github-actions[bot]
080d2e37ac
chore: Update NAPI-RS binaries for all platforms
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Built from commit 8e60cf9e53🤖 Generated by GitHub Actions
2026-02-12 18:51:15 +00:00
rUv
990091b927
chore(ruqu): bump to v2.0.5 with updated READMEs
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- Updated ruqu-core README with 5 simulation backends, cost-model planner,
QEC control plane, OpenQASM 3.0, cryptographic witnesses, transpiler
- Fixed ruqu-wasm npm badge and imports to use @ruvector/ruqu-wasm scope
- Published to crates.io: ruqu-core, ruqu-algorithms, ruqu-exotic, ruqu-wasm
- Published to npm: @ruvector/ruqu-wasm@2.0.5
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 18:44:22 +00:00
github-actions[bot]
0cc59a8203
chore: Update NAPI-RS binaries for all platforms
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Built from commit 740e87579c🤖 Generated by GitHub Actions
2026-02-12 18:10:19 +00:00
rUv
988db53bd0
chore(ruqu): bump all quantum crates to v2.0.4
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Published to crates.io: ruqu-core, ruqu-algorithms, ruqu-exotic, ruqu-wasm
Published to npm: @ruvector/ruqu-wasm@2.0.4
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 18:03:46 +00:00
github-actions[bot]
5fe1d078ee
chore: Update NAPI-RS binaries for all platforms
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Built from commit e6d4330008🤖 Generated by GitHub Actions
2026-02-12 18:01:45 +00:00
rUv
470c62d568
feat(ruqu): add quantum execution intelligence engine with 5 backends
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Transforms ruqu from classical coherence monitor into full-stack quantum execution intelligence engine (~2K to ~24K lines).
New: StateVector, Stabilizer, TensorNetwork, Clifford+T, and Hardware simulation backends. Cost-model planner, surface code decoder (union-find O(n*alpha(n))), QEC scheduler, noise models, OpenQASM 3.0 export, deterministic replay, and cross-backend verification.
PR #161
2026-02-12 12:55:21 -05:00
github-actions[bot]
98c471dc7e
chore: Update NAPI-RS binaries for all platforms
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Built from commit cb1b6de3be🤖 Generated by GitHub Actions
2026-02-12 16:21:06 +00:00
rUv
9db3693a44
docs: add missing crates and examples to root README
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Crates added:
- ruvector-delta-core, delta-graph, delta-index, delta-consensus,
delta-wasm (behavioral change tracking subsystem)
- profiling (real-time coherence diagnostics)
Examples added:
- dna (rvDNA genomic analysis)
- delta-behavior (change tracking math)
- data (dataset discovery framework)
- prime-radiant (coherence engine demos)
- benchmarks (temporal reasoning benchmarks)
- vwm-viewer (visual vector world model viewer)
Updated counts: 70 crates, 34 examples, 34 capabilities.
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 16:17:02 +00:00
github-actions[bot]
784f5ea361
chore: Update NAPI-RS binaries for all platforms
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Built from commit 4d6f9abbc4🤖 Generated by GitHub Actions
2026-02-12 16:03:29 +00:00
github-actions[bot]
94090f132f
chore: Update NAPI-RS binaries for all platforms
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Built from commit c30c3dd8ef🤖 Generated by GitHub Actions
2026-02-12 15:59:36 +00:00
rUv
2c9f8e7b09
docs: add rvDNA to all root README sections
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- Capabilities: new "Genomics & Health" section (items 22-25)
- Installation table: cargo add rvdna, npm install @ruvector/rvdna
- npm Packages: @ruvector/rvdna under "Genomics & Health"
- Rust Crates: rvdna with crates.io badge and feature summary
- Updated capability count from 30+ to 34
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 15:59:02 +00:00
github-actions[bot]
d0122be670
chore: Update NAPI-RS binaries for all platforms
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Built from commit 1c503b9f45🤖 Generated by GitHub Actions
2026-02-12 15:55:43 +00:00
rUv
8bd20aa32f
docs(rvdna): add health mission, npm/crate details, mermaid diagrams
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- Add "Why This Exists" section: AI for instant, private, free
genomic diagnostics available to everyone
- Add install table with crates.io and npm links
- Add full npm API table with JS examples and NAPI-RS platform matrix
- Replace ASCII architecture with 4 mermaid diagrams in collapsed
sections: pipeline, .rvdna format layout, data flow, WASM deployment
- Add collapsed rvDNA section to root README.md
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 15:55:02 +00:00
rUv
a06c877b78
docs(rvdna): rewrite npm README for JavaScript users
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Tailored README with JS/TS code examples, API reference tables,
WASM tutorial (browser + bundler setup), platform support table,
format comparison, and speed benchmarks. Bump to v0.1.1.
