@optave/codegraph 3.3.1 → 3.4.1

package/dist/graph/algorithms/leiden/cpm.d.ts

@@ -0,0 +1,28 @@
+/**
+ * CPM (Constant Potts Model) quality functions.
+ * Vendored from ngraph.leiden (MIT) — no external dependencies.
+ */
+/**
+ * Minimal view of a partition needed by CPM quality functions.
+ */
+export interface PartitionView {
+    readonly communityCount: number;
+    nodeCommunity: Int32Array;
+    readonly communityInternalEdgeWeight: Float64Array;
+    readonly communityTotalSize: Float64Array;
+    getOutEdgeWeightToCommunity(c: number): number;
+    getInEdgeWeightFromCommunity(c: number): number;
+    getNeighborEdgeWeightToCommunity(c: number): number;
+}
+/**
+ * Minimal view of a graph needed by CPM quality functions.
+ */
+export interface GraphView {
+    n: number;
+    directed: boolean;
+    selfLoop: Float64Array;
+    size: Float64Array;
+}
+export declare function diffCPM(part: PartitionView, g: GraphView, v: number, c: number, gamma?: number): number;
+export declare function qualityCPM(part: PartitionView, _g: GraphView, gamma?: number): number;
+//# sourceMappingURL=cpm.d.ts.map

package/dist/graph/algorithms/leiden/cpm.d.ts.map

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package/dist/graph/algorithms/leiden/cpm.js

@@ -0,0 +1,48 @@
+/**
+ * CPM (Constant Potts Model) quality functions.
+ * Vendored from ngraph.leiden (MIT) — no external dependencies.
+ */
+// Typed array safe-access helper (see adapter.ts for rationale)
+function fget(a, i) {
+    return a[i];
+}
+function iget(a, i) {
+    return a[i];
+}
+export function diffCPM(part, g, v, c, gamma = 1.0) {
+    const oldC = iget(part.nodeCommunity, v);
+    if (c === oldC)
+        return 0;
+    let w_old;
+    let w_new;
+    let selfCorrection = 0;
+    if (g.directed) {
+        w_old =
+            (part.getOutEdgeWeightToCommunity(oldC) || 0) +
+                (part.getInEdgeWeightFromCommunity(oldC) || 0);
+        w_new =
+            c < g.n
+                ? (part.getOutEdgeWeightToCommunity(c) || 0) + (part.getInEdgeWeightFromCommunity(c) || 0)
+                : 0;
+        // Self-loop weight appears in both out and in arrays for oldC,
+        // making w_old include 2x selfLoop. Correct to match moveNodeToCommunity.
+        selfCorrection = 2 * (fget(g.selfLoop, v) || 0);
+    }
+    else {
+        w_old = part.getNeighborEdgeWeightToCommunity(oldC) || 0;
+        w_new = c < g.n ? part.getNeighborEdgeWeightToCommunity(c) || 0 : 0;
+    }
+    const s_v = fget(g.size, v) || 1;
+    const S_old = fget(part.communityTotalSize, oldC) || 0;
+    const S_new = c < part.communityTotalSize.length ? fget(part.communityTotalSize, c) : 0;
+    return w_new - w_old + selfCorrection - gamma * s_v * (S_new - S_old + s_v);
+}
+export function qualityCPM(part, _g, gamma = 1.0) {
+    let sum = 0;
+    for (let c = 0; c < part.communityCount; c++) {
+        const S = fget(part.communityTotalSize, c) || 0;
+        sum += fget(part.communityInternalEdgeWeight, c) - (gamma * (S * (S - 1))) / 2;
+    }
+    return sum;
+}
+//# sourceMappingURL=cpm.js.map

