@graphty/algorithms 2.1.2 → 2.2.0

package/dist/src/clustering/k-core-legacy.js

@@ -0,0 +1,191 @@
+/**
+ * The k-core decomposition as it was before `kCoreDecomposition` delegated to
+ * `indexed.kCoreDecomposition`, unchanged. The facade in `k-core.ts` still calls it for the graphs
+ * the port cannot answer the same way (a directed graph, a self-loop, a NaN weight, ids spelled alike), its facade
+ * test uses it as the oracle, and the other k-core functions read the graph through
+ * `graphToAdjacencySet`.
+ */
+/**
+ * Convert Graph to adjacency set representation
+ * @param graph - The input graph to convert
+ * @returns Map of node IDs to sets of neighbor node IDs
+ */
+export function graphToAdjacencySet(graph) {
+    const adjacency = new Map();
+    // Initialize all nodes
+    for (const node of graph.nodes()) {
+        adjacency.set(String(node.id), new Set());
+    }
+    // Add edges
+    for (const edge of graph.edges()) {
+        const source = String(edge.source);
+        const target = String(edge.target);
+        const sourceSet = adjacency.get(source);
+        if (sourceSet) {
+            sourceSet.add(target);
+        }
+        // For undirected graphs, add reverse edge
+        if (!graph.isDirected) {
+            const targetSet = adjacency.get(target);
+            if (targetSet) {
+                targetSet.add(source);
+            }
+        }
+    }
+    return adjacency;
+}
+/**
+ * Internal implementation of K-Core decomposition algorithm
+ * @param graph - Adjacency map representation of the graph
+ * @returns K-core decomposition result with cores, coreness values, and maximum core number
+ */
+function kCoreDecompositionImpl(graph) {
+    if (graph.size === 0) {
+        return { cores: new Map(), coreness: new Map(), maxCore: 0 };
+    }
+    const n = graph.size;
+    const nodes = Array.from(graph.keys());
+    const nodeToIndex = new Map();
+    nodes.forEach((node, i) => nodeToIndex.set(node, i));
+    // Initialize data structures
+    const degree = new Array(n).fill(0);
+    const pos = new Array(n).fill(0);
+    const vert = new Array(n).fill(0);
+    const coreness = new Map();
+    // Initialize coreness for all nodes to 0
+    for (let i = 0; i < n; i++) {
+        const node = nodes[i];
+        if (node !== undefined) {
+            coreness.set(node, 0);
+        }
+    }
+    // Compute initial degrees
+    let maxDegree = 0;
+    for (let i = 0; i < n; i++) {
+        const node = nodes[i];
+        if (!node) {
+            continue;
+        }
+        const neighbors = graph.get(node);
+        const nodeSize = neighbors ? neighbors.size : 0;
+        degree[i] = nodeSize;
+        maxDegree = Math.max(maxDegree, nodeSize);
+    }
+    // Count nodes of each degree
+    const bin = new Array(maxDegree + 1).fill(0);
+    for (let i = 0; i < n; i++) {
+        const deg = degree[i];
+        if (deg !== undefined && deg >= 0 && deg < bin.length) {
+            const currentCount = bin[deg];
+            if (currentCount !== undefined) {
+                bin[deg] = currentCount + 1;
+            }
+        }
+    }
+    // Starting position of each degree in sorted array
+    let start = 0;
+    for (let d = 0; d <= maxDegree; d++) {
+        const temp = bin[d] ?? 0;
+        bin[d] = start;
+        start += temp;
+    }
+    // Sort nodes by degree
+    for (let i = 0; i < n; i++) {
+        const deg = degree[i];
+        if (deg !== undefined && deg >= 0 && deg < bin.length) {
+            const posIndex = bin[deg] ?? 0;
+            pos[i] = posIndex;
+            vert[posIndex] = i;
+            const currentBin = bin[deg];
+            if (currentBin !== undefined) {
+                bin[deg] = currentBin + 1;
+            }
+        }
+        else {
+            // If we can't properly place the node in vert, set its position to -1
+            // This shouldn't happen with our fixes, but just in case
+            pos[i] = -1;
+        }
+    }
+    // Recover starting positions
+    for (let d = maxDegree; d > 0; d--) {
+        bin[d] = bin[d - 1] ?? 0;
+    }
+    bin[0] = 0;
+    // Main algorithm
+    for (let i = 0; i < n; i++) {
+        const v = vert[i];
+        if (v === undefined) {
+            continue;
+        }
+        const node = nodes[v];
+        if (node === undefined) {
+            continue;
+        }
+        const degreeV = degree[v];
+        if (degreeV !== undefined) {
+            coreness.set(node, degreeV);
+        }
+        // Process neighbors
+        const neighbors = graph.get(node);
+        if (!neighbors) {
+            // Node has no neighbors, skip neighbor processing but coreness is already set
+            continue;
+        }
+        for (const neighbor of neighbors) {
+            const u = nodeToIndex.get(neighbor);
+            if (u === undefined) {
+                continue;
+            }
+            const degreeU = degree[u];
+            const degreeV = degree[v];
+            if (degreeU !== undefined && degreeV !== undefined && degreeU > degreeV) {
+                const du = degreeU;
+                const pu = pos[u];
+                const pw = bin[du] ?? 0;
+                const w = vert[pw];
+                if (u !== w && w !== undefined && pw < n && pu !== undefined) {
+                    // Swap u and w in the sorted order
+                    vert[pu] = w;
+                    vert[pw] = u;
+                    pos[u] = pw;
+                    pos[w] = pu;
+                }
+                const currentBin = bin[du];
+                if (currentBin !== undefined) {
+                    bin[du] = currentBin + 1;
+                }
+                degree[u] = degreeU - 1;
+            }
+        }
+    }
+    // Build cores map
+    const cores = new Map();
+    let maxCore = 0;
+    for (const [node, core] of coreness) {
+        if (!cores.has(core)) {
+            cores.set(core, new Set());
+        }
+        const coreSet = cores.get(core);
+        if (coreSet) {
+            coreSet.add(node);
+        }
+        maxCore = Math.max(maxCore, core);
+    }
+    return { cores, coreness, maxCore };
+}
+/**
+ * K-Core decomposition algorithm
+ * Finds all k-cores in the graph and assigns coreness values to nodes
+ * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
+ * @returns K-core decomposition results
+ *
+ * Time Complexity: O(V + E)
+ * Space Complexity: O(V)
+ */
+export function kCoreDecomposition(graph) {
+    // Convert Graph to adjacency set representation
+    const adjacencySet = graphToAdjacencySet(graph);
+    return kCoreDecompositionImpl(adjacencySet);
+}
+//# sourceMappingURL=k-core-legacy.js.map

