Migrate Track 1 simulation kernel into renunney

README.md

@@ -24,6 +24,7 @@ plane and the Track 1 runner/API boundary are now local to `renunney`.
 - a local Track 1 runner and config/API layer,
 - a local Track 1 analysis layer for tracking summaries and loci-regression,
 - a local Track 1 threshold/search layer for Nunney-style threshold checks,
+- a local Track 1 simulation kernel,
 - a Makefile for common tasks,
 - migration notes for pulling code into this repo in stages.
 
@@ -86,8 +87,10 @@ The current state is split:
 - Track 1 runner and config/API layer: local to `renunney`
 - Track 1 analysis layer: local to `renunney`
 - Track 1 threshold/search layer: local to `renunney`
-- Track 1 simulation backend: still in the older `cost_of_substitution`
-  directory and imported through the local compatibility layer
+- Track 1 simulation kernel: local to `renunney`
+- Track 1 report, dataset, fit, and extinction-model helpers: still imported
+  from the older `cost_of_substitution` directory through the local
+  compatibility layer
 
 This repo is now the clean operational entry point while the simulation code is
 migrated in later stages.

docs/MIGRATION.md

@@ -31,16 +31,14 @@ Operational code still lives in:
    - `src/renunney/track1_analysis.py`
 5. Track 1 threshold/search boundary has been migrated locally:
    - `src/renunney/track1_threshold.py`
-6. Keep the Track 1 simulation backend in the legacy path until real multi-host runs are stable.
-7. Migrate the Track 1 simulation core after the runner path is stable:
-   - `python/track1_reference.py`
-   - `python/track1_threshold.py`
-   - `python/track1_analysis.py`
-8. Migrate report, dataset, fit, and orchestration-adjacent Track 1 modules after the kernel boundary is stable:
+6. Track 1 simulation kernel has been migrated locally:
+   - `src/renunney/track1_reference.py`
+7. Migrate report, dataset, fit, and orchestration-adjacent Track 1 modules next:
    - `python/track1_report.py`
    - `python/track1_dataset.py`
    - `python/track1_fit.py`
    - `python/track1_extinction.py`
+8. Reduce or remove the remaining compatibility-layer imports after those modules are local.
 9. Migrate docs and example configs last, after path references are updated.
 
 ## Constraint

docs/WORKFLOW.md

@@ -47,8 +47,9 @@ make status
 ## Current Assumption
 
 The Makefile now drives the local orchestration code in `renunney`, while the
-Track 1 runner/API boundary, analysis layer, and threshold/search layer are
-also local to `renunney`. The simulation kernel is still imported from the
-legacy `cost_of_substitution` directory through the compatibility layer in
+Track 1 runner/API boundary, analysis layer, threshold/search layer, and
+simulation kernel are also local to `renunney`. The remaining Track 1
+report/dataset/fit helpers are still imported from the legacy
+`cost_of_substitution` directory through the compatibility layer in
 `src/renunney/legacy.py`. The paper-scale Figure 1 configs used for submission
 are now local to `renunney/config`.

src/renunney/__init__.py

@@ -28,6 +28,26 @@ from .track1_analysis import (
     sweep_number_of_loci,
 )
 from .track1_api import Track1RunConfig, config_from_mapping, load_config, run_config, save_payload
+from .track1_reference import (
+    GenerationSummary,
+    PopulationState,
+    Track1Parameters,
+    allele_tracking_metrics,
+    approximate_ne,
+    expected_female_productivity,
+    expected_mutations_for_population,
+    female_fecundity,
+    female_fraction,
+    generation_metrics,
+    genotype_fitness,
+    initialize_population,
+    is_extinct,
+    paper_mutation_supply_M,
+    realize_birth_counts,
+    simulate_one_generation,
+    simulate_run,
+    summarize_generation,
+)
 from .track1_threshold import (
     ThresholdCheck,
     ThresholdSearchResult,
@@ -56,6 +76,8 @@ __all__ = [
     "LinearCostFit",
     "LocusThresholdRow",
     "NumberOfLociSweep",
+    "GenerationSummary",
+    "PopulationState",
     "repo_root",
     "run_one_job",
     "run_worker_loop",
@@ -64,17 +86,33 @@ __all__ = [
     "ThresholdCheck",
     "ThresholdSearchResult",
     "TrackingSummary",
+    "Track1Parameters",
     "Track1RunConfig",
+    "allele_tracking_metrics",
+    "approximate_ne",
     "config_from_mapping",
+    "expected_female_productivity",
+    "expected_mutations_for_population",
     "evaluate_threshold_candidate",
+    "female_fecundity",
+    "female_fraction",
     "fit_linear_cost_by_loci",
+    "generation_metrics",
+    "genotype_fitness",
+    "initialize_population",
+    "is_extinct",
     "load_config",
     "nunney_threshold_accepts",
+    "paper_mutation_supply_M",
     "published_threshold_accepts",
+    "realize_birth_counts",
     "run_config",
+    "simulate_one_generation",
+    "simulate_run",
     "run_extinction_check",
     "save_payload",
     "search_threshold_over_candidates",
     "summarize_tracking",
+    "summarize_generation",
     "sweep_number_of_loci",
 ]