package/dist/graph/algorithms/leiden/cpm.js.map

@@ -0,0 +1 @@
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package/dist/graph/algorithms/leiden/index.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Leiden community detection — vendored from ngraph.leiden (MIT).
+ * Adapted to work directly with CodeGraph (no external graph library dependency).
+ *
+ * Original: https://github.com/anvaka/ngraph.leiden
+ * License:  MIT — see LICENSE in this directory.
+ */
+import type { CodeGraph } from '../../model.js';
+import type { LeidenOptions } from './optimiser.js';
+export type { LeidenOptions } from './optimiser.js';
+export type DetectClustersOptions = LeidenOptions;
+export interface DetectClustersResult {
+    getClass(nodeId: string | number): number | undefined;
+    getCommunities(): Map<number, string[]>;
+    quality(): number;
+    toJSON(): {
+        membership: Record<string, number>;
+        meta: {
+            levels: number;
+            quality: number;
+            options: DetectClustersOptions;
+        };
+    };
+}
+/**
+ * Detect communities in a CodeGraph using the Leiden algorithm.
+ *
+ * Note on `quality()`: For modularity, `quality()` always evaluates at gamma=1.0
+ * (standard Newman-Girvan modularity) regardless of the `resolution` used during
+ * optimization. This makes quality values comparable across runs with different
+ * resolutions. For CPM, `quality()` uses the caller-specified resolution since gamma
+ * is intrinsic to the CPM metric. Do not use modularity `quality()` values to
+ * compare partitions found at different resolutions — they reflect Q at gamma=1.0,
+ * not the objective that was actually optimized.
+ */
+export declare function detectClusters(graph: CodeGraph, options?: DetectClustersOptions): DetectClustersResult;
+//# sourceMappingURL=index.d.ts.map

package/dist/graph/algorithms/leiden/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/graph/algorithms/leiden/index.js