package/dist/src/clustering/k-core-legacy.js.map

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package/dist/src/clustering/k-core.d.ts

@@ -4,13 +4,13 @@
  * Finds the k-core subgraph where each node has at least k neighbors
  * within the subgraph. Used for identifying cohesive groups and
  * understanding graph structure.
+ *
+ * `kCoreDecomposition` (and `getKCore` through it) delegates to `indexed.kCoreDecomposition` on an
+ * undirected graph; the result equals the pre-migration implementation in `k-core-legacy.ts`.
  */
 import type { Graph } from "../core/graph.js";
-export interface KCoreResult<T> {
-    cores: Map<number, Set<T>>;
-    coreness: Map<T, number>;
-    maxCore: number;
-}
+import { type KCoreResult } from "./k-core-legacy.js";
+export type { KCoreResult } from "./k-core-legacy.js";
 /**
  * Extract the k-core subgraph
  * Returns nodes that belong to k-core or higher
@@ -51,8 +51,9 @@ export declare function toUndirected<T>(directedGraph: Map<T, Map<T, number>>):
 /**
  * K-Core decomposition algorithm
  * Finds all k-cores in the graph and assigns coreness values to nodes
- * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
- * @returns K-core decomposition results
+ * @param graph - Undirected graph. A directed graph is peeled over out-neighbours only, as it
+ *   always was.
+ * @returns K-core decomposition results, keyed by `String(id)` in node order
  *
  * Time Complexity: O(V + E)
  * Space Complexity: O(V)

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package/dist/src/clustering/k-core.js

