FEAT-1b: add first test project (xUnit) for Inzuchtkoeffizient
GerbilManager.Tests (net10.0), added to slnx. Reference pedigrees verified against textbook F: parent-offspring 0.25, full sibs 0.25, half sibs 0.125, first cousins 0.0625, unknown 0, plus deep multi-path (0.375) and generationsAvailable checks. 8/8 green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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GerbilManager.Tests/GerbilManager.Tests.csproj
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GerbilManager.Tests/GerbilManager.Tests.csproj
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<Project Sdk="Microsoft.NET.Sdk">
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<PropertyGroup>
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<TargetFramework>net10.0</TargetFramework>
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<ImplicitUsings>enable</ImplicitUsings>
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<Nullable>enable</Nullable>
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<IsPackable>false</IsPackable>
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</PropertyGroup>
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<ItemGroup>
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<PackageReference Include="coverlet.collector" Version="6.0.4" />
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<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.14.1" />
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<PackageReference Include="xunit" Version="2.9.3" />
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<PackageReference Include="xunit.runner.visualstudio" Version="3.1.4" />
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</ItemGroup>
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<ItemGroup>
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<Using Include="Xunit" />
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</ItemGroup>
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<ItemGroup>
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<ProjectReference Include="..\GerbilManagerWebAPI\GerbilManagerWebAPI.csproj" />
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</ItemGroup>
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</Project>
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GerbilManager.Tests/PedigreeCalculatorTests.cs
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GerbilManager.Tests/PedigreeCalculatorTests.cs
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using GerbilManagerWebAPI.Genetics;
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namespace GerbilManager.Tests
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{
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/// <summary>
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/// Exact-math checks for the inbreeding coefficient (Inzuchtkoeffizient) against
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/// the textbook reference values for canonical pedigrees.
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/// </summary>
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public class PedigreeCalculatorTests
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{
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private const int Precision = 10;
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[Fact]
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public void UnknownAncestry_IsZero()
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{
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var ped = new PedigreeBuilder();
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var lonely = ped.Add("Lonely");
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var calc = ped.Build();
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var result = calc.ForIndividual(lonely);
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Assert.Equal(0.0, result.Coefficient, Precision);
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Assert.Equal(0, result.GenerationsAvailable);
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Assert.Empty(result.CommonAncestors);
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}
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[Fact]
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public void OneKnownParent_IsZero()
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{
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var ped = new PedigreeBuilder();
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var sire = ped.Add("Sire");
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var calc = ped.Build();
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// Only one parent known → no inbreeding can be established.
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var result = calc.ForOffspringOf(sire, null);
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Assert.Equal(0.0, result.Coefficient, Precision);
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Assert.Empty(result.CommonAncestors);
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}
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[Fact]
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public void ParentOffspring_IsQuarter()
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{
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// Z is the offspring of P mated with its own daughter C.
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var ped = new PedigreeBuilder();
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var p = ped.Add("P");
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var mate = ped.Add("Mate");
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var c = ped.AddChild("C", p, mate);
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var calc = ped.Build();
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var result = calc.ForOffspringOf(p, c);
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Assert.Equal(0.25, result.Coefficient, Precision);
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Assert.Equal(25.0, result.Percent, Precision);
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var ancestor = Assert.Single(result.CommonAncestors);
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Assert.Equal(p, ancestor.Id);
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Assert.Equal(0.25, ancestor.Contribution, Precision);
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}
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[Fact]
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public void FullSiblings_IsQuarter()
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{
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// Parents S and D are full siblings (both children of GF and GM).
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var ped = new PedigreeBuilder();
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var gf = ped.Add("GF");
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var gm = ped.Add("GM");
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var s = ped.AddChild("S", gf, gm);
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var d = ped.AddChild("D", gf, gm);
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var calc = ped.Build();
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var result = calc.ForOffspringOf(s, d);
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Assert.Equal(0.25, result.Coefficient, Precision);
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Assert.Equal(2, result.CommonAncestors.Count);
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Assert.All(result.CommonAncestors, a => Assert.Equal(0.125, a.Contribution, Precision));
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}
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[Fact]
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public void HalfSiblings_IsEighth()
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{
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// Parents S and D share only GF (other parents unrelated).