Co-Authored-By: claude-flow <ruv@ruv.net>
2026-02-12 15:50:34 +00:00
rUv
691748e2e1
feat(rvdna): rename package to rvdna, publish to crates.io and npm
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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
github-actions[bot]
68933665da
chore: Update NAPI-RS binaries for all platforms
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Built from commit 244bbffe54🤖 Generated by GitHub Actions
2026-02-12 15:38:32 +00:00
rUv
6af4200a60
feat: add package.json for rvdna example with WASM bindings and build scripts
2026-02-12 15:32:55 +00:00
github-actions[bot]
2cf6624a90
chore: Update NAPI-RS binaries for all platforms
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Built from commit c51726238c🤖 Generated by GitHub Actions
2026-02-12 01:19:28 +00:00
rUv
66790bcdfd
Merge pull request #159 from ruvnet/claude/dna-analyzer-example-ZgAiv
2026-02-11 20:14:30 -05:00
Claude
e46d742999
perf(dna): 1.8x kmer speedup, 10x SW memory reduction
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Smith-Waterman: rolling 2-row DP replaces 3 full (Q+1)*(R+1) matrices.
Only prev+curr rows for H/E, single scalar for F. Memory drops from
~600KB to ~12KB for 100x500bp alignment, fitting L1 cache. Traceback
matrix retained (tb==0 encodes stop condition, no full H needed).
K-mer encoding: zero-allocation canonical hashing eliminates Vec alloc
per k-mer in MinHash::sketch() via dual MurmurHash3 (fwd + rc strands).
types.rs to_kmer_vector: rolling polynomial hash computes O(1) per
k-mer instead of O(k). Removes leading nucleotide, shifts, adds
trailing in constant time using precomputed 5^(k-1).
Benchmarks (100bp query x 500bp ref / k=11):
kmer/encode_1kb: 4.1µs → 2.3µs (1.78x)
kmer/encode_100kb: 364µs → 199µs (1.83x)
smith_waterman: 416µs → 386µs (1.08x, 10x less memory)
full pipeline: 1.98ms → 1.52ms (1.30x end-to-end)
95 tests pass, zero failures.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 13:59:26 +00:00
Claude
d5c3fb810f
feat(dna): implement missing capabilities + optimize hot paths
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- Affine gap scoring: 3-matrix Smith-Waterman (H/E/F) with flat 1D
arrays for cache-friendly access, direct slice indexing
- Indel detection: call_indel() for insertion/deletion from pileup data
- VCF output: VCFv4.3 format with proper CHROM/POS/REF/ALT/QUAL columns
- CYP2C19 pharmacogenomics: star allele calling (*1/*2/*3/*17),
phenotype prediction, drug recommendations (clopidogrel, voriconazole)
- Cancer signal detection: methylation entropy + extreme ratio scoring,
CancerSignalDetector with configurable risk threshold
- Molecular weight: monoisotopic Da for all 20 amino acids
- Isoelectric point: Henderson-Hasselbalch bisection with sidechain pKa
- K-mer encoding: zero-allocation canonical hashing (hash both strands,
take min) eliminates O(n) Vec allocs per sliding window
- CRC32: lookup table replaces bit-by-bit (~8x faster header checksums)
- Benchmarks: added RVDNA, epigenomics, protein analysis groups
95 tests pass (54 lib + 12 kmer + 17 pipeline + 12 security)
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 05:31:16 +00:00
Claude
7674e6aafc
docs(dna): rewrite README with RVDNA format, real gene data, benchmarks
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Complete README rewrite reflecting the final state of the project:
- Added "What It Does" section showing actual 8-stage demo output
- Added RVDNA AI-native format section with format comparison table
- Added real gene data section (HBB, TP53, BRCA1, CYP2D6, INS)
