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4 commits

Author SHA1 Message Date
rUv
161f890ddb fix: apply cargo fmt across workspace and fix CI issues 
- Run cargo fmt --all to fix formatting in 362 files across the entire workspace
- Add PGDG repository for PostgreSQL 17 in CI test-all-features and benchmark jobs
- Add missing rvf dependency crates to standalone Dockerfile for domain-expansion
- Add sona-learning and domain-expansion features to standalone Dockerfile build
- Create npu.rs stub for ruvector-sparse-inference (fixes rustfmt resolution error)

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-21 20:56:38 +00:00
rUv
829ca9f014 feat(rvdna): rename package to rvdna, publish to crates.io and npm 
Rename dna-analyzer-example to rvdna across all source files, tests,
and benchmarks. Add crates.io metadata (repository, docs, keywords).
Publish rvdna v0.1.0 to crates.io and @ruvector/rvdna v0.1.0 to npm
with NAPI-RS platform loader, JS fallbacks, and TypeScript definitions.

Also publishes workspace deps at v2.0.2: ruvector-math, ruvector-core,
ruvector-filter, ruvector-collections, ruvector-graph, ruvector-gnn.

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-12 15:47:00 +00:00
rUv
244bbffe54 feat: add package.json for rvdna example with WASM bindings and build scripts 2026-02-12 15:32:55 +00:00
Claude
541fc85e4b feat(dna): complete SOTA genomic analysis pipeline with full test suite 
Implements a comprehensive DNA analyzer demonstrating RuVector's vector
computing capabilities for bioinformatics:

Modules (9):
- types: Core domain types (DnaSequence, Nucleotide, ProteinSequence, etc.)
- kmer: HNSW k-mer indexing with FNV-1a hashing and MinHash sketching
- alignment: Smith-Waterman local alignment with CIGAR generation
- variant: SNP calling from pileup data with genotype classification
- protein: DNA-to-protein translation with contact graph prediction
- epigenomics: Horvath clock biological age prediction from CpG methylation
- pharma: CYP2D6 star allele calling and metabolizer phenotype prediction
- pipeline: DAG-based genomic analysis orchestration
- error: Typed error handling across all modules

Testing (41 tests, 0 mocks):
- 12 k-mer integration tests (encoding, HNSW search, MinHash Jaccard)
- 17 pipeline e2e tests (alignment, variant calling, pharmacogenomics)
- 12 security tests (buffer overflow, path traversal, concurrency, bounds)

Benchmarks: Criterion suite for kmer, alignment, variant, protein, pipeline

Binary: 7-stage demo (sequence gen, k-mer search, alignment, variant
calling, protein analysis, epigenomics, pharmacogenomics)

https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
 2026-02-11 04:29:28 +00:00