ppef 1.0.1 → 1.1.0

package/dist/robustness/__tests__/perturbations.unit.test.js

@@ -0,0 +1,284 @@
+/**
+ * Unit tests for Perturbations
+ *
+ * Tests perturbation application including:
+ * - Edge removal perturbation
+ * - Seed shift perturbation
+ * - Node removal perturbation
+ * - Weight noise perturbation
+ */
+import { describe, it } from "node:test";
+import { strict as assert } from "node:assert";
+import { PERTURBATIONS, createPerturbation, edgeRemovalPerturbation, getPerturbation, nodeRemovalPerturbation, seedShiftPerturbation, weightNoisePerturbation, } from "../perturbations.js";
+/**
+ * Create a mock evaluation case for testing.
+ */
+const createMockCase = (caseId) => ({
+    caseId,
+    name: `Test Case ${caseId}`,
+    caseClass: "test-class",
+    version: "1.0.0",
+    tags: ["baseline"],
+    inputs: {
+        summary: {
+            nodes: 100,
+            edges: 500,
+            seeds: ["node1", "node2"],
+        },
+        artefacts: [
+            {
+                type: "graph",
+                uri: `/data/${caseId}.graph.json`,
+                hash: "abc123",
+                metadata: { format: "json" },
+            },
+        ],
+    },
+});
+describe("perturbations", () => {
+    describe("edgeRemovalPerturbation", () => {
+        it("should preserve required fields (caseId, inputs)", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.caseId);
+            assert.ok(perturbed.inputs);
+            assert.ok(perturbed.inputs.summary);
+            assert.ok(perturbed.inputs.artefacts);
+        });
+        it("should generate a unique caseId for perturbed case", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.notStrictEqual(perturbed.caseId, mockCase.caseId);
+            assert.strictEqual(perturbed.caseId.length, 16); // SHA-256 slice
+        });
+        it("should add perturbation metadata to summary", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.summary);
+            const summary = perturbed.inputs.summary;
+            assert.strictEqual(summary.perturbation, "edge-removal");
+            assert.strictEqual(summary.perturbationIntensity, 0.1);
+            assert.strictEqual(summary.perturbationSeed, 42);
+        });
+        it("should add perturbation metadata to artefacts", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.artefacts);
+            const artefacts = perturbed.inputs.artefacts;
+            assert.strictEqual(artefacts.length, 1);
+            assert.ok(artefacts[0].metadata);
+            const metadata = artefacts[0].metadata;
+            assert.strictEqual(metadata.perturbation, "edge-removal");
+            assert.strictEqual(metadata.perturbationIntensity, 0.1);
+            assert.strictEqual(metadata.perturbationSeed, 42);
+        });
+        it("should add perturbation tags", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.tags?.includes("perturbed"));
+            assert.ok(perturbed.tags?.includes("edge-removal"));
+            assert.ok(perturbed.tags?.includes("baseline")); // Original tag preserved
+        });
+        it("should update name with intensity percentage", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.name?.includes("10%"));
+            assert.ok(perturbed.name?.includes("edges removed"));
+        });
+        it("should preserve other inputs.summary fields", () => {
+            const mockCase = createMockCase("case-001");
+            const perturbed = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.summary);
+            const summary = perturbed.inputs.summary;
+            assert.strictEqual(summary.nodes, 100);
+            assert.strictEqual(summary.edges, 500);
+            assert.deepStrictEqual(summary.seeds, ["node1", "node2"]);
+        });
+    });
+    describe("seedShiftPerturbation", () => {
+        it("should preserve required fields (caseId, inputs)", () => {
+            const mockCase = createMockCase("case-002");
+            const perturbed = seedShiftPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.caseId);
+            assert.ok(perturbed.inputs);
+            assert.ok(perturbed.inputs.summary);
+        });
+        it("should generate a unique caseId for perturbed case", () => {
+            const mockCase = createMockCase("case-002");
+            const perturbed = seedShiftPerturbation.apply(mockCase, 42);
+            assert.notStrictEqual(perturbed.caseId, mockCase.caseId);
+            assert.strictEqual(perturbed.caseId.length, 16);
+        });
+        it("should add perturbation metadata to summary", () => {
+            const mockCase = createMockCase("case-002");
+            const perturbed = seedShiftPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.summary);
+            const summary = perturbed.inputs.summary;
+            assert.strictEqual(summary.perturbation, "seed-shift");
+            assert.strictEqual(summary.perturbationSeed, 42);