- Added actual Criterion benchmark numbers (155ns SNP, 12ms full pipeline)
- Fixed Quick Start to match working binary commands
- Added collapsible module guides with accurate line counts
- Added test suite summary (87 tests, zero mocks)
- Added project structure tree with all 13 source files
- Added 13 ADR index table
- Updated architecture diagram to include RVDNA output stage
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 05:03:43 +00:00
Claude
c12b3c1b42
feat(dna): add RVDNA AI-native format, real gene data, 8-stage pipeline
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New RVDNA binary format (.rvdna) purpose-built for AI genomic analysis:
- 2-bit nucleotide encoding (4x compression vs ASCII FASTA)
- Pre-computed k-mer vectors with int8 quantization for instant HNSW search
- Sparse attention matrices in COO format for direct tensor consumption
- Variant probability tensors with f16 genotype likelihoods
- Zero-copy memory-mappable with 64-byte aligned sections
- CRC32 checksums, section-level integrity verification
Real human gene sequences from NCBI RefSeq:
- HBB (hemoglobin beta, NM_000518.5) - sickle cell gene
- TP53 (tumor suppressor, NM_000546.6) - exons 5-8 hotspot
- BRCA1 (DNA repair, NM_007294.4) - exon 11 fragment
- CYP2D6 (drug metabolism, NM_000106.6) - pharmacogenomic
- INS (insulin, NM_000207.3) - preproinsulin
Pipeline upgraded to 8 stages using real data:
1. Load 5 real human genes (2,340 bp total)
2. K-mer similarity matrix across gene panel
3. Smith-Waterman alignment on HBB
4. Sickle cell variant detection at HBB codon 6
5. HBB → hemoglobin beta translation (MVHLTPEEKSAVTALWGKVN verified)
6. Horvath epigenetic clock
7. CYP2D6 *4/*10 pharmacogenomics
8. RVDNA format conversion with pre-computed vectors
87 tests, 0 failures. ADR-013 documents the format specification.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 04:48:28 +00:00
Claude
605aa7da55
chore(dna): add .gitignore for VectorDB database artifacts
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Ignores :memory: and *.db files created during test runs and binary execution.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 04:30:48 +00:00
Claude
9638ba38de
feat(dna): complete SOTA genomic analysis pipeline with full test suite
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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
Claude
c188316ff3
feat(dna): optimize all 12 ADRs + add DDD docs, README
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All ADRs updated with:
- Implementation Status sections (Working/Buildable/Research)
- SOTA algorithm references with citations
- Crate API mappings to actual RuVector functions
- Concrete performance math and targets
New documents:
- ADR-011: Performance targets and benchmark suite (755 lines)
- ADR-012: Genomic security and privacy (596 lines)
- DDD Bounded Context Map (602 lines)
- DDD Domain Model with Rust types (1,047 lines)
- README with features, comparisons, QuickStart (541 lines)
9,326 lines of architecture documentation total.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 04:02:06 +00:00
Claude
2bd81953aa
feat(dna): add ADR-006 temporal epigenomics, ADR-008 WASM edge, ADR-010 pharmacogenomics
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ADR-006: Temporal Epigenomic & Lifespan Analysis Engine (1,177 lines)
ADR-008: WebAssembly Edge Genomics & Universal Deployment (1,117 lines)
ADR-010: Quantum-Enhanced Pharmacogenomics & Precision Medicine (1,136 lines)
10 of 15 documents now complete (10,935 total lines).
