Squashed 'vendor/ruvector/' content from commit b64c2172

git-subtree-dir: vendor/ruvector
git-subtree-split: b64c21726f2bb37286d9ee36a7869fef60cc6900

examples/dna/benches/biomarker_bench.rs

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+//! Criterion benchmarks for Biomarker Analysis Engine
+//!
+//! Performance benchmarks covering ADR-014 targets:
+//! - Risk scoring (<50 μs)
+//! - Profile vector encoding (<100 μs)
+//! - Population generation (<500ms for 10k)
+//! - Streaming throughput (>100k readings/sec)
+//! - Z-score and classification (<5 μs)
+
+use criterion::{black_box, criterion_group, criterion_main, Criterion};
+use rvdna::biomarker::*;
+use rvdna::biomarker_stream::*;
+use std::collections::HashMap;
+
+// ============================================================================
+// Helpers
+// ============================================================================
+
+fn sample_genotypes() -> HashMap<String, String> {
+    let mut gts = HashMap::new();
+    gts.insert("rs429358".into(), "TT".into());
+    gts.insert("rs7412".into(), "CC".into());
+    gts.insert("rs4680".into(), "AG".into());
+    gts.insert("rs1799971".into(), "AA".into());
+    gts.insert("rs762551".into(), "AA".into());
+    gts.insert("rs1801133".into(), "AG".into());
+    gts.insert("rs1801131".into(), "TT".into());
+    gts.insert("rs1042522".into(), "CG".into());
+    gts.insert("rs80357906".into(), "DD".into());
+    gts.insert("rs4363657".into(), "TT".into());
+    gts
+}
+
+fn full_panel_genotypes() -> HashMap<String, String> {
+    // All 17 SNPs from health.rs
+    let mut gts = sample_genotypes();
+    gts.insert("rs28897696".into(), "GG".into());
+    gts.insert("rs11571833".into(), "AA".into());
+    gts.insert("rs4988235".into(), "AG".into());
+    gts.insert("rs53576".into(), "GG".into());
+    gts.insert("rs6311".into(), "CT".into());
+    gts.insert("rs1800497".into(), "AG".into());
+    gts.insert("rs1800566".into(), "CC".into());
+    gts
+}
+
+// ============================================================================
+// Risk Scoring Benchmarks (target: <50 μs)
+// ============================================================================
+
+fn risk_scoring_benchmarks(c: &mut Criterion) {
+    let mut group = c.benchmark_group("biomarker_scoring");
+
+    // Setup: create a representative genotype map
+    let gts = sample_genotypes();
+
+    group.bench_function("compute_risk_scores", |b| {
+        b.iter(|| black_box(compute_risk_scores(&gts)));
+    });
+
+    group.bench_function("compute_risk_scores_full_panel", |b| {
+        let full_gts = full_panel_genotypes();
+        b.iter(|| black_box(compute_risk_scores(&full_gts)));
+    });
+
+    group.finish();
+}
+
+// ============================================================================
+// Profile Vector Benchmarks (target: <100 μs)
+// ============================================================================
+
+fn vector_encoding_benchmarks(c: &mut Criterion) {
+    let mut group = c.benchmark_group("biomarker_vector");
+
+    let gts = sample_genotypes();
+    let profile = compute_risk_scores(&gts);
+
+    group.bench_function("encode_profile_vector", |b| {
+        b.iter(|| black_box(encode_profile_vector(&profile)));
+    });
+
+    group.finish();
+}
+
+// ============================================================================
+// Population Generation Benchmarks (target: <500ms for 10k)
+// ============================================================================
+
+fn population_benchmarks(c: &mut Criterion) {
+    let mut group = c.benchmark_group("biomarker_population");
+
+    group.bench_function("generate_100", |b| {
+        b.iter(|| black_box(generate_synthetic_population(100, 42)));
+    });
+
+    group.bench_function("generate_1000", |b| {
+        b.iter(|| black_box(generate_synthetic_population(1000, 42)));
+    });
+
+    group.finish();
+}
+
+// ============================================================================
+// Streaming Benchmarks (target: >100k readings/sec)
+// ============================================================================
+
+fn streaming_benchmarks(c: &mut Criterion) {
+    let mut group = c.benchmark_group("biomarker_streaming");
+
+    group.bench_function("generate_1000_readings", |b| {
+        let config = StreamConfig::default();
+        b.iter(|| black_box(generate_readings(&config, 1000, 42)));
+    });
+
+    group.bench_function("process_1000_readings", |b| {
+        let config = StreamConfig::default();
+        let readings = generate_readings(&config, 1000, 42);
+        b.iter(|| {
+            let mut processor = StreamProcessor::new(config.clone());
+            for reading in &readings {
+                black_box(processor.process_reading(reading));
+            }
+        });
+    });
+
+    group.bench_function("ring_buffer_1000_push", |b| {
+        b.iter(|| {
+            let mut rb: RingBuffer<f64> = RingBuffer::new(100);
+            for i in 0..1000 {
+                rb.push(black_box(i as f64));
+            }
+        });
+    });
+
+    group.finish();
+}
+
+// ============================================================================
+// Z-Score and Classification Benchmarks (target: <5 μs)
+// ============================================================================
+
+fn classification_benchmarks(c: &mut Criterion) {
+    let mut group = c.benchmark_group("biomarker_classification");
+    let refs = biomarker_references();
+
+    group.bench_function("z_score_single", |b| {
+        let r = &refs[0];
+        b.iter(|| black_box(z_score(180.0, r)));
+    });
+
+    group.bench_function("classify_single", |b| {
+        let r = &refs[0];
+        b.iter(|| black_box(classify_biomarker(180.0, r)));
+    });
+
+    group.bench_function("z_score_all_biomarkers", |b| {
+        b.iter(|| {
+            for r in refs {
+                let mid = (r.normal_low + r.normal_high) / 2.0;
+                black_box(z_score(mid, r));
+            }
+        });
+    });
+
+    group.finish();
+}
+
+// ============================================================================
+// Criterion Configuration
+// ============================================================================
+
+criterion_group!(
+    benches,
+    risk_scoring_benchmarks,
+    vector_encoding_benchmarks,
+    population_benchmarks,
+    streaming_benchmarks,
+    classification_benchmarks,
+);
+criterion_main!(benches);