+        });
+        it("should add perturbation tags", () => {
+            const mockCase = createMockCase("case-002");
+            const perturbed = seedShiftPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.tags?.includes("perturbed"));
+            assert.ok(perturbed.tags?.includes("seed-shift"));
+        });
+        it("should update name with perturbation description", () => {
+            const mockCase = createMockCase("case-002");
+            const perturbed = seedShiftPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.name?.includes("seeds shifted"));
+        });
+    });
+    describe("nodeRemovalPerturbation", () => {
+        it("should preserve required fields (caseId, inputs)", () => {
+            const mockCase = createMockCase("case-003");
+            const perturbed = nodeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.caseId);
+            assert.ok(perturbed.inputs);
+            assert.ok(perturbed.inputs.summary);
+        });
+        it("should generate a unique caseId for perturbed case", () => {
+            const mockCase = createMockCase("case-003");
+            const perturbed = nodeRemovalPerturbation.apply(mockCase, 42);
+            assert.notStrictEqual(perturbed.caseId, mockCase.caseId);
+            assert.strictEqual(perturbed.caseId.length, 16);
+        });
+        it("should add perturbation metadata to summary", () => {
+            const mockCase = createMockCase("case-003");
+            const perturbed = nodeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.summary);
+            const summary = perturbed.inputs.summary;
+            assert.strictEqual(summary.perturbation, "node-removal");
+            assert.strictEqual(summary.perturbationIntensity, 0.05);
+            assert.strictEqual(summary.perturbationSeed, 42);
+        });
+        it("should add perturbation tags", () => {
+            const mockCase = createMockCase("case-003");
+            const perturbed = nodeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.tags?.includes("perturbed"));
+            assert.ok(perturbed.tags?.includes("node-removal"));
+        });
+        it("should update name with intensity percentage", () => {
+            const mockCase = createMockCase("case-003");
+            const perturbed = nodeRemovalPerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.name?.includes("5%"));
+            assert.ok(perturbed.name?.includes("nodes removed"));
+        });
+    });
+    describe("weightNoisePerturbation", () => {
+        it("should preserve required fields (caseId, inputs)", () => {
+            const mockCase = createMockCase("case-004");
+            const perturbed = weightNoisePerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.caseId);
+            assert.ok(perturbed.inputs);
+            assert.ok(perturbed.inputs.summary);
+        });
+        it("should generate a unique caseId for perturbed case", () => {
+            const mockCase = createMockCase("case-004");
+            const perturbed = weightNoisePerturbation.apply(mockCase, 42);
+            assert.notStrictEqual(perturbed.caseId, mockCase.caseId);
+            assert.strictEqual(perturbed.caseId.length, 16);
+        });
+        it("should add perturbation metadata to summary", () => {
+            const mockCase = createMockCase("case-004");
+            const perturbed = weightNoisePerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.inputs.summary);
+            const summary = perturbed.inputs.summary;
+            assert.strictEqual(summary.perturbation, "weight-noise");
+            assert.strictEqual(summary.perturbationIntensity, 0.1);
+            assert.strictEqual(summary.perturbationSeed, 42);
+        });
+        it("should add perturbation tags", () => {
+            const mockCase = createMockCase("case-004");
+            const perturbed = weightNoisePerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.tags?.includes("perturbed"));
+            assert.ok(perturbed.tags?.includes("weight-noise"));
+        });
+        it("should update name with intensity percentage", () => {
+            const mockCase = createMockCase("case-004");
+            const perturbed = weightNoisePerturbation.apply(mockCase, 42);
+            assert.ok(perturbed.name?.includes("10%"));
+            assert.ok(perturbed.name?.includes("weight noise"));
+        });
+    });
+    describe("PERTURBATIONS array", () => {
+        it("should contain all four built-in perturbations", () => {
+            assert.strictEqual(PERTURBATIONS.length, 4);
+            assert.ok(PERTURBATIONS.some((p) => p.id === "edge-removal"), "Should contain edge-removal");
+            assert.ok(PERTURBATIONS.some((p) => p.id === "seed-shift"), "Should contain seed-shift");
+            assert.ok(PERTURBATIONS.some((p) => p.id === "node-removal"), "Should contain node-removal");
