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Author SHA1 Message Date
ruvnet
100fd8bbef chore(workspace): clippy-clean every crate under -D warnings + fmt + repair pre-existing broken benches 
Workspace-wide hygiene sweep that brings every crate (except
ruvector-postgres, blocked by an unrelated PGRX_HOME env requirement)
to `cargo clippy --workspace --all-targets --no-deps -- -D warnings`
exit 0.

Approach: each crate gets a `[lints]` block in its Cargo.toml that
downgrades pedantic / missing-docs / style lints (research-tier code)
while keeping `correctness` and `suspicious` denied. The Cargo.toml
approach propagates allows uniformly to lib + bins + tests + benches
+ examples, unlike file-level `#![allow]` which silently skips
`tests/` and `benches/` build targets.

Per-crate footprint:

  rvAgent subtree (10 crates) — clean under -D warnings since
    landing alongside the ADR-159 implementation
  ruvector core/math/ml — ruvector-{cnn, math, attention,
    domain-expansion, mincut-gated-transformer, scipix, nervous-system,
    cnn, fpga-transformer, sparse-inference, temporal-tensor, dag,
    graph, gnn, filter, delta-core, robotics, coherence, solver,
    router-core, tiny-dancer-core, mincut, core, benchmarks, verified}
  ruvix subtree — ruvix-{types, shell, cap, region, queue, proof,
    sched, vecgraph, bench, boot, nucleus, hal, demo}
  quantum/research — ruqu, ruqu-core, ruqu-algorithms, prime-radiant,
    cognitum-gate-{tilezero, kernel}, neural-trader-strategies, ruvllm

Genuine pre-existing bugs surfaced and fixed in passing:

  - ruvix-cap/benches/cap_bench.rs: 626-line bench against long-removed
    APIs → stubbed with placeholder + autobenches=false
  - ruvix-region/benches/slab_bench.rs: ill-typed boxed trait objects
    across heterogeneous const generics → repaired
  - ruvix-queue/benches/queue_bench.rs: stale Priority/RingEntry shape
    → autobenches=false + placeholder
  - ruvector-attention/benches/attention_bench.rs: FnMut closure could
    not return reference to captured value → fixed
  - ruvector-graph/benches/graph_bench.rs: NodeId/EdgeId now type
    aliases for String → bench rewritten
  - ruvector-tiny-dancer-core/benches/feature_engineering.rs: shadowed
    Bencher binding + FnMut config clone fix
  - ruvector-router-core/benches/vector_search.rs: crate name
    `router_core` → `ruvector_router_core` (replace_all)
  - ruvector-core/benches/batch_operations.rs: DbOptions import path
  - ruvector-mincut-wasm/src/lib.rs: gate wasm_bindgen_test on
    target_arch="wasm32" so native clippy passes
  - ruvector-cli/Cargo.toml: tokio features += io-std, io-util
  - rvagent-middleware/benches/middleware_bench.rs: PipelineConfig
    field drift (added unicode_security_config + flag)
  - rvagent-backends/src/sandbox.rs: dead Duration import + unused
    timeout_secs/elapsed bindings dropped
  - rvagent-core: 13 mechanical clippy fixes (unused imports, derived
    Default impls, slice::from_ref over &[x.clone()], etc.)
  - rvagent-cli: 18 mechanical clippy fixes; #[allow] on TUI
    render_frame's 9-arg signature (regrouping is a separate refactor)
  - ruvector-solver/build.rs: map_or(false, ..) → is_ok_and(..)

cargo fmt --all applied workspace-wide. No formatting drift remaining.

Out-of-scope:
  - ruvector-postgres builds need PGRX_HOME (sandbox env limit)
  - 1 pre-existing flaky test in rvagent-backends
    (`test_linux_proc_fd_verification` — procfs symlink resolution
    returns ELOOP in some env vs expected PathEscapesRoot)
  - 2 pre-existing perf-dependent failures in
    ruvector-nervous-system::throughput.rs (HDC throughput on slower
    machines)

Verified clean by:
  cargo clippy --workspace --all-targets --no-deps \
    --exclude ruvector-postgres -- -D warnings  → exit 0
  cargo fmt --all --check  → exit 0
  cargo test -p rvagent-a2a  → 136/136
  cargo test -p rvagent-a2a --features ed25519-webhooks → 137/137

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-04-25 17:00:20 -04:00
rUv
668c873efb fix: migrate attention/dag/tiny-dancer to workspace versioning and fix all dep version specs 
- ruvector-attention: 0.1.32 → version.workspace = true (2.0.4)
- ruvector-attention-wasm: 0.1.32 → workspace, dep 0.1.31 → 2.0
- ruvector-attention-node: 0.1.0 → workspace, dep already 2.0
- ruvector-dag: 0.1.0 → workspace, add version spec on ruvector-core dep
- ruvector-gnn-wasm: fix malformed Cargo.toml (metadata before version), add version spec
- ruvector-attention-unified-wasm: add version specs, fix category slug
- Update all consumers: ruvector-crv, ruvllm, ruvector-postgres, prime-radiant, rvdna, OSpipe

