun 24, 2026
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@goruha goruha merged commit 879e227 into main Jun 25, 2026
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@goruha goruha deleted the 002-decompose-intervals-pipeline branch June 25, 2026 08:20
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