Release seqtree 1.1.0: consolidate native reductions and text calibration

[mikessh]

Consolidates the pending seqtree APIs into release 1.1.0: exact batched edit histograms, symmetric positional weights and group penalties, gap-block balls/counts/linear mass/linked sum reductions, streaming group audits, stable Poisson tails, and distinct-record TextIndex E-values and cutoffs. Existing unweighted scoring and identity exclusion remain intact; duplicate reference rows retain their multiplicity. Supersedes #7–#12.

TextIndex record reduction runs in one GIL-released native call. Native batches resolve one CPU budget, respect detected allocations, reject excessive positive requests, and use the caller plus B−1 workers for a budget of B. Serial execution is inline; pools close before returning. Setup combines extras and propagates installation failures. Internal notes remain local, while public data provenance is preserved in the Sphinx docs.

Validation: 603 Python tests passed locally (4 platform/optional skips), all 70 C++ test cases passed, Sphinx built with zero warnings, oracle/performance gates passed, distribution contents and metadata checked, and clean wheel smoke checks passed. Live-thread measurements on 512 queries × 8,000 references peaked at exactly 1, 2 and 16 threads for serial, explicit two-core and automatic modes; counts matched and peak RSS stayed below 30 MiB. Linux CI exercises restricted one-CPU affinity and excessive-request rejection. Final cross-platform CI is required before merge.

Copilot's two documentation findings were fixed and their threads resolved. Review focus: native score/overflow bounds, histogram equivalence, positional symmetry, grouped and linked reduction semantics, record deduplication/exclusion, GIL and resource cleanup.

[Copilot]

🟡 Changes recommended

Removed documentation leaves dangling references and provenance unavailable, while gap-block documentation contradicts the new paired-sum API.

2 open findings

• Narrow positional-weight limitation statement to affected reducers · New
• Preserve or update references to removed tracked documents · New

What changed in this PR

Consolidates native reductions, positional/group scoring, stable calibration, and TextIndex E-values for the 1.1.0 release.

Changes:

• Adds native edit histograms and expanded gap-block reductions.
• Adds distinct-record TextIndex calibration and stable Poisson tails.
• Updates packaging, setup, documentation, and regression coverage.

File	Description
.gitignore	Ignores local planning files.
CHANGELOG.md	Documents release 1.1.0.
CLAUDE.md	Removes repository instructions.
ROADMAP.md	Removes downstream roadmap.
SOURCES.md	Removes data provenance document.
docs/​api.rst	Documents histogram and text calibration APIs.
docs/​design/​text_index.md	Updates TextIndex adoption status.
docs/​gapblock.rst	Documents new scoring geometry and reductions.
docs/​roadmap.rst	Updates significance roadmap.
docs/​text-index.rst	Introduces TextIndex calibration.
include/​seqtree/​seqtree.hpp	Declares histogram and gap-block APIs.
include/​seqtree/​text_index.hpp	Declares record-distance reduction.
pyproject.toml	Bumps version and adjusts sdist exclusions.
python/​seqtree/​__init__.py	Exports text calibration functions.
python/​seqtree/​evalue.py	Stabilizes Poisson probabilities.
python/​seqtree/​gapblock.py	Exposes new gap-block options and reducers.
python/​seqtree/​text_evalue.py	Implements TextIndex E-values and cutoffs.
setup.sh	Combines extras and propagates failures.
skills/​seqtree/​SKILL.md	Removes agent API reference.
src/​_bindings.cpp	Binds the new native APIs.
src/​count_unit.hpp	Implements unit-edit histogram acceleration.
src/​gapblock.cpp	Implements weighted/grouped reductions.
src/​index.cpp	Implements edit histogram batching.
src/​text_index.cpp	Implements distinct-record reduction.
tests/​python/​test_doc_coverage.py	Registers text calibration documentation.
tests/​python/​test_edit_histogram.py	Tests histogram equivalence.
tests/​python/​test_evalue.py	Tests stable probability tails.
tests/​python/​test_gapblock_group_audit.py	Tests streaming audits.
tests/​python/​test_gapblock_group_offsets.py	Tests group penalties.
tests/​python/​test_gapblock_linear_mass.py	Tests linear mass reduction.
tests/​python/​test_gapblock_paired_sum.py	Tests linked sum reductions.
tests/​python/​test_gapblock_position_weights.py	Tests length-based weights.
tests/​python/​test_gapblock_sequence_weights.py	Tests per-input weights.
tests/​python/​test_setup.py	Tests setup behavior.
tests/​python/​test_text_evalue.py	Tests TextIndex calibration.
tests/​python/​test_unit_histogram_fastpath.py	Tests histogram fast path.

🧠 Review effort: Balanced

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