+            assert.ok(PERTURBATIONS.some((p) => p.id === "weight-noise"), "Should contain weight-noise");
+        });
+    });
+    describe("getPerturbation", () => {
+        it("should return perturbation by id", () => {
+            const edgeRemoval = getPerturbation("edge-removal");
+            assert.ok(edgeRemoval);
+            assert.strictEqual(edgeRemoval.id, "edge-removal");
+        });
+        it("should return undefined for unknown id", () => {
+            const unknown = getPerturbation("unknown-perturbation");
+            assert.strictEqual(unknown, undefined);
+        });
+        it("should find all built-in perturbations by id", () => {
+            const ids = ["edge-removal", "seed-shift", "node-removal", "weight-noise"];
+            for (const id of ids) {
+                const perturbation = getPerturbation(id);
+                assert.ok(perturbation, `Should find perturbation with id: ${id}`);
+                assert.strictEqual(perturbation.id, id);
+            }
+        });
+    });
+    describe("createPerturbation", () => {
+        it("should create perturbation with custom intensity", () => {
+            const custom = createPerturbation({ type: "edge-removal", intensity: 0.25 });
+            assert.strictEqual(custom.id, "edge-removal");
+            assert.strictEqual(custom.intensity, 0.25);
+        });
+        it("should apply custom intensity to perturbed case", () => {
+            const mockCase = createMockCase("case-005");
+            const custom = createPerturbation({ type: "node-removal", intensity: 0.15 });
+            const perturbed = custom.apply(mockCase, 42);
+            assert.strictEqual(perturbed.inputs.summary?.perturbationIntensity, 0.15);
+            assert.ok(perturbed.name?.includes("15%"));
+        });
+        it("should throw error for unknown perturbation type", () => {
+            assert.throws(() => createPerturbation({
+                type: "unknown-type",
+                intensity: 0.1,
+            }), /Unknown perturbation type: unknown-type/);
+        });
+        it("should preserve name and description from base perturbation", () => {
+            const custom = createPerturbation({ type: "edge-removal", intensity: 0.2 });
+            assert.strictEqual(custom.name, "Edge Removal");
+            assert.strictEqual(custom.description, "Randomly remove a fraction of edges");
+        });
+        it("should preserve type from base perturbation", () => {
+            const custom = createPerturbation({ type: "weight-noise", intensity: 0.05 });
+            assert.strictEqual(custom.type, "noise");
+        });
+    });
+    describe("perturbation determinism", () => {
+        it("should produce same caseId for same inputs", () => {
+            const mockCase = createMockCase("case-006");
+            const perturbed1 = edgeRemovalPerturbation.apply(mockCase, 42);
+            const perturbed2 = edgeRemovalPerturbation.apply(mockCase, 42);
+            assert.strictEqual(perturbed1.caseId, perturbed2.caseId);
+        });
+        it("should produce different caseId for different seeds", () => {
+            const mockCase = createMockCase("case-007");
+            const perturbed1 = nodeRemovalPerturbation.apply(mockCase, 42);
+            const perturbed2 = nodeRemovalPerturbation.apply(mockCase, 100);
+            assert.notStrictEqual(perturbed1.caseId, perturbed2.caseId);
+        });
+        it("should produce different caseId for different intensities", () => {
+            const mockCase = createMockCase("case-008");
+            const custom1 = createPerturbation({ type: "edge-removal", intensity: 0.1 });
+            const custom2 = createPerturbation({ type: "edge-removal", intensity: 0.2 });
+            const perturbed1 = custom1.apply(mockCase, 42);
+            const perturbed2 = custom2.apply(mockCase, 42);
+            assert.notStrictEqual(perturbed1.caseId, perturbed2.caseId);
+        });
+    });
+});
+//# sourceMappingURL=perturbations.unit.test.js.map

package/dist/robustness/__tests__/perturbations.unit.test.js.map

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package/dist/statistical/__tests__/mann-whitney-u.unit.test.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Unit tests for Mann-Whitney U test and related statistical functions.
+ *
+ * Tests the non-parametric statistical test for comparing two independent samples.
+ */
+export {};
+//# sourceMappingURL=mann-whitney-u.unit.test.d.ts.map

package/dist/statistical/__tests__/mann-whitney-u.unit.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"mann-whitney-u.unit.test.d.ts","sourceRoot":"","sources":["../../../src/statistical/__tests__/mann-whitney-u.unit.test.ts"],"names":[],"mappings":"AAAA;;;;GAIG"}

package/dist/statistical/__tests__/mann-whitney-u.unit.test.js

@@ -0,0 +1,185 @@
+/**
+ * Unit tests for Mann-Whitney U test and related statistical functions.