src/renunney/track1_analysis.py

@@ -14,13 +14,9 @@ from typing import Iterable, Optional
 
 import numpy as np
 
-from .legacy import ensure_legacy_python_path
+from .track1_reference import GenerationSummary, Track1Parameters
 from .track1_threshold import ThresholdSearchResult, search_threshold_over_candidates
 
-ensure_legacy_python_path()
-
-from track1_reference import GenerationSummary, Track1Parameters
-
 
 @dataclass(frozen=True)
 class LocusThresholdRow:

src/renunney/track1_api.py

@@ -16,13 +16,13 @@ from typing import Any, Optional
 
 from .legacy import ensure_legacy_python_path
 from .track1_analysis import summarize_tracking, sweep_number_of_loci
+from .track1_reference import Track1Parameters, simulate_run
 from .track1_threshold import evaluate_threshold_candidate, search_threshold_over_candidates
 
 ensure_legacy_python_path()
 
 from track1_dataset import generate_extinction_dataset
 from track1_fit import class_balance, fit_payload_from_jsonl, load_jsonl
-from track1_reference import Track1Parameters, simulate_run
 from track1_report import generate_report_bundle
 
 

src/renunney/track1_reference.py

@@ -0,0 +1,428 @@
+"""
+track1_reference.py
+
+Local Track 1 reference module for renunney.
+
+This is the historically faithful Nunney-style simulation kernel used by the
+local analysis, threshold, and orchestration layers.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Optional
+
+import numpy as np
+
+
+@dataclass(frozen=True, init=False)
+class Track1Parameters:
+    """Reference parameters for the Track 1 baseline."""
+
+    K: int
+    N0: int
+    n: int
+    u: float
+    R: float
+    T: int
+    epochs: int = 8
+    p: float = 0.5
+    a_max: Optional[int] = None
+
+    def __init__(
+        self,
+        K: int,
+        N0: int,
+        n: int,
+        u: float | None = None,
+        R: float = 10.0,
+        T: int = 300,
+        epochs: int = 8,
+        p: float = 0.5,
+        a_max: Optional[int] = None,
+        M: float | None = None,
+    ) -> None:
+        if u is None:
+            if M is None:
+                raise ValueError("Track1Parameters requires u, or convenience M to derive u.")
+            u = float(M / (2.0 * K))
+        object.__setattr__(self, "K", int(K))
+        object.__setattr__(self, "N0", int(N0))
+        object.__setattr__(self, "n", int(n))
+        object.__setattr__(self, "u", float(u))
+        object.__setattr__(self, "R", float(R))
+        object.__setattr__(self, "T", int(T))
+        object.__setattr__(self, "epochs", int(epochs))
+        object.__setattr__(self, "p", float(p))
+        object.__setattr__(self, "a_max", a_max)
+
+    @property
+    def M(self) -> float:
+        return float(2.0 * self.K * self.u)
+
+    def resolved_a_max(self) -> int:
+        if self.a_max is not None:
+            return self.a_max
+        return self.epochs
+
+    def intrinsic_growth_rate(self) -> float:
+        return float(np.log(self.R / 2.0))
+
+    def total_generations(self) -> int:
+        return self.epochs * self.T + (self.T // 2)
+
+
+@dataclass
+class PopulationState:
+    """Diploid population state for one generation."""
+
+    genomes: np.ndarray
+    sexes: np.ndarray
+
+    @property
+    def size(self) -> int:
+        return int(self.genomes.shape[0])
+
+
+@dataclass(frozen=True)
+class GenerationSummary:
+    """Per-generation diagnostics for Track 1."""
+
+    t: int
+    N: int
+    female_fraction: float
+    male_count: int
+    female_count: int
+    fecundity: float
+    mean_fitness: float
+    mean_expected_female_productivity: float
+    target_value: float
+    mean_allele_value: float
+    mean_genotype_value: float
+    mean_tracking_gap: float
+    paper_M: float
+    expected_mutations_current_N: float
+    realized_mutation_count: int
+    realized_mutation_rate_per_allele: float
+    birth_count: int
+    surviving_offspring_count: int
+    ne_approx: float
+    extinct: bool
+
+
+def initialize_population(params: Track1Parameters, rng: np.random.Generator) -> PopulationState:
+    genomes = np.zeros((params.N0, 2, params.n), dtype=np.int16)
+    sexes = rng.binomial(1, 1.0 - params.p, size=params.N0).astype(np.int8)
+    return PopulationState(genomes=genomes, sexes=sexes)
+
+
+def female_fecundity(r: float, N: int, K: int) -> float:
+    return float(2.0 * np.exp(r * (1.0 - (N / K) ** (1.0 / r))))
+
+
+def genotype_fitness(genomes: np.ndarray, r: float, T: int, t: int) -> np.ndarray:
+    target = t / T
+    locus_means = 0.5 * (genomes[:, 0, :] + genomes[:, 1, :])
+    squared_distance = np.square(locus_means - target, dtype=np.float64)
+    return np.exp(-(r / genomes.shape[2]) * np.sum(squared_distance, axis=1))
+
+
+def expected_female_productivity(fecundity: float, fitness: np.ndarray) -> np.ndarray:
+    return fecundity * fitness
+
+
+def paper_mutation_supply_M(K: int, u: float) -> float:
+    return float(2.0 * K * u)
+
+
+def expected_mutations_for_population(N: int, n: int, u: float) -> float:
+    return float(2.0 * N * n * u)
+
+
+def allele_tracking_metrics(genomes: np.ndarray, T: int, t: int) -> tuple[float, float, float, float]:
+    target_value = float(t / T)
+    if genomes.size == 0:
+        return target_value, 0.0, 0.0, -target_value
+    mean_allele_value = float(np.mean(genomes))
+    genotype_values = 0.5 * (genomes[:, 0, :] + genomes[:, 1, :])
+    mean_genotype_value = float(np.mean(genotype_values))
+    mean_tracking_gap = mean_genotype_value - target_value
+    return target_value, mean_allele_value, mean_genotype_value, mean_tracking_gap
+
+
+def approximate_ne(N: int, female_fraction: float) -> float:
+    male_fraction = 1.0 - female_fraction
+    denom = female_fraction + male_fraction
+    if N <= 0 or female_fraction <= 0.0 or male_fraction <= 0.0 or denom == 0.0:
+        return 0.0
+    return float((2.0 * N * female_fraction * male_fraction) / denom)
+
+
+def female_fraction(sexes: np.ndarray) -> float:
+    if sexes.size == 0:
+        return 0.0
+    return float(np.sum(sexes == 0) / sexes.size)
+
+
+def is_extinct(state: PopulationState) -> bool:
+    if state.size == 0:
+        return True
+    female_count = int(np.sum(state.sexes == 0))
+    male_count = int(np.sum(state.sexes == 1))
+    return female_count == 0 or male_count == 0
+
+
+def choose_gamete(parent: np.ndarray, rng: np.random.Generator) -> np.ndarray:
+    n = parent.shape[1]
+    picks = rng.integers(0, 2, size=n)
+    gamete = np.empty(n, dtype=parent.dtype)
+    gamete[:] = parent[picks, np.arange(n)]
+    return gamete
+
+
+def choose_mutant_allele(current: int, a_max: int, rng: np.random.Generator) -> int:
+    if a_max <= 0:
+        return current
+    draw = int(rng.integers(0, a_max))
+    return draw if draw < current else draw + 1
+
+
+def mutate_zygote(zygote: np.ndarray, params: Track1Parameters, rng: np.random.Generator) -> np.ndarray:
+    a_max = params.resolved_a_max()
+    out = zygote.copy()
+    for chrom in range(out.shape[0]):
+        for locus in range(out.shape[1]):
+            if rng.random() <= params.u:
+                out[chrom, locus] = choose_mutant_allele(int(out[chrom, locus]), a_max, rng)
+    return out
+
+
+def produce_offspring(
+    mother: np.ndarray,
+    father: np.ndarray,
+    params: Track1Parameters,
+    rng: np.random.Generator,
+    locus_indices: np.ndarray,
+) -> tuple[np.ndarray, int]:
+    n = params.n
+    offspring = np.empty((2, n), dtype=mother.dtype)
+    maternal_picks = rng.integers(0, 2, size=n)
+    paternal_picks = rng.integers(0, 2, size=n)
+    offspring[0, :] = mother[maternal_picks, locus_indices]
+    offspring[1, :] = father[paternal_picks, locus_indices]
+    a_max = params.resolved_a_max()
+    mutation_count = 0
+    for chrom in range(2):
+        for locus in range(n):
+            if rng.random() <= params.u:
+                offspring[chrom, locus] = choose_mutant_allele(int(offspring[chrom, locus]), a_max, rng)
+                mutation_count += 1
+    return offspring, mutation_count
+
+
