Add foapy.partials package for partial-sequence interval analysis

[goruha]

Summary

• Adds foapy.partials subpackage — the position-preserving counterpart to foapy.core and foapy.ma for sequences with gap positions (numpy masked arrays)
• Gap positions are preserved throughout the pipeline; interval distances are measured using actual full-array indices (gaps count toward distance)
• Exports order, alphabet, intervals_chain, intervals_tuple — all returning masked 1-D arrays of the same length as input

Key semantic distinction

	foapy.ma	foapy.partials
Gap handling	Compressed out before computing	Preserved; count toward interval distance
order() output	2-D masked matrix	1-D masked array (same length as input)
lossy output length	Shorter (boundaries dropped)	Same length (boundaries masked in-place)
redundant output length	n+k using compressed positions	n+k using actual full-array positions

Files changed

New source files: src/foapy/partials/ — __init__, _order, _alphabet, _intervals_chain, _intervals_tuple

Modified: src/foapy/__init__.py — lazy submodule registration for foapy.partials

New tests: 5 test files covering all functions, all binding × chain_mode × tuple_mode combinations, gap semantics, error handling, and no-mask passthrough consistency with core.

Test plan

• tox -e default — 503 tests passing, 0 failures
• pre-commit run --all-files — black, isort, flake8 all pass
• Quickstart examples execute without error

🤖 Generated with Claude Code

[coveralls]

Coverage Report for CI Build 24638355903

Coverage increased (+0.7%) to 94.595%

Details

• Coverage increased (+0.7%) from the base build.
• Patch coverage: 5 uncovered changes across 3 files (271 of 276 lines covered, 98.19%).
• 1 coverage regression across 1 file.

Uncovered Changes

File	Changed	Covered	%
src/foapy/init.py	9	6	66.67%
src/foapy/core/_intervals_tuple.py	37	36	97.3%
src/foapy/partials/init.py	12	11	91.67%

Coverage Regressions

1 previously-covered line in 1 file lost coverage.

File	Lines Losing Coverage	Coverage
src/foapy/init.py	1	53.49%

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Coverage Stats

Relevant Lines:	555
Covered Lines:	525
Line Coverage:	94.59%
Coverage Strength:	5.64 hits per line

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💛 - Coveralls

[github-actions]