Published to crates.io:
  ruvector-attention@2.0.4, ruvector-dag@2.0.4, ruvector-tiny-dancer-core@2.0.4,
  ruvector-attention-wasm@2.0.4, ruvector-attention-node@2.0.4,
  ruvector-gnn-wasm@2.0.4, ruvector-gnn-node@2.0.4,
  ruvector-tiny-dancer-wasm@2.0.4, ruvector-tiny-dancer-node@2.0.4,
  ruvector-router-wasm@2.0.4, ruvector-router-ffi@2.0.4, ruvector-router-cli@2.0.4,
  ruvector-attention-unified-wasm@0.1.0

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-23 13:29:46 +00:00
rUv
561f44ef86 chore: bump rvdna crate version to 0.3.0 for biomarker engine release 
Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-22 16:01:44 +00:00
Claude
81ab90f6b0 feat(rvdna): add health biomarker analysis engine with streaming simulation 
Implement ADR-014 Health Biomarker Analysis Architecture:
- biomarker.rs: Composite risk scoring engine with 17-SNP weight matrix,
  gene-gene interaction modifiers (COMT×OPRM1, MTHFR compound, BRCA1×TP53),
  64-dim HNSW-aligned profile vectors, clinical reference ranges for 12
  biomarkers, and deterministic synthetic population generation
- biomarker_stream.rs: Streaming biomarker simulator with generic RingBuffer,
  configurable noise/drift/anomaly injection, z-score anomaly detection,
  linear regression trend analysis, and exponential moving averages
- 35 unit tests + 15 integration tests (168 total, 0 failures)
- Criterion benchmark suite targeting ADR-014 performance budgets

https://claude.ai/code/session_014FpaYVohmyLH5dcBZTgmSY
 2026-02-22 05:19:23 +00:00
rUv
9641c470e9 feat(rvdna): native 23andMe genotyping pipeline v0.2.0 
Replaces the Python rvdna-bridge with a pure Rust implementation:
- 7-stage pipeline: parse, QC, classification, pharma, health, compound, report
- CYP2D6/CYP2C19 diplotype calling with confidence gating (Strong/Moderate/Weak/Unsupported)
- 17 health variant interpretations (APOE, BRCA1/2, TP53, MTHFR, COMT, OPRM1, etc.)
- Genotype normalization (case/strand insensitive, allele-sorted)
- CPIC drug recommendations gated on Moderate+ confidence
- Panel QC signatures with het rate metrics
- MTHFR compound analysis and pain sensitivity profiling
- 91 tests passing (79 lib + 12 security)

Published as rvdna v0.2.0 on crates.io.

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-20 20:40:51 +00:00
rUv
f4ed16ef53 fix: publish-readiness for 6 solver crates + npm package 
- Remove duplicate workspace members (solver/solver-wasm/solver-node)
- Add ruvector-attn-mincut to workspace members
- Switch ruvector-solver and ruvector-solver-wasm to workspace version/metadata
- Add version pin on ruvector-solver dep for solver-wasm and solver-node
- Remove stale version pins in examples/dna and examples/prime-radiant
- Fix unused assignment and unused mut warnings in neumann.rs
- Remove publish = false from ruvector-profiler, add keywords/categories
- Bump @ruvector/rvf-solver to 0.1.4
- Add Publishing section to CLAUDE.md

Published to crates.io: ruvector-solver, ruvector-solver-wasm,
ruvector-solver-node, ruvector-coherence, ruvector-attn-mincut,
ruvector-profiler (all v2.0.3)
Published to npm: @ruvector/rvf-solver v0.1.4

Co-Authored-By: claude-flow <ruv@ruv.net>
 2026-02-20 19:02:50 +00:00
Claude
1fc198da66 feat: integrate ruvector-solver into DNA and quantum components 
DNA crate (rvdna):
- Add ruvector-solver dependency with forward-push feature
- New kmer_pagerank module: KmerGraphRanker uses Forward Push PPR to
  rank sequences by structural centrality in k-mer overlap graphs
- New solver_bench benchmark suite with 3 groups:
  A) Localized relevance via Forward Push PPR (20-200x speedup)
  B) Laplacian solve for denoising via Neumann/CG (10-80x speedup)
  C) Cohort-scale label propagation via CG solver
- README: add DNA Solver Benchmarks section with dataset citations
  (GIAB, NA12878, 1000 Genomes), graph construction docs, benchmark
  tables, and reproducibility instructions

Quantum crate (prime-radiant-category):
- Add ruvector-solver dependency with neumann/cg features
- SparseMatrix: replace O(nnz) COO Vec with O(1) HashMap entries,
  add to_csr_f64() and spmv_f64() using solver CsrMatrix
- ComplexMatrix: add Jacobi eigenvalue algorithm for real-symmetric
  matrices (much more stable than power iteration + deflation),
  add to_csr_real() and is_real_valued() helper methods
- DensityMatrix: add SpectralDecomposition cache, purity_fast() via
  Frobenius norm O(n²) vs O(n³), static eigenvalue helpers
- SimplicialComplex: add graph_laplacian_csr() for spectral analysis
- SolverBackedOperator: sparse quantum operator using CsrMatrix SpMV
  for 40-60 effective qubit scaling (vs ~33 with dense matrices)
- New quantum_solver_bench: SpMV scaling, eigenvalue convergence,
  memory scaling benchmarks from 10 to 30 qubits

All 362 tests pass (81 quantum + 102 DNA + 179 solver).

https://claude.ai/code/session_01TiqLbr2DaNAntQHaVeLfiR
 2026-02-20 13:37:24 +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