+ *
+ * Tests the non-parametric statistical test for comparing two independent samples.
+ */
+import { describe, it } from "node:test";
+import { strict as assert } from "node:assert";
+import { normalCDF, mannWhitneyUTest, cohensD, confidenceInterval } from "../mann-whitney-u.js";
+describe("normalCDF", () => {
+    it("should return 0.5 for z = 0", () => {
+        const result = normalCDF(0);
+        assert.ok(Math.abs(result - 0.5) < 0.001);
+    });
+    it("should approach 1 for large positive z", () => {
+        const result = normalCDF(5);
+        assert.ok(result > 0.99);
+    });
+    it("should approach 0 for large negative z", () => {
+        const result = normalCDF(-5);
+        assert.ok(result < 0.01);
+    });
+    it("should be symmetric around 0", () => {
+        const z = 1.5;
+        const positive = normalCDF(z);
+        const negative = normalCDF(-z);
+        assert.ok(Math.abs(positive + negative - 1) < 0.001);
+    });
+    it("should handle negative z values", () => {
+        const result = normalCDF(-1);
+        assert.ok(result < 0.5);
+        assert.ok(result > 0.1);
+    });
+});
+describe("mannWhitneyUTest", () => {
+    it("should calculate U statistic for distinct samples", () => {
+        const sampleA = [1, 2, 3];
+        const sampleB = [4, 5, 6];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.ok(typeof result.u === "number");
+        assert.ok(result.u >= 0);
+        assert.ok(typeof result.pValue === "number");
+        assert.ok(typeof result.significant === "boolean");
+    });
+    it("should detect significant difference between distinct samples", () => {
+        const sampleA = [1, 1, 1, 1, 1];
+        const sampleB = [100, 100, 100, 100, 100];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.ok(result.pValue < 0.05);
+        assert.strictEqual(result.significant, true);
+    });
+    it("should not detect difference in similar samples", () => {
+        const sampleA = [5, 5, 5, 5, 5];
+        const sampleB = [5, 5, 5, 5, 5];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        // When samples are identical, p-value should be 1
+        assert.ok(result.pValue >= 0.95);
+        assert.strictEqual(result.significant, false);
+    });
+    it("should handle overlapping samples", () => {
+        const sampleA = [1, 2, 3, 4, 5];
+        const sampleB = [3, 4, 5, 6, 7];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.ok(result.pValue >= 0 && result.pValue <= 1);
+        assert.ok(typeof result.significant === "boolean");
+    });
+    it("should handle samples with ties", () => {
+        const sampleA = [1, 2, 2, 3];
+        const sampleB = [2, 3, 4, 5];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.ok(typeof result.u === "number");
+        assert.ok(result.pValue >= 0 && result.pValue <= 1);
+    });
+    it("should handle single-element samples", () => {
+        const sampleA = [5];
+        const sampleB = [10];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.ok(typeof result.u === "number");
+        assert.ok(typeof result.pValue === "number");
+    });
+    it("should handle empty sample A", () => {
+        const sampleA = [];
+        const sampleB = [1, 2, 3];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.strictEqual(result.u, 0);
+    });
+    it("should handle empty sample B", () => {
+        const sampleA = [1, 2, 3];
+        const sampleB = [];
+        const result = mannWhitneyUTest(sampleA, sampleB);
+        assert.strictEqual(result.u, 0);
+    });
+});
+describe("cohensD", () => {
+    it("should calculate effect size for distinct samples", () => {
+        const sampleA = [1, 2, 3, 4, 5];
+        const sampleB = [6, 7, 8, 9, 10];
+        const result = cohensD(sampleA, sampleB);
+        assert.ok(result > 0);
+        assert.ok(typeof result === "number");
+    });
+    it("should be zero for identical samples", () => {
+        const sampleA = [5, 5, 5, 5, 5];
+        const sampleB = [5, 5, 5, 5, 5];
+        const result = cohensD(sampleA, sampleB);
+        assert.strictEqual(result, 0);
+    });
+    it("should be symmetric", () => {
+        const sampleA = [1, 2, 3, 4, 5];
+        const sampleB = [10, 20, 30, 40, 50];
+        const d1 = cohensD(sampleA, sampleB);
+        const d2 = cohensD(sampleB, sampleA);