@@ -4,176 +4,13 @@
  * Finds the k-core subgraph where each node has at least k neighbors
  * within the subgraph. Used for identifying cohesive groups and
  * understanding graph structure.
+ *
+ * `kCoreDecomposition` (and `getKCore` through it) delegates to `indexed.kCoreDecomposition` on an
+ * undirected graph; the result equals the pre-migration implementation in `k-core-legacy.ts`.
  */
-/**
- * Convert Graph to adjacency set representation
- * @param graph - The input graph to convert
- * @returns Map of node IDs to sets of neighbor node IDs
- */
-function graphToAdjacencySet(graph) {
-    const adjacency = new Map();
-    // Initialize all nodes
-    for (const node of graph.nodes()) {
-        adjacency.set(String(node.id), new Set());
-    }
-    // Add edges
-    for (const edge of graph.edges()) {
-        const source = String(edge.source);
-        const target = String(edge.target);
-        const sourceSet = adjacency.get(source);
-        if (sourceSet) {
-            sourceSet.add(target);
-        }
-        // For undirected graphs, add reverse edge
-        if (!graph.isDirected) {
-            const targetSet = adjacency.get(target);
-            if (targetSet) {
-                targetSet.add(source);
-            }
-        }
-    }
-    return adjacency;
-}
-/**
- * Internal implementation of K-Core decomposition algorithm
- * @param graph - Adjacency map representation of the graph
- * @returns K-core decomposition result with cores, coreness values, and maximum core number
- */
-function kCoreDecompositionImpl(graph) {
-    if (graph.size === 0) {
-        return { cores: new Map(), coreness: new Map(), maxCore: 0 };
-    }
-    const n = graph.size;
-    const nodes = Array.from(graph.keys());
-    const nodeToIndex = new Map();
-    nodes.forEach((node, i) => nodeToIndex.set(node, i));
-    // Initialize data structures
-    const degree = new Array(n).fill(0);
-    const pos = new Array(n).fill(0);
-    const vert = new Array(n).fill(0);
-    const coreness = new Map();
-    // Initialize coreness for all nodes to 0
-    for (let i = 0; i < n; i++) {
-        const node = nodes[i];
-        if (node !== undefined) {
-            coreness.set(node, 0);
-        }
-    }
-    // Compute initial degrees
-    let maxDegree = 0;
-    for (let i = 0; i < n; i++) {
-        const node = nodes[i];
-        if (!node) {
-            continue;
-        }
-        const neighbors = graph.get(node);
-        const nodeSize = neighbors ? neighbors.size : 0;
-        degree[i] = nodeSize;
-        maxDegree = Math.max(maxDegree, nodeSize);
-    }
-    // Count nodes of each degree
-    const bin = new Array(maxDegree + 1).fill(0);
-    for (let i = 0; i < n; i++) {
-        const deg = degree[i];
-        if (deg !== undefined && deg >= 0 && deg < bin.length) {
-            const currentCount = bin[deg];
-            if (currentCount !== undefined) {
-                bin[deg] = currentCount + 1;
-            }
-        }
-    }
-    // Starting position of each degree in sorted array
-    let start = 0;
-    for (let d = 0; d <= maxDegree; d++) {
-        const temp = bin[d] ?? 0;
-        bin[d] = start;
-        start += temp;
-    }
-    // Sort nodes by degree
-    for (let i = 0; i < n; i++) {
-        const deg = degree[i];
-        if (deg !== undefined && deg >= 0 && deg < bin.length) {
-            const posIndex = bin[deg] ?? 0;
-            pos[i] = posIndex;
-            vert[posIndex] = i;
-            const currentBin = bin[deg];
-            if (currentBin !== undefined) {
-                bin[deg] = currentBin + 1;
-            }
-        }
-        else {
-            // If we can't properly place the node in vert, set its position to -1
-            // This shouldn't happen with our fixes, but just in case
-            pos[i] = -1;
-        }
-    }
-    // Recover starting positions
-    for (let d = maxDegree; d > 0; d--) {
-        bin[d] = bin[d - 1] ?? 0;
-    }
-    bin[0] = 0;
-    // Main algorithm
-    for (let i = 0; i < n; i++) {
-        const v = vert[i];
-        if (v === undefined) {
-            continue;
-        }
-        const node = nodes[v];
-        if (node === undefined) {
-            continue;
-        }
-        const degreeV = degree[v];
-        if (degreeV !== undefined) {
-            coreness.set(node, degreeV);
-        }
-        // Process neighbors
-        const neighbors = graph.get(node);
-        if (!neighbors) {
-            // Node has no neighbors, skip neighbor processing but coreness is already set
-            continue;
-        }
-        for (const neighbor of neighbors) {
-            const u = nodeToIndex.get(neighbor);
-            if (u === undefined) {
-                continue;
-            }
-            const degreeU = degree[u];
-            const degreeV = degree[v];
-            if (degreeU !== undefined && degreeV !== undefined && degreeU > degreeV) {
-                const du = degreeU;
-                const pu = pos[u];
-                const pw = bin[du] ?? 0;
-                const w = vert[pw];
-                if (u !== w && w !== undefined && pw < n && pu !== undefined) {
-                    // Swap u and w in the sorted order
-                    vert[pu] = w;
-                    vert[pw] = u;
-                    pos[u] = pw;
-                    pos[w] = pu;
-                }
-                const currentBin = bin[du];
-                if (currentBin !== undefined) {
-                    bin[du] = currentBin + 1;
-                }
-                degree[u] = degreeU - 1;
-            }
-        }
-    }
-    // Build cores map
-    const cores = new Map();
-    let maxCore = 0;
-    for (const [node, core] of coreness) {
-        if (!cores.has(core)) {
-            cores.set(core, new Set());
-        }
-        const coreSet = cores.get(core);
-        if (coreSet) {
-            coreSet.add(node);
-        }
-        maxCore = Math.max(maxCore, core);
-    }
-    return { cores, coreness, maxCore };
-}
+import { kCoreDecomposition as indexedKCoreDecomposition } from "../indexed/k-core.js";
+import { needsLegacyCode, toSnapshot } from "../indexed/to-snapshot.js";
+import { graphToAdjacencySet, kCoreDecomposition as legacyKCoreDecomposition, } from "./k-core-legacy.js";
 /**
  * Extract the k-core subgraph
  * Returns nodes that belong to k-core or higher
@@ -401,15 +238,37 @@ export function toUndirected(directedGraph) {
 /**
  * K-Core decomposition algorithm
  * Finds all k-cores in the graph and assigns coreness values to nodes
- * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
- * @returns K-core decomposition results
+ * @param graph - Undirected graph. A directed graph is peeled over out-neighbours only, as it
+ *   always was.
+ * @returns K-core decomposition results, keyed by `String(id)` in node order
  *
  * Time Complexity: O(V + E)
  * Space Complexity: O(V)
  */
 export function kCoreDecomposition(graph) {
-    // Convert Graph to adjacency set representation
-    const adjacencySet = graphToAdjacencySet(graph);
-    return kCoreDecompositionImpl(adjacencySet);
+    // The port refuses a directed graph and does not count a self-loop as a neighbour, where the old
+    // code counts one towards the node's degree; ids spelled alike are one key of the result.
+    if (graph.isDirected || needsLegacyCode(graph)) {
+        return legacyKCoreDecomposition(graph);
+    }
+    const s = toSnapshot(graph);
+    if (s.flags.hasSelfLoops) {
+        return legacyKCoreDecomposition(graph);
+    }
+    const { coreness, maxCore } = indexedKCoreDecomposition(s);
+    const byNode = new Map();
+    const cores = new Map();
+    for (let u = 0; u < s.nodeCount; u++) {
+        const id = String(s.ids.idOf(u));
+        const k = coreness[u];
+        byNode.set(id, k);
+        let members = cores.get(k);
+        if (members === undefined) {
+            members = new Set();
+            cores.set(k, members);
+        }
+        members.add(id);
+    }
+    return { cores, coreness: byNode, maxCore };
 }
 //# sourceMappingURL=k-core.js.map