Change	Before [58bd76e] <0.0.22>	After [79a5d0f]	Ratio	Benchmark (Parameter)
-	17.2±0.1μs	15.4±0.1μs	0.9	bench_alphabet.AlphabetSuite.time_alphabet(500, 'DNA')
-	17.5±0.09μs	15.4±0.09μs	0.88	bench_alphabet.AlphabetSuite.time_alphabet(500, 'Normal')
-	19.8±0.1μs	15.8±0.1μs	0.8	bench_alphabet.AlphabetSuite.time_alphabet(500, 'Worst')
-	28.8±0.2μs	24.7±0.05μs	0.86	bench_alphabet.AlphabetSuite.time_alphabet(5000, 'Best')
-	156±1μs	119±0.7μs	0.76	bench_alphabet.AlphabetSuite.time_alphabet(5000, 'DNA')
-	264±0.4μs	126±0.9μs	0.48	bench_alphabet.AlphabetSuite.time_alphabet(5000, 'Normal')
-	345±0.8μs	133±0.9μs	0.39	bench_alphabet.AlphabetSuite.time_alphabet(5000, 'Worst')
-	4.69±0.1ms	3.90±0.1ms	0.83	bench_alphabet.AlphabetSuite.time_alphabet(500000, 'Best')
-	49.4±0.1μs	38.1±0.2μs	0.77	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5, 'Best')
-	64.2±2μs	45.6±0.4μs	0.71	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5, 'DNA')
-	50.1±2μs	39.3±0.8μs	0.78	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5, 'Normal')
-	52.7±0.6μs	40.1±0.5μs	0.76	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5, 'Worst')
-	50.7±0.7μs	39.1±0.07μs	0.77	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(50, 'Best')
-	65.9±1μs	45.8±0.2μs	0.7	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(50, 'DNA')
-	54.5±0.5μs	41.8±0.2μs	0.77	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(50, 'Normal')
-	54.7±0.4μs	42.6±0.4μs	0.78	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(50, 'Worst')
-	55.3±0.2μs	42.7±0.2μs	0.77	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(500, 'Best')
-	80.0±0.6μs	57.8±0.4μs	0.72	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(500, 'DNA')
-	74.1±0.7μs	56.8±0.2μs	0.77	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(500, 'Normal')
-	75.9±0.2μs	59.1±0.2μs	0.78	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(500, 'Worst')
-	92.9±0.5μs	72.3±0.6μs	0.78	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5000, 'Best')
-	390±4μs	226±20μs	0.58	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5000, 'Normal')
-	427±3μs	270±10μs	0.63	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(5000, 'Worst')
-	53.6±0.4μs	35.4±0.2μs	0.66	bench_ma_order.MaOrderSuite.time_order(5, 'Best')
-	60.3±2μs	39.8±0.2μs	0.66	bench_ma_order.MaOrderSuite.time_order(5, 'DNA')
-	55.4±1μs	35.8±1μs	0.65	bench_ma_order.MaOrderSuite.time_order(5, 'Normal')
-	61.3±0.5μs	39.4±1μs	0.64	bench_ma_order.MaOrderSuite.time_order(5, 'Worst')
-	55.0±0.2μs	36.8±0.6μs	0.67	bench_ma_order.MaOrderSuite.time_order(50, 'Best')
-	64.6±0.5μs	42.3±0.3μs	0.66	bench_ma_order.MaOrderSuite.time_order(50, 'DNA')
-	65.7±0.9μs	42.3±0.2μs	0.64	bench_ma_order.MaOrderSuite.time_order(50, 'Normal')
-	67.2±0.4μs	45.2±0.8μs	0.67	bench_ma_order.MaOrderSuite.time_order(50, 'Worst')
-	61.9±0.4μs	42.5±0.2μs	0.69	bench_ma_order.MaOrderSuite.time_order(500, 'Best')
-	83.8±0.7μs	57.9±0.4μs	0.69	bench_ma_order.MaOrderSuite.time_order(500, 'DNA')
-	140±0.6μs	117±3μs	0.83	bench_ma_order.MaOrderSuite.time_order(500, 'Normal')
-	264±2μs	226±4μs	0.86	bench_ma_order.MaOrderSuite.time_order(500, 'Worst')
-	120±0.3μs	92.4±0.3μs	0.77	bench_ma_order.MaOrderSuite.time_order(5000, 'Best')
-	288±5μs	223±6μs	0.77	bench_ma_order.MaOrderSuite.time_order(5000, 'DNA')
-	10.9±0.4ms	8.53±0.1ms	0.78	bench_ma_order.MaOrderSuite.time_order(5000, 'Normal')
-	39.1±0.3ms	28.8±0.4ms	0.74	bench_ma_order.MaOrderSuite.time_order(5000, 'Worst')
-	15.2±0.2μs	12.9±0.02μs	0.85	bench_order.OrderSuite.time_order(5, 'Best')
-	15.5±0.05μs	13.2±0.03μs	0.85	bench_order.OrderSuite.time_order(5, 'DNA')
-	15.3±0.07μs	13.0±0.02μs	0.85	bench_order.OrderSuite.time_order(5, 'Normal')
-	15.5±0.1μs	13.2±0.04μs	0.85	bench_order.OrderSuite.time_order(5, 'Worst')
-	16.0±0.2μs	13.5±0.03μs	0.85	bench_order.OrderSuite.time_order(50, 'Best')
-	17.1±0.04μs	14.5±0.1μs	0.85	bench_order.OrderSuite.time_order(50, 'DNA')
-	16.8±0.08μs	14.2±0.09μs	0.85	bench_order.OrderSuite.time_order(50, 'Normal')
-	16.9±0.3μs	14.4±0.06μs	0.85	bench_order.OrderSuite.time_order(50, 'Worst')
-	21.2±0.06μs	18.9±0.08μs	0.89	bench_order.OrderSuite.time_order(500, 'Best')
-	30.2±0.1μs	26.7±0.1μs	0.89	bench_order.OrderSuite.time_order(500, 'DNA')
-	31.5±0.1μs	27.1±0.1μs	0.86	bench_order.OrderSuite.time_order(500, 'Normal')
-	33.9±0.2μs	28.4±0.3μs	0.84	bench_order.OrderSuite.time_order(500, 'Worst')
-	208±3μs	163±3μs	0.78	bench_order.OrderSuite.time_order(5000, 'DNA')
-	309±1μs	177±1μs	0.57	bench_order.OrderSuite.time_order(5000, 'Normal')
-	397±0.8μs	202±1μs	0.51	bench_order.OrderSuite.time_order(5000, 'Worst')
-	12.0±0.5ms	10.8±0.08ms	0.9	bench_order.OrderSuite.time_order(500000, 'Best')
Change	Before [58bd76e] <0.0.22>	After [79a5d0f]	Ratio	Benchmark (Parameter)
----------	------------------------------	---------------------	---------	-----------------------------------------------------------------
+	50.9±0.9ms	57.2±2ms	1.12	bench_alphabet.AlphabetSuite.time_alphabet(500000, 'Normal')
+	70.7±0.8ms	80.1±0.5ms	1.13	bench_alphabet.AlphabetSuite.time_alphabet(500000, 'Worst')
+	4.71±0.02ms	5.27±0.06ms	1.12	bench_ma_alphabet.MaAlphabetSuite.time_alphabet(50000, 'Worst')
+	83.0±0.3ms	93.2±0.6ms	1.12	bench_order.OrderSuite.time_order(500000, 'Worst')