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 03:43:38 +00:00
Claude
ddb9eec42c
feat(dna): add 7 ADR documents for DNA analyzer architecture
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ADR-001: Vision & Context - world's fastest DNA analyzer strategy
ADR-002: Quantum Genomics Engine - Grover's, QAOA, VQE for genomics
ADR-003: HNSW Genomic Vector Index - hyperbolic space phylogenetics
ADR-004: Flash Attention Genomic Architecture - hierarchical 6-level
ADR-005: GNN Protein Structure Engine - SE(3)-equivariant folding
ADR-007: Distributed Genomics Consensus - global biosurveillance
ADR-009: Zero-False-Negative Variant Calling Pipeline
7,505 lines of scientifically-grounded architecture decisions.
Remaining ADRs (006, 008, 010-012) and DDD docs in progress.
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 01:32:49 +00:00
Claude
38e56633d3
feat(dna): scaffold DNA analyzer example with claude-flow init
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- Initialize claude-flow v3 with hierarchical-mesh swarm (15 agents)
- Create examples/dna/ directory structure for ADR/DDD documents
- Update .claude/ agents, helpers, settings, and skills from init --force
- 15-agent swarm actively producing ADR-001 through ADR-012 and DDD docs
https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
2026-02-11 00:25:19 +00:00
github-actions[bot]
2f1df0e788
chore: Update NAPI-RS binaries for all platforms
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Built from commit 8c36eae2da🤖 Generated by GitHub Actions
2026-02-08 22:43:26 +00:00
rUv
244b7b76ef
feat(vwm-viewer): add hyper-realistic Super Bowl LX visualization
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4D Gaussian splatting demo deployed to Cloud Run at
ruvector-vwm-875130704813.us-central1.run.app
- football.html: Patriots vs Seahawks with 4000+ gaussians/frame,
ESPN-style scorebug, 5 camera modes, play simulation engine,
particle effects, atmospheric fog, post-processing pipeline
- canvas-viewer.html: Canvas2D fallback for generic VWM viewing
- Dockerfile + nginx.conf: Cloud Run deployment config
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-02-08 22:39:31 +00:00
github-actions[bot]
20aae511e4
chore: Update NAPI-RS binaries for all platforms
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Built from commit 70f3ba6707🤖 Generated by GitHub Actions
2026-02-08 20:54:25 +00:00
rUv
ec157847ca
chore: add auto-memory bridge, upgrade settings, and operational guidance
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Install @claude-flow/memory as local dependency to enable the auto-memory
bridge that was silently skipping. Update settings.json with Agent Teams
hooks (TeammateIdle, TaskCompleted), SessionStart/End memory sync, and
verified v3 configuration. Add operational guidance to CLAUDE.md covering
disk space management, upgrade procedures, and health check reference.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-02-08 20:49:35 +00:00
rUv
a68f5b9e10
docs: fix metadata and README issues from deep review
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- ruvllm: Add missing keywords, categories, readme field
- ruvector-sona: Fix docs.rs URL (was "sona", now "ruvector-sona")
- ruvector-crv: Add badges, installation, related crates
- graph-wasm npm: Add npm and license badges
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 20:49:15 +00:00
rUv
f8ffa1295d
chore(graph-node): bump npm version to 2.0.2
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Aligns npm package version with crates.io release.