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package/dist/src/clustering/mcl-legacy.d.ts

@@ -0,0 +1,42 @@
+import type { Graph } from "../core/graph.js";
+import type { NodeId } from "../types/index.js";
+/**
+ * Markov Clustering (MCL) algorithm implementation
+ *
+ * MCL simulates flow in graphs and finds clusters based on the notion that
+ * random walks stay within clusters and rarely move between clusters.
+ * The algorithm alternates between expansion (matrix squaring) and
+ * inflation (element-wise powering and normalization).
+ *
+ * Time complexity: O(V³) per iteration
+ * Space complexity: O(V²)
+ */
+export interface MCLOptions {
+    expansion?: number;
+    inflation?: number;
+    maxIterations?: number;
+    tolerance?: number;
+    pruningThreshold?: number;
+    selfLoops?: boolean;
+}
+export interface MCLResult {
+    communities: NodeId[][];
+    attractors: Set<NodeId>;
+    iterations: number;
+    converged: boolean;
+}
+/**
+ * Perform Markov Clustering on a graph
+ * @param graph - The input graph to cluster
+ * @param options - MCL algorithm options (expansion, inflation, iterations, etc.)
+ * @returns MCL clustering result with communities, attractors, and convergence info
+ */
+export declare function markovClustering(graph: Graph, options?: MCLOptions): MCLResult;
+/**
+ * Calculate modularity of MCL clustering result
+ * @param graph - The original graph that was clustered
+ * @param communities - Array of communities (each community is an array of node IDs)
+ * @returns Modularity score between -0.5 and 1.0
+ */
+export declare function calculateMCLModularity(graph: Graph, communities: NodeId[][]): number;
+//# sourceMappingURL=mcl-legacy.d.ts.map

package/dist/src/clustering/mcl-legacy.d.ts.map

@@ -0,0 +1 @@
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