optave-codegraph 3.13.0

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

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+/**
+ * Core Leiden/Louvain community detection optimiser.
+ * Vendored from ngraph.leiden (MIT) — adapted to use CodeGraph + local RNG.
+ */
+import { CodeGraph } from '../../model.js';
+import { makeGraphAdapter } from './adapter.js';
+import { diffCPM } from './cpm.js';
+import { diffModularity } from './modularity.js';
+import { makePartition } from './partition.js';
+import { createRng } from './rng.js';
+// Mirrored in DEFAULTS.community (src/infrastructure/config.js) for user override
+// via .codegraphrc.json. Callers (e.g. louvain.ts) can pass overrides through options.
+const DEFAULT_MAX_LEVELS = 50;
+const DEFAULT_MAX_LOCAL_PASSES = 20;
+const GAIN_EPSILON = 1e-12;
+const CandidateStrategy = {
+    Neighbors: 0,
+    All: 1,
+    RandomAny: 2,
+    RandomNeighbor: 3,
+};
+export function runLouvainUndirectedModularity(graph, optionsInput = {}) {
+    const options = normalizeOptions(optionsInput);
+    const rngSource = createRng(options.randomSeed);
+    const random = () => rngSource.nextDouble();
+    const baseGraphAdapter = makeGraphAdapter(graph, {
+        directed: options.directed,
+        ...optionsInput,
+    });
+    const origN = baseGraphAdapter.n;
+    const originalToCurrent = new Int32Array(origN);
+    for (let i = 0; i < origN; i++)
+        originalToCurrent[i] = i;
+    const fixedNodeMask = buildFixedNodeMask(baseGraphAdapter, options.fixedNodes);
+    const levels = [];
+    let currentGraph = graph;
+    for (let level = 0; level < options.maxLevels; level++) {
+        const graphAdapter = level === 0
+            ? baseGraphAdapter
+            : makeGraphAdapter(currentGraph, { directed: options.directed, ...optionsInput });
+        const levelOutcome = runLevel(graphAdapter, options, random, level === 0 ? fixedNodeMask : null);
+        levels.push({ graph: graphAdapter, partition: levelOutcome.effectivePartition });
+        applyFineToCoarseMapping(originalToCurrent, levelOutcome.effectivePartition.nodeCommunity);
+        if (levelOutcome.terminate)
+            break;
+        currentGraph = buildCoarseGraph(graphAdapter, levelOutcome.effectivePartition);
+    }
+    const last = levels[levels.length - 1];
+    return {
+        graph: last.graph,
+        partition: last.partition,
+        levels,
+        originalToCurrent,
+        originalNodeIds: baseGraphAdapter.nodeIds,
+        baseGraph: baseGraphAdapter,
+    };
+}
+/**
+ * Build a fixed-node mask aligned with the base graph adapter's node indices.
+ * Returns null when no fixed nodes are configured.
+ */
+function buildFixedNodeMask(baseGraphAdapter, fixedNodes) {
+    if (!fixedNodes)
+        return null;
+    const mask = new Uint8Array(baseGraphAdapter.n);
+    const asSet = fixedNodes instanceof Set ? fixedNodes : new Set(fixedNodes);
+    for (const id of asSet) {
+        const idx = baseGraphAdapter.idToIndex.get(String(id));
+        if (idx != null)
+            mask[idx] = 1;
+    }
+    return mask;
+}
+/**
+ * Run one level of the Louvain/Leiden pipeline: greedy local-move phase,
+ * optional Leiden refinement, and a termination check. Returns the
+ * partition that feeds the next coarse graph plus a `terminate` flag set
+ * when no further coarsening is possible.
+ */
+function runLevel(graphAdapter, options, random, fixedNodeMask) {
+    const partition = makePartition(graphAdapter);
+    partition.graph = graphAdapter;
+    partition.initializeAggregates();
+    runLocalMovePhase(graphAdapter, partition, options, random, fixedNodeMask);
+    renumberCommunities(partition, options.preserveLabels);
+    let effectivePartition = partition;
+    if (options.refine) {
+        const refined = refineWithinCoarseCommunities(graphAdapter, partition, random, options, fixedNodeMask);
+        // Post-refinement: split any disconnected communities into their
+        // connected components. This is the cheap O(V+E) alternative to
+        // checking gamma-connectedness on every candidate during refinement.
+        // A disconnected community violates even basic connectivity, so
+        // splitting is always correct.
+        splitDisconnectedCommunities(graphAdapter, refined);
+        renumberCommunities(refined, options.preserveLabels);
+        effectivePartition = refined;
+    }
+    // Terminate when no further coarsening is possible. Check both the
+    // move-phase partition (did the greedy phase find merges?) and the
+    // effective partition that feeds buildCoarseGraph (would coarsening
+    // actually reduce the graph?). When refine is enabled the refined
+    // partition starts from singletons and may have more communities than
+    // the move phase found, so checking only effectivePartition would
+    // cause premature termination.
+    const terminate = partition.communityCount === graphAdapter.n &&
+        effectivePartition.communityCount === graphAdapter.n;
+    return { effectivePartition, terminate };
+}
+/**
+ * Greedy local-move phase: iterate randomly over nodes, moving each to the
+ * best community among the candidate set. Loops until no improvement or
+ * `maxLocalPasses` is reached.