@@ -0,0 +1,142 @@
+/**
+ * Leiden community detection — vendored from ngraph.leiden (MIT).
+ * Adapted to work directly with CodeGraph (no external graph library dependency).
+ *
+ * Original: https://github.com/anvaka/ngraph.leiden
+ * License:  MIT — see LICENSE in this directory.
+ */
+import { qualityCPM } from './cpm.js';
+import { qualityModularity } from './modularity.js';
+import { runLouvainUndirectedModularity } from './optimiser.js';
+// Typed array safe-access helpers (see adapter.ts for rationale)
+function fget(a, i) {
+    return a[i];
+}
+function iget(a, i) {
+    return a[i];
+}
+/**
+ * Detect communities in a CodeGraph using the Leiden algorithm.
+ *
+ * Note on `quality()`: For modularity, `quality()` always evaluates at gamma=1.0
+ * (standard Newman-Girvan modularity) regardless of the `resolution` used during
+ * optimization. This makes quality values comparable across runs with different
+ * resolutions. For CPM, `quality()` uses the caller-specified resolution since gamma
+ * is intrinsic to the CPM metric. Do not use modularity `quality()` values to
+ * compare partitions found at different resolutions — they reflect Q at gamma=1.0,
+ * not the objective that was actually optimized.
+ */
+export function detectClusters(graph, options = {}) {
+    const { levels, originalToCurrent, originalNodeIds, baseGraph } = runLouvainUndirectedModularity(graph, options);
+    const idToClass = new Map();
+    for (let i = 0; i < originalNodeIds.length; i++) {
+        const comm = iget(originalToCurrent, i);
+        idToClass.set(originalNodeIds[i], comm);
+    }
+    return {
+        getClass(nodeId) {
+            return idToClass.get(String(nodeId));
+        },
+        getCommunities() {
+            const out = new Map();
+            for (const [id, c] of idToClass) {
+                if (!out.has(c))
+                    out.set(c, []);
+                out.get(c).push(id);
+            }
+            return out;
+        },
+        quality() {
+            // Compute quality on the original (level-0) graph with the final
+            // partition mapped back. Computing on the last coarse-level graph
+            // produces inflated values because the modularity null model depends
+            // on the degree distribution, which changes after coarsening.
+            const part = buildOriginalPartition(baseGraph, originalToCurrent);
+            const q = (options.quality || 'modularity').toLowerCase();
+            if (q === 'cpm') {
+                const gamma = typeof options.resolution === 'number' ? options.resolution : 1.0;
+                return qualityCPM(part, baseGraph, gamma);
+            }
+            // Always evaluate at gamma=1.0 for standard Newman-Girvan modularity
+            return qualityModularity(part, baseGraph, 1.0);
+        },
+        toJSON() {
+            const membershipObj = {};
+            for (const [id, c] of idToClass)
+                membershipObj[id] = c;
+            return {
+                membership: membershipObj,
+                meta: { levels: levels.length, quality: this.quality(), options },
+            };
+        },
+    };
+}
+function buildOriginalPartition(g, communityMap) {
+    const n = g.n;
+    let maxC = 0;
+    for (let i = 0; i < n; i++) {
+        const ci = iget(communityMap, i);
+        if (ci > maxC)
+            maxC = ci;
+    }
+    const cc = maxC + 1;
+    const nodeCommunity = communityMap;
+    const internalWeight = new Float64Array(cc);
+    const totalStr = new Float64Array(cc);
+    const totalOutStr = new Float64Array(cc);
+    const totalInStr = new Float64Array(cc);
+    const totalSize = new Float64Array(cc);
+    for (let i = 0; i < n; i++) {
+        const c = iget(communityMap, i);
+        totalSize[c] = fget(totalSize, c) + fget(g.size, i);
+        if (g.directed) {
+            totalOutStr[c] = fget(totalOutStr, c) + fget(g.strengthOut, i);
+            totalInStr[c] = fget(totalInStr, c) + fget(g.strengthIn, i);
+        }
+        else {
+            totalStr[c] = fget(totalStr, c) + fget(g.strengthOut, i);
+        }
+        if (fget(g.selfLoop, i))
+            internalWeight[c] = fget(internalWeight, c) + fget(g.selfLoop, i);
+    }
+    if (g.directed) {
+        for (let i = 0; i < n; i++) {
+            const ci = iget(communityMap, i);
+            const list = g.outEdges[i];
+            for (let k = 0; k < list.length; k++) {
+                const { to: j, w } = list[k];
+                if (i === j)
+                    continue;
+                if (ci === iget(communityMap, j))
+                    internalWeight[ci] = fget(internalWeight, ci) + w;
+            }
+        }
+    }
+    else {
+        for (let i = 0; i < n; i++) {
+            const ci = iget(communityMap, i);
+            const list = g.outEdges[i];
+            for (let k = 0; k < list.length; k++) {
+                const { to: j, w } = list[k];
+                if (j <= i)
+                    continue;
+                if (ci === iget(communityMap, j))
+                    internalWeight[ci] = fget(internalWeight, ci) + w;
+            }
+        }
+    }
+    return {
+        communityCount: cc,
+        nodeCommunity,
+        communityInternalEdgeWeight: internalWeight,
+        communityTotalStrength: totalStr,
+        communityTotalOutStrength: totalOutStr,
+        communityTotalInStrength: totalInStr,
+        communityTotalSize: totalSize,
+        // Stubs — quality functions only read the aggregate arrays, not these methods
+        getNeighborEdgeWeightToCommunity: () => 0,
+        getOutEdgeWeightToCommunity: () => 0,
+        getInEdgeWeightFromCommunity: () => 0,
+    };
+}
+//# sourceMappingURL=index.js.map

package/dist/graph/algorithms/leiden/index.js.map

@@ -0,0 +1 @@
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package/dist/graph/algorithms/leiden/modularity.d.ts

@@ -0,0 +1,33 @@
+/**
+ * Modularity quality functions.
+ * Vendored from ngraph.leiden (MIT) — no external dependencies.
+ */
+/**
+ * Minimal view of a partition needed by modularity quality functions.
+ */
+export interface PartitionView {
+    readonly communityCount: number;
+    nodeCommunity: Int32Array;
+    readonly communityInternalEdgeWeight: Float64Array;
+    readonly communityTotalStrength: Float64Array;
+    readonly communityTotalOutStrength: Float64Array;
+    readonly communityTotalInStrength: Float64Array;
+    getNeighborEdgeWeightToCommunity(c: number): number;
+    getOutEdgeWeightToCommunity(c: number): number;
+    getInEdgeWeightFromCommunity(c: number): number;
+}
+/**
+ * Minimal view of a graph needed by modularity quality functions.
+ */
+export interface GraphView {
+    n: number;
+    directed: boolean;
+    totalWeight: number;
+    strengthOut: Float64Array;
+    strengthIn: Float64Array;
+    selfLoop: Float64Array;
+}
+export declare function diffModularity(part: PartitionView, g: GraphView, v: number, c: number, gamma?: number): number;
+export declare function diffModularityDirected(part: PartitionView, g: GraphView, v: number, c: number, gamma?: number): number;
+export declare function qualityModularity(part: PartitionView, g: GraphView, gamma?: number): number;
+//# sourceMappingURL=modularity.d.ts.map