+def realize_birth_counts(fecundity: float, sexes: np.ndarray, rng: np.random.Generator) -> np.ndarray:
+    female_mask = sexes == 0
+    counts = np.zeros(sexes.shape[0], dtype=np.int32)
+    counts[female_mask] = rng.poisson(fecundity, size=int(np.sum(female_mask)))
+    return counts
+
+
+def summarize_generation(state: PopulationState, params: Track1Parameters, t: int) -> GenerationSummary:
+    if state.size == 0:
+        return GenerationSummary(
+            t=t,
+            N=0,
+            female_fraction=0.0,
+            male_count=0,
+            female_count=0,
+            fecundity=0.0,
+            mean_fitness=0.0,
+            mean_expected_female_productivity=0.0,
+            target_value=float(t / params.T),
+            mean_allele_value=0.0,
+            mean_genotype_value=0.0,
+            mean_tracking_gap=float(-(t / params.T)),
+            paper_M=params.M,
+            expected_mutations_current_N=0.0,
+            realized_mutation_count=0,
+            realized_mutation_rate_per_allele=0.0,
+            birth_count=0,
+            surviving_offspring_count=0,
+            ne_approx=0.0,
+            extinct=True,
+        )
+    fit, fec, exp_fp, ff, female_count, male_count = generation_metrics(state, params, t)
+    mean_expected_fp = float(np.mean(exp_fp[state.sexes == 0])) if female_count > 0 else 0.0
+    target_value, mean_allele_value, mean_genotype_value, mean_tracking_gap = allele_tracking_metrics(
+        state.genomes,
+        T=params.T,
+        t=t,
+    )
+    return GenerationSummary(
+        t=t,
+        N=state.size,
+        female_fraction=ff,
+        male_count=male_count,
+        female_count=female_count,
+        fecundity=fec,
+        mean_fitness=float(np.mean(fit)),
+        mean_expected_female_productivity=mean_expected_fp,
+        target_value=target_value,
+        mean_allele_value=mean_allele_value,
+        mean_genotype_value=mean_genotype_value,
+        mean_tracking_gap=mean_tracking_gap,
+        paper_M=params.M,
+        expected_mutations_current_N=expected_mutations_for_population(state.size, params.n, params.u),
+        realized_mutation_count=0,
+        realized_mutation_rate_per_allele=0.0,
+        birth_count=0,
+        surviving_offspring_count=0,
+        ne_approx=approximate_ne(state.size, ff),
+        extinct=is_extinct(state),
+    )
+
+
+def generation_metrics(
+    state: PopulationState,
+    params: Track1Parameters,
+    t: int,
+) -> tuple[np.ndarray, float, np.ndarray, float, int, int]:
+    r = params.intrinsic_growth_rate()
+    fit = genotype_fitness(state.genomes, r=r, T=params.T, t=t)
+    fec = female_fecundity(r=r, N=state.size, K=params.K)
+    exp_fp = expected_female_productivity(fec, fit)
+    female_count = int(np.sum(state.sexes == 0))
+    male_count = int(state.size - female_count)
+    ff = float(female_count / state.size) if state.size > 0 else 0.0
+    return fit, fec, exp_fp, ff, female_count, male_count
+
+
+def simulate_one_generation(
+    state: PopulationState,
+    params: Track1Parameters,
+    t: int,
+    rng: np.random.Generator,
+) -> tuple[PopulationState, GenerationSummary]:
+    if state.size == 0:
+        summary = summarize_generation(state, params, t)
+        return state, summary
+
+    fit, fec, exp_fp, ff, female_count, male_count = generation_metrics(state, params, t)
+    extinct = female_count == 0 or male_count == 0
+    target_value, mean_allele_value, mean_genotype_value, mean_tracking_gap = allele_tracking_metrics(
+        state.genomes,
+        T=params.T,
+        t=t,
+    )
+    expected_mutations_current_N = expected_mutations_for_population(state.size, params.n, params.u)
+    summary = GenerationSummary(
+        t=t,
+        N=state.size,
+        female_fraction=ff,
+        male_count=male_count,
+        female_count=female_count,
+        fecundity=fec,
+        mean_fitness=float(np.mean(fit)),
+        mean_expected_female_productivity=float(np.mean(exp_fp[state.sexes == 0])) if female_count > 0 else 0.0,
+        target_value=target_value,