+ */
+function runLocalMovePhase(graphAdapter, partition, options, random, fixedNodeMask) {
+    const order = new Int32Array(graphAdapter.n);
+    for (let i = 0; i < graphAdapter.n; i++)
+        order[i] = i;
+    const strategyCode = options.candidateStrategyCode;
+    let improved = true;
+    let localPasses = 0;
+    while (improved) {
+        improved = false;
+        localPasses++;
+        shuffleArrayInPlace(order, random);
+        for (let idx = 0; idx < order.length; idx++) {
+            const nodeIndex = order[idx];
+            if (fixedNodeMask?.[nodeIndex])
+                continue;
+            const candidateCount = partition.accumulateNeighborCommunityEdgeWeights(nodeIndex);
+            const { bestCommunityId, bestGain } = findBestCommunityMove(partition, graphAdapter, nodeIndex, candidateCount, strategyCode, options, random);
+            if (bestCommunityId !== partition.nodeCommunity[nodeIndex] && bestGain > GAIN_EPSILON) {
+                partition.moveNodeToCommunity(nodeIndex, bestCommunityId);
+                improved = true;
+            }
+        }
+        if (localPasses >= options.maxLocalPasses)
+            break;
+    }
+}
+/**
+ * Compose the running `originalToCurrent` mapping with this level's
+ * fine→coarse community labels, in place.
+ */
+function applyFineToCoarseMapping(originalToCurrent, fineToCoarse) {
+    for (let i = 0; i < originalToCurrent.length; i++) {
+        originalToCurrent[i] = fineToCoarse[originalToCurrent[i]];
+    }
+}
+/**
+ * Evaluate all candidate communities for a node and return the best move.
+ * Encapsulates the four candidate-selection strategies (All, RandomAny,
+ * RandomNeighbor, Neighbors) and the optional new-community probe.
+ */
+function findBestCommunityMove(partition, graphAdapter, nodeIndex, candidateCount, strategyCode, options, random) {
+    let bestCommunityId = partition.nodeCommunity[nodeIndex];
+    let bestGain = 0;
+    const maxCommunitySize = options.maxCommunitySize;
+    const evaluateCandidate = (communityId) => {
+        if (communityId === partition.nodeCommunity[nodeIndex])
+            return;
+        if (maxCommunitySize < Infinity &&
+            partition.getCommunityTotalSize(communityId) + graphAdapter.size[nodeIndex] >
+                maxCommunitySize)
+            return;
+        const gain = computeQualityGain(partition, nodeIndex, communityId, options);
+        if (gain > bestGain) {
+            bestGain = gain;
+            bestCommunityId = communityId;
+        }
+    };
+    if (strategyCode === CandidateStrategy.All) {
+        for (let communityId = 0; communityId < partition.communityCount; communityId++) {
+            evaluateCandidate(communityId);
+        }
+    }
+    else if (strategyCode === CandidateStrategy.RandomAny) {
+        const tries = Math.min(10, Math.max(1, partition.communityCount));
+        for (let trialIndex = 0; trialIndex < tries; trialIndex++) {
+            evaluateCandidate((random() * partition.communityCount) | 0);
+        }
+    }
+    else if (strategyCode === CandidateStrategy.RandomNeighbor) {
+        const tries = Math.min(10, Math.max(1, candidateCount));
+        for (let trialIndex = 0; trialIndex < tries; trialIndex++) {
+            evaluateCandidate(partition.getCandidateCommunityAt((random() * candidateCount) | 0));
+        }
+    }
+    else {
+        for (let trialIndex = 0; trialIndex < candidateCount; trialIndex++) {
+            evaluateCandidate(partition.getCandidateCommunityAt(trialIndex));
+        }
+    }
+    if (options.allowNewCommunity) {
+        const newCommunityId = partition.communityCount;
+        const gain = computeQualityGain(partition, nodeIndex, newCommunityId, options);
+        if (gain > bestGain) {
+            bestGain = gain;
+            bestCommunityId = newCommunityId;
+        }
+    }
+    return { bestCommunityId, bestGain };
+}
+/**
+ * Run a BFS on the subgraph induced by `inCommunity` starting from `start`.
+ * Returns the list of visited nodes. Works on both directed (weak connectivity
+ * via both outEdges and inEdges) and undirected graphs.
+ */
+function bfsComponent(g, start, inCommunity, visited) {
+    const queue = [start];
+    visited[start] = 1;
+    let head = 0;
+    while (head < queue.length) {
+        const v = queue[head++];
+        const out = g.outEdges[v];
+        for (let k = 0; k < out.length; k++) {
+            const w = out[k].to;
+            if (inCommunity[w] && !visited[w]) {
+                visited[w] = 1;
+                queue.push(w);
+            }
+        }
+        if (g.directed) {
+            const inc = g.inEdges[v];
+            for (let k = 0; k < inc.length; k++) {
+                const w = inc[k].from;
+                if (inCommunity[w] && !visited[w]) {
+                    visited[w] = 1;
+                    queue.