package/dist/graph/algorithms/leiden/modularity.d.ts.map

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package/dist/graph/algorithms/leiden/modularity.js

@@ -0,0 +1,80 @@
+/**
+ * Modularity quality functions.
+ * Vendored from ngraph.leiden (MIT) — no external dependencies.
+ */
+// Typed array safe-access helper (see adapter.ts for rationale)
+function fget(a, i) {
+    return a[i];
+}
+function iget(a, i) {
+    return a[i];
+}
+export function diffModularity(part, g, v, c, gamma = 1.0) {
+    if (g.directed)
+        return diffModularityDirected(part, g, v, c, gamma);
+    const oldC = iget(part.nodeCommunity, v);
+    if (c === oldC)
+        return 0;
+    const k_v = fget(g.strengthOut, v);
+    const m2 = g.totalWeight;
+    const k_v_in_new = part.getNeighborEdgeWeightToCommunity(c) || 0;
+    const k_v_in_old = part.getNeighborEdgeWeightToCommunity(oldC) || 0;
+    const wTot_new = c < part.communityTotalStrength.length ? fget(part.communityTotalStrength, c) : 0;
+    const wTot_old = fget(part.communityTotalStrength, oldC);
+    const gain_remove = -(k_v_in_old / m2 - (gamma * (k_v * wTot_old)) / (m2 * m2));
+    const gain_add = k_v_in_new / m2 - (gamma * (k_v * wTot_new)) / (m2 * m2);
+    return gain_remove + gain_add;
+}
+export function diffModularityDirected(part, g, v, c, gamma = 1.0) {
+    const oldC = iget(part.nodeCommunity, v);
+    if (c === oldC)
+        return 0;
+    const m = g.totalWeight;
+    const k_out = fget(g.strengthOut, v);
+    const k_in = fget(g.strengthIn, v);
+    const w_new_in = c < g.n ? part.getInEdgeWeightFromCommunity(c) || 0 : 0;
+    const w_new_out = c < g.n ? part.getOutEdgeWeightToCommunity(c) || 0 : 0;
+    const w_old_in = part.getInEdgeWeightFromCommunity(oldC) || 0;
+    const w_old_out = part.getOutEdgeWeightToCommunity(oldC) || 0;
+    const T_new = c < part.communityTotalInStrength.length ? fget(part.communityTotalInStrength, c) : 0;
+    const F_new = c < part.communityTotalOutStrength.length ? fget(part.communityTotalOutStrength, c) : 0;
+    const T_old = fget(part.communityTotalInStrength, oldC);
+    const F_old = fget(part.communityTotalOutStrength, oldC);
+    // Self-loop correction: the self-loop edge (v->v) appears in both
+    // outEdgeWeightToCommunity[oldC] and inEdgeWeightFromCommunity[oldC],
+    // making w_old include 2x selfLoop. Since the self-loop moves with the
+    // node, add it back to match moveNodeToCommunity's directed accounting.
+    const selfW = fget(g.selfLoop, v) || 0;
+    const deltaInternal = (w_new_in + w_new_out - w_old_in - w_old_out + 2 * selfW) / m;
+    // The full delta(F*T) expansion includes a constant 2*k_out*k_in term that
+    // doesn't depend on the target community but does affect the move-vs-stay
+    // decision. Without it, coarse-level merges can appear profitable when
+    // they actually decrease quality.
+    const deltaExpected = (gamma * (k_out * (T_new - T_old) + k_in * (F_new - F_old) + 2 * k_out * k_in)) / (m * m);
+    return deltaInternal - deltaExpected;
+}
+export function qualityModularity(part, g, gamma = 1.0) {
+    const m2 = g.totalWeight;
+    let sum = 0;
+    if (g.directed) {
+        for (let c = 0; c < part.communityCount; c++)
+            sum +=
+                fget(part.communityInternalEdgeWeight, c) / m2 -
+                    (gamma *
+                        (fget(part.communityTotalOutStrength, c) * fget(part.communityTotalInStrength, c))) /
+                        (m2 * m2);
+    }
+    else {
+        // communityInternalEdgeWeight counts each undirected edge once (j > i),
+        // but m2 = totalWeight = 2m (sum of symmetrized degrees). The standard
+        // Newman-Girvan formula is Q = sum_c [2*L_c/(2m) - gamma*(d_c/(2m))^2], so
+        // we multiply lc by 2 to match.
+        for (let c = 0; c < part.communityCount; c++) {
+            const lc = fget(part.communityInternalEdgeWeight, c);
+            const dc = fget(part.communityTotalStrength, c);
+            sum += (2 * lc) / m2 - (gamma * (dc * dc)) / (m2 * m2);
+        }
+    }
+    return sum;
+}
+//# sourceMappingURL=modularity.js.map