+        mean_allele_value=mean_allele_value,
+        mean_genotype_value=mean_genotype_value,
+        mean_tracking_gap=mean_tracking_gap,
+        paper_M=paper_mutation_supply_M(params.K, params.u),
+        expected_mutations_current_N=expected_mutations_current_N,
+        realized_mutation_count=0,
+        realized_mutation_rate_per_allele=0.0,
+        birth_count=0,
+        surviving_offspring_count=0,
+        ne_approx=approximate_ne(state.size, ff),
+        extinct=extinct,
+    )
+    if extinct:
+        return state, summary
+
+    birth_counts = realize_birth_counts(fec, state.sexes, rng)
+
+    female_indices = np.flatnonzero(state.sexes == 0)
+    male_indices = np.flatnonzero(state.sexes == 1)
+    total_births = int(np.sum(birth_counts[female_indices]))
+
+    new_genomes = np.zeros((total_births, 2, params.n), dtype=np.int16)
+    new_sexes = np.zeros(total_births, dtype=np.int8)
+    locus_indices = np.arange(params.n)
+    r = params.intrinsic_growth_rate()
+    offspring_t = t + 1
+
+    survivor_cursor = 0
+    realized_mutation_count = 0
+    for mother_index in female_indices:
+        count = int(birth_counts[mother_index])
+        if count == 0:
+            continue
+        father_index = int(male_indices[rng.integers(0, male_indices.size)])
+        for _ in range(count):
+            offspring, offspring_mutations = produce_offspring(
+                state.genomes[mother_index],
+                state.genomes[father_index],
+                params,
+                rng,
+                locus_indices,
+            )
+            realized_mutation_count += offspring_mutations
+            offspring_fitness = float(
+                genotype_fitness(offspring[np.newaxis, :, :], r=r, T=params.T, t=offspring_t)[0]
+            )
+            if rng.random() <= offspring_fitness:
+                new_genomes[survivor_cursor] = offspring
+                new_sexes[survivor_cursor] = int(rng.binomial(1, 1.0 - params.p))
+                survivor_cursor += 1
+
+    allele_exposures = 2 * total_births * params.n
+    next_state = PopulationState(genomes=new_genomes[:survivor_cursor], sexes=new_sexes[:survivor_cursor])
+    summary = GenerationSummary(
+        t=summary.t,
+        N=summary.N,
+        female_fraction=summary.female_fraction,
+        male_count=summary.male_count,
+        female_count=summary.female_count,
+        fecundity=summary.fecundity,
+        mean_fitness=summary.mean_fitness,
+        mean_expected_female_productivity=summary.mean_expected_female_productivity,
+        target_value=summary.target_value,
+        mean_allele_value=summary.mean_allele_value,
+        mean_genotype_value=summary.mean_genotype_value,
+        mean_tracking_gap=summary.mean_tracking_gap,
+        paper_M=summary.paper_M,
+        expected_mutations_current_N=summary.expected_mutations_current_N,
+        realized_mutation_count=realized_mutation_count,
+        realized_mutation_rate_per_allele=0.0
+        if allele_exposures == 0
+        else float(realized_mutation_count / allele_exposures),
+        birth_count=total_births,
+        surviving_offspring_count=survivor_cursor,
+        ne_approx=summary.ne_approx,
+        extinct=summary.extinct,
+    )
+    return next_state, summary
+
+
+def simulate_run(
+    params: Track1Parameters,
+    seed: Optional[int] = None,
+) -> list[GenerationSummary]:
+    rng = np.random.default_rng(seed)
+    state = initialize_population(params, rng)
+    t = -(params.T // 2)
+    summaries: list[GenerationSummary] = []
+
+    for _ in range(params.total_generations()):
+        state, summary = simulate_one_generation(state, params, t, rng)
+        summaries.append(summary)
+        if is_extinct(state):
+            terminal_t = t if summary.extinct else t + 1
+            terminal_summary = summarize_generation(state, params, terminal_t)
+            if summaries[-1] != terminal_summary:
+                summaries.append(terminal_summary)
+            break
+        t += 1
+
+    return summaries