Updates platform dependencies to match.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 20:49:15 +00:00
github-actions[bot]
91dafc1b7f
chore: Update NAPI-RS binaries for all platforms
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Built from commit b67f3c9962🤖 Generated by GitHub Actions
2026-02-08 17:18:26 +00:00
rUv
1e3035c289
feat: add READMEs and publish ruqu packages v2.0.3
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Crates.io (v2.0.3):
- ruqu-core: High-performance quantum circuit simulator
- ruqu-algorithms: VQE, Grover, QAOA, Surface Code
- ruqu-exotic: Quantum-classical hybrid algorithms
- ruqu-wasm: WebAssembly bindings
npm (@ruvector/ruqu-wasm v2.0.3):
- Browser-native quantum simulation
- 25-qubit support with 105KB WASM bundle
- TypeScript definitions included
SEO-optimized READMEs with:
- Performance benchmarks
- API documentation
- Code examples
- ADR links
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 17:13:57 +00:00
github-actions[bot]
f08991b7a2
chore: Update NAPI-RS binaries for all platforms
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Built from commit 00aa395976🤖 Generated by GitHub Actions
2026-02-08 17:11:50 +00:00
github-actions[bot]
2faa0bb1d0
chore: Update NAPI-RS binaries for all platforms
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Built from commit fcbe23fe55🤖 Generated by GitHub Actions
2026-02-08 17:10:01 +00:00
github-actions[bot]
edddeee1ee
chore: Update NAPI-RS binaries for all platforms
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Built from commit 00e8fc3f1e🤖 Generated by GitHub Actions
2026-02-08 17:07:51 +00:00
rUv
96c84f422e
feat: publish ruQu quantum simulation engine crates
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Published crates:
- ruqu-core v2.0.2 - State-vector simulator
- ruqu-algorithms v2.0.2 - VQE, Grover, QAOA, Surface Code
- ruqu-exotic v2.0.2 - Quantum-classical hybrids
- ruqu-wasm v2.0.2 - WebAssembly bindings
Updated README with quantum engine section linking ADRs:
- QE-001 to QE-012: Core architecture to MinCut coherence
- Code example for GHZ state creation
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 17:06:58 +00:00
github-actions[bot]
7970c07036
chore: Update NAPI-RS binaries for all platforms
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Built from commit 8cfb2e8393🤖 Generated by GitHub Actions
2026-02-08 17:06:47 +00:00
rUv
efd0f70f56
Merge pull request #154 from ruvnet/claude/quantum-engine-adrs-6OsEO
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feat: Add quantum simulation engine ADR series (QE-001 to QE-012) and DDD design documents
2026-02-08 12:05:03 -05:00
rUv
4a59e7e4de
Merge origin/main into claude/quantum-engine-adrs-6OsEO - resolve Cargo.toml conflict
2026-02-08 17:04:57 +00:00
rUv
7781e10c0e
docs: expand temporal tensor store section with PR #156 details
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Added ADR links (018-023) and DDD reference for:
- Block-based storage engine
- Tiered quantization formats
- Temporal scoring tier migration
- Delta compression reconstruction
- WASM API cross-platform
- Benchmarking acceptance criteria
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 17:03:22 +00:00
rUv
239f22214c
docs: update README with new crates and BitNet features
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Added:
- ruvector-temporal-tensor: Temporal tensor store with tiered quantization
- ruvector-crv: CRV signal line protocol for vector search
- BitNet 1.58-bit quantization features to ruvllm description
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 17:02:09 +00:00
rUv
2c607c7327
chore: bump versions for BitNet integration publish
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- Workspace version: 2.0.1 → 2.0.2
- ruvector-sona: 0.1.4 → 0.1.5 (adds Debug impl for SonaEngine)
- ruvllm: 2.0.2 (BitNet integration from PR #151 )
Published crates:
- ruvector-sona v0.1.5
- ruvllm v2.0.2
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-02-08 17:00:26 +00:00
github-actions[bot]
c0b610dcd1
chore: Update NAPI-RS binaries for all platforms
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Built from commit 593b44a543🤖 Generated by GitHub Actions
2026-02-08 16:59:58 +00:00
github-actions[bot]
445dace141
chore: Update NAPI-RS binaries for all platforms
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Built from commit e98ce26da3🤖 Generated by GitHub Actions
2026-02-08 16:58:30 +00:00
github-actions[bot]
926376e227
chore: Update NAPI-RS binaries for all platforms
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Built from commit 0989957d15🤖 Generated by GitHub Actions
2026-02-08 16:55:50 +00:00