package/dist/graph/algorithms/leiden/modularity.js.map

@@ -0,0 +1 @@
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package/dist/graph/algorithms/leiden/optimiser.d.ts

@@ -0,0 +1,62 @@
+/**
+ * Core Leiden/Louvain community detection optimiser.
+ * Vendored from ngraph.leiden (MIT) — adapted to use CodeGraph + local RNG.
+ */
+import { CodeGraph } from '../../model.js';
+import type { GraphAdapter, GraphAdapterOptions } from './adapter.js';
+import type { Partition } from './partition.js';
+declare const CandidateStrategy: {
+    readonly Neighbors: 0;
+    readonly All: 1;
+    readonly RandomAny: 2;
+    readonly RandomNeighbor: 3;
+};
+type CandidateStrategyCode = (typeof CandidateStrategy)[keyof typeof CandidateStrategy];
+export interface LeidenOptions {
+    directed?: boolean;
+    randomSeed?: number;
+    maxLevels?: number;
+    maxLocalPasses?: number;
+    allowNewCommunity?: boolean;
+    candidateStrategy?: 'neighbors' | 'all' | 'random' | 'random-neighbor';
+    quality?: string;
+    resolution?: number;
+    refine?: boolean;
+    preserveLabels?: boolean | Map<number, number>;
+    maxCommunitySize?: number;
+    refinementTheta?: number;
+    fixedNodes?: Set<string> | string[];
+    linkWeight?: GraphAdapterOptions['linkWeight'];
+    nodeSize?: GraphAdapterOptions['nodeSize'];
+    baseNodeIds?: string[];
+}
+export interface NormalizedOptions {
+    directed: boolean;
+    randomSeed: number;
+    maxLevels: number;
+    maxLocalPasses: number;
+    allowNewCommunity: boolean;
+    candidateStrategyCode: CandidateStrategyCode;
+    quality: string;
+    resolution: number;
+    refine: boolean;
+    preserveLabels: boolean | Map<number, number> | undefined;
+    maxCommunitySize: number;
+    refinementTheta: number;
+    fixedNodes: Set<string> | string[] | undefined;
+}
+export interface LevelEntry {
+    graph: GraphAdapter;
+    partition: Partition;
+}
+export interface LouvainResult {
+    graph: GraphAdapter;
+    partition: Partition;
+    levels: LevelEntry[];
+    originalToCurrent: Int32Array;
+    originalNodeIds: string[];
+    baseGraph: GraphAdapter;
+}
+export declare function runLouvainUndirectedModularity(graph: CodeGraph, optionsInput?: LeidenOptions): LouvainResult;
+export {};
+//# sourceMappingURL=optimiser.d.ts.map

package/dist/graph/algorithms/leiden/optimiser.d.ts.map

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