src/renunney/track1_threshold.py

@@ -15,11 +15,7 @@ import json
 from pathlib import Path
 from typing import Iterable, Optional
 
-from .legacy import ensure_legacy_python_path
-
-ensure_legacy_python_path()
-
-from track1_reference import Track1Parameters, simulate_run
+from .track1_reference import Track1Parameters, simulate_run
 
 
 @dataclass(frozen=True)

tests/test_track1_dynamics.py

@@ -0,0 +1,95 @@
+import sys
+from pathlib import Path
+
+import numpy as np
+
+ROOT = Path(__file__).resolve().parents[1]
+SRC_DIR = ROOT / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
+
+import renunney.track1_reference as ref
+
+
+def test_zero_mutation_preserves_zero_alleles_in_one_generation():
+    params = ref.Track1Parameters(K=5000, N0=2, n=2, u=0.0, R=10.0, T=20)
+    state = ref.PopulationState(
+        genomes=np.zeros((2, 2, 2), dtype=np.int16),
+        sexes=np.array([0, 1], dtype=np.int8),
+    )
+    next_state, summary = ref.simulate_one_generation(state, params, t=0, rng=np.random.default_rng(1))
+    assert summary.mean_allele_value == 0.0
+    assert int(next_state.genomes.sum()) == 0
+
+
+def test_zero_offspring_fitness_prevents_survival(monkeypatch):
+    params = ref.Track1Parameters(K=5000, N0=2, n=1, u=0.0, R=10.0, T=20)
+    state = ref.PopulationState(
+        genomes=np.zeros((2, 2, 1), dtype=np.int16),
+        sexes=np.array([0, 1], dtype=np.int8),
+    )
+
+    def fake_fitness(genomes, r, T, t):
+        if genomes.shape[0] == 1:
+            return np.zeros(1, dtype=float)
+        return np.ones(genomes.shape[0], dtype=float)
+
+    monkeypatch.setattr(ref, "genotype_fitness", fake_fitness)
+    monkeypatch.setattr(ref, "female_fecundity", lambda r, N, K: 4.0)
+    monkeypatch.setattr(ref, "realize_birth_counts", lambda fecundity, sexes, rng: np.array([3, 0], dtype=np.int32))
+
+    next_state, _ = ref.simulate_one_generation(state, params, t=0, rng=np.random.default_rng(2))
+    assert next_state.size == 0
+
+
+def test_unit_offspring_fitness_keeps_all_births(monkeypatch):
+    params = ref.Track1Parameters(K=5000, N0=2, n=1, u=0.0, R=10.0, T=20)
+    state = ref.PopulationState(
+        genomes=np.zeros((2, 2, 1), dtype=np.int16),
+        sexes=np.array([0, 1], dtype=np.int8),
+    )
+
+    monkeypatch.setattr(ref, "genotype_fitness", lambda genomes, r, T, t: np.ones(genomes.shape[0], dtype=float))
+    monkeypatch.setattr(ref, "female_fecundity", lambda r, N, K: 4.0)
+    monkeypatch.setattr(ref, "realize_birth_counts", lambda fecundity, sexes, rng: np.array([3, 0], dtype=np.int32))
+
+    next_state, summary = ref.simulate_one_generation(state, params, t=0, rng=np.random.default_rng(2))
+    assert summary.female_count == 1
+    assert next_state.size == 3
+
+
+def test_one_father_is_used_per_female_reproductive_event(monkeypatch):
+    params = ref.Track1Parameters(K=5000, N0=3, n=2, u=0.0, R=10.0, T=20)
+    state = ref.PopulationState(
+        genomes=np.array(
+            [
+                [[0, 0], [0, 0]],
+                [[1, 1], [1, 1]],
+                [[2, 2], [2, 2]],
+            ],
+            dtype=np.int16,
+        ),
+        sexes=np.array([0, 1, 1], dtype=np.int8),
+    )
+
+    monkeypatch.setattr(ref, "genotype_fitness", lambda genomes, r, T, t: np.ones(genomes.shape[0], dtype=float))
+    monkeypatch.setattr(ref, "female_fecundity", lambda r, N, K: 4.0)
+    monkeypatch.setattr(ref, "realize_birth_counts", lambda fecundity, sexes, rng: np.array([3, 0, 0], dtype=np.int32))
+
+    next_state, _ = ref.simulate_one_generation(state, params, t=0, rng=np.random.default_rng(3))
+    paternal_alleles = next_state.genomes[:, 1, :]
+    assert next_state.size == 3
+    assert np.unique(paternal_alleles).size == 1
+
+
+def test_absence_of_males_or_females_counts_as_extinction():
+    female_only = ref.PopulationState(
+        genomes=np.zeros((2, 2, 1), dtype=np.int16),
+        sexes=np.array([0, 0], dtype=np.int8),
+    )
+    male_only = ref.PopulationState(
+        genomes=np.zeros((2, 2, 1), dtype=np.int16),
+        sexes=np.array([1, 1], dtype=np.int8),
+    )
+    assert ref.is_extinct(female_only) is True
+    assert ref.is_extinct(male_only) is True

tests/test_track1_reference.py

@@ -0,0 +1,59 @@
+import sys
+from pathlib import Path
+
+ROOT = Path(__file__).resolve().parents[1]
+SRC_DIR = ROOT / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
+
+import renunney.track1_reference as ref
+
+
+def test_fecundity_matches_r_definition():
+    params = ref.Track1Parameters(K=5000, N0=50, n=1, u=5e-6, R=10.0, T=40)
+    r = params.intrinsic_growth_rate()
+    assert ref.female_fecundity(r, N=0, K=params.K) == pytest_approx(10.0)
+
+
+def test_initialize_population_shapes_and_allele_zero_fixation():
+    params = ref.Track1Parameters(K=5000, N0=12, n=3, u=5e-6, R=10.0, T=40)
+    state = ref.initialize_population(params, ref.np.random.default_rng(1))
+    assert state.genomes.shape == (12, 2, 3)
+    assert state.sexes.shape == (12,)
+    assert int(state.genomes.sum()) == 0
+
+
+def test_simulate_run_returns_generation_summaries():
+    params = ref.Track1Parameters(K=5000, N0=20, n=1, u=5e-6, R=10.0, T=20)
+    out = ref.simulate_run(params, seed=2)
+    assert out
+    assert out[0].N == 20
+    assert out[0].t == -(params.T // 2)
+
+
+def test_generation_summary_reports_tracking_fields_for_initial_population():
+    params = ref.Track1Parameters(K=5000, N0=20, n=2, u=5e-6, R=10.0, T=20)
+    out = ref.simulate_run(params, seed=2)
+    first = out[0]
+    assert first.mean_allele_value == pytest_approx(0.0)
+    assert first.mean_genotype_value == pytest_approx(0.0)
+    assert first.target_value == pytest_approx(-0.5)
+    assert first.mean_tracking_gap == pytest_approx(0.5)
+    assert first.paper_M == pytest_approx(0.05)
+    assert first.expected_mutations_current_N == pytest_approx(0.0004)
+
+
+def test_generation_summary_reports_realized_mutations_for_high_u():
+    params = ref.Track1Parameters(K=5000, N0=20, n=1, u=0.5, R=10.0, T=20)
+    out = ref.simulate_run(params, seed=2)
+    first = out[0]
+    assert first.realized_mutation_count >= 0
+    assert 0.0 <= first.realized_mutation_rate_per_allele <= 1.0
+
+
+def pytest_approx(value: float, tol: float = 1e-9):
+    class Approx:
+        def __eq__(self, other):
+            return abs(other - value) <= tol
+
+    return Approx()