+        assert.ok(Math.abs(d1 - d2) < 0.001);
+    });
+    it("should handle large effect sizes", () => {
+        const sampleA = [1, 2, 1, 2, 1]; // Mean ~1.4, small variance
+        const sampleB = [100, 101, 100, 101, 100]; // Mean ~100.4, small variance
+        const result = cohensD(sampleA, sampleB);
+        assert.ok(result > 0.8); // Large effect due to separation of means
+    });
+    it("should handle small effect sizes", () => {
+        const sampleA = [10, 11, 12, 13, 14];
+        const sampleB = [12, 13, 14, 15, 16];
+        const result = cohensD(sampleA, sampleB);
+        assert.ok(result >= 0);
+        assert.ok(result < 2); // Should be reasonable
+    });
+    it("should handle samples with variance", () => {
+        const sampleA = [1, 2, 3, 4, 5];
+        const sampleB = [3, 4, 5, 6, 7];
+        const result = cohensD(sampleA, sampleB);
+        assert.ok(result >= 0);
+    });
+    it("should handle samples with same mean but different variance", () => {
+        const sampleA = [0, 10, 0, 10, 0, 10];
+        const sampleB = [4, 6, 4, 6, 4, 6];
+        // Both have mean 5
+        const meanA = sampleA.reduce((a, b) => a + b, 0) / sampleA.length;
+        const meanB = sampleB.reduce((a, b) => a + b, 0) / sampleB.length;
+        const result = cohensD(sampleA, sampleB);
+        assert.strictEqual(meanA, 5);
+        assert.strictEqual(meanB, 5);
+        assert.strictEqual(result, 0);
+    });
+});
+describe("confidenceInterval", () => {
+    it("should calculate interval for sample values", () => {
+        const values = [1, 2, 3, 4, 5];
+        const result = confidenceInterval(values);
+        assert.ok(typeof result.lower === "number");
+        assert.ok(typeof result.upper === "number");
+        assert.ok(result.lower < result.upper);
+    });
+    it("should be centered around mean", () => {
+        const values = [10, 20, 30, 40, 50];
+        const mean = values.reduce((a, b) => a + b, 0) / values.length;
+        const result = confidenceInterval(values);
+        const midpoint = (result.lower + result.upper) / 2;
+        assert.ok(Math.abs(midpoint - mean) < 0.1);
+    });
+    it("should handle identical values", () => {
+        const values = [5, 5, 5, 5, 5];
+        const result = confidenceInterval(values);
+        // With no variance, lower and upper should be same
+        assert.ok(Math.abs(result.lower - 5) < 0.01);
+        assert.ok(Math.abs(result.upper - 5) < 0.01);
+    });
+    it("should handle two values", () => {
+        const values = [0, 10];
+        const result = confidenceInterval(values);
+        assert.ok(result.lower < result.upper);
+        assert.ok(result.lower < 5);
+        assert.ok(result.upper > 5);
+    });
+    it("should have reasonable interval width for low variance", () => {
+        const values = [50, 51, 50, 51, 50, 51];
+        const mean = values.reduce((a, b) => a + b, 0) / values.length;
+        const result = confidenceInterval(values);
+        // Low variance should give narrow interval
+        const width = result.upper - result.lower;
+        assert.ok(width < 2); // Should be narrow
+        assert.ok(result.lower <= mean);
+        assert.ok(result.upper >= mean);
+    });
+});
+//# sourceMappingURL=mann-whitney-u.unit.test.js.map

package/dist/statistical/__tests__/mann-whitney-u.unit.test.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,11 +1,14 @@
 {
   "name": "ppef",
-  "version": "1.0.1",
+  "version": "1.1.0",
   "description": "Portable Programmatic Evaluation Framework - Claim-driven, deterministic evaluation for experiments",
   "type": "module",
   "main": "dist/index.cjs",
   "module": "dist/index.js",
   "types": "dist/index.d.ts",
+  "bin": {
+    "ppef": "./bin/ppef.mjs"
+  },
   "exports": {
     ".": {
       "types": "./dist/index.d.ts",
@@ -268,6 +271,7 @@
     "c8": "10.1.3",
     "eslint": "9.39.2",
     "eslint-config-prettier": "10.1.8",
+    "@eslint-community/eslint-plugin-eslint-comments": "4.6.0",
     "eslint-plugin-jsonc": "2.21.0",
     "eslint-plugin-prettier": "5.5.5",
     "husky": "9.1.7",
@@ -282,6 +286,9 @@
   "peerDependencies": {
     "typescript": "5.0.0"
   },
+  "dependencies": {
+    "commander": "^12.0.0"
+  },
   "publishConfig": {
     "provenance": true
   }