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var ped = new PedigreeBuilder();
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var gf = ped.Add("GF");
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var x = ped.Add("X");
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var y = ped.Add("Y");
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var s = ped.AddChild("S", gf, x);
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var d = ped.AddChild("D", gf, y);
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var calc = ped.Build();
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var result = calc.ForOffspringOf(s, d);
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Assert.Equal(0.125, result.Coefficient, Precision);
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var ancestor = Assert.Single(result.CommonAncestors);
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Assert.Equal(gf, ancestor.Id);
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Assert.Equal(0.125, ancestor.Contribution, Precision);
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}
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[Fact]
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public void FirstCousins_IsSixteenth()
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{
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// Parents S and D are first cousins: their respective parents A1 and B1
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// are full siblings (children of GF and GM).
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var ped = new PedigreeBuilder();
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var gf = ped.Add("GF");
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var gm = ped.Add("GM");
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var a1 = ped.AddChild("A1", gf, gm);
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var b1 = ped.AddChild("B1", gf, gm);
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var x = ped.Add("X");
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var y = ped.Add("Y");
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var s = ped.AddChild("S", a1, x);
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var d = ped.AddChild("D", b1, y);
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var calc = ped.Build();
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var result = calc.ForOffspringOf(s, d);
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Assert.Equal(0.0625, result.Coefficient, Precision);
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Assert.Equal(2, result.CommonAncestors.Count);
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Assert.All(result.CommonAncestors, a => Assert.Equal(0.03125, a.Contribution, Precision));
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}
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[Fact]
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public void DeepCommonAncestry_SumsAllDisjointPaths()
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{
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// Full siblings S and D whose shared parents (GF, GM) are themselves full
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// siblings (children of GGF, GGM). GF and GM are NOT inbred (their parents
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// are unrelated founders, so F_GF = F_GM = 0), but the great-grandparents
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// are reached by additional disjoint paths:
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// GF + GM: 2 * (1/2)^3 = 0.25
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// GGF: 2 * (1/2)^5 = 0.0625 (S-GF-GGF / D-GM-GGF and swap)
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// GGM: 2 * (1/2)^5 = 0.0625
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// ---------------------------------------------
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// F = 0.375 (verified against the recursive kinship method)
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var ped = new PedigreeBuilder();
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var ggf = ped.Add("GGF");
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var ggm = ped.Add("GGM");
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var gf = ped.AddChild("GF", ggf, ggm);
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var gm = ped.AddChild("GM", ggf, ggm);
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var s = ped.AddChild("S", gf, gm);
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var d = ped.AddChild("D", gf, gm);
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var calc = ped.Build();
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var result = calc.ForOffspringOf(s, d);
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Assert.Equal(0.375, result.Coefficient, Precision);
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// Four common ancestors: GF, GM, GGF, GGM.
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Assert.Equal(4, result.CommonAncestors.Count);
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Assert.Equal(0.375, result.CommonAncestors.Sum(a => a.Contribution), Precision);
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// Deepest known generation above the offspring: S/D (1) → GF/GM (2) → GGF/GGM (3).
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Assert.Equal(3, result.GenerationsAvailable);
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}
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[Fact]
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public void GenerationsAvailable_CountsDeepestKnownGeneration()
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{
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var ped = new PedigreeBuilder();
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var gf = ped.Add("GF");
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var gm = ped.Add("GM");
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var father = ped.AddChild("Father", gf, gm);
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var mother = ped.Add("Mother");
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var calc = ped.Build();
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var result = calc.ForOffspringOf(father, mother);
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// Father side reaches grandparents (2 generations); mother side reaches 1.
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Assert.Equal(2, result.GenerationsAvailable);
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}
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/// <summary>Small helper to assemble a pedigree of plain GUIDs for the calculator.</summary>
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private sealed class PedigreeBuilder
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{
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private readonly Dictionary<Guid, (Guid? Father, Guid? Mother)> _parents = new();
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private readonly Dictionary<Guid, string> _names = new();
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public Guid Add(string name)
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{
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var id = Guid.NewGuid();
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_parents[id] = (null, null);
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_names[id] = name;
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return id;
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}
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public Guid AddChild(string name, Guid father, Guid mother)
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{
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var id = Add(name);
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_parents[id] = (father, mother);
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return id;
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}
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public PedigreeCalculator Build() => new(_parents, _names);
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}
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}
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}
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@@ -1,5 +1,6 @@
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<Solution>
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<Project Path="GerbilManager.AppHost/GerbilManager.AppHost.csproj" />
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<Project Path="GerbilManager.ServiceDefaults/GerbilManager.ServiceDefaults.csproj" />
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<Project Path="GerbilManager.Tests/GerbilManager.Tests.csproj" />
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<Project Path="GerbilManagerWebAPI/GerbilManagerWebAPI.csproj" />
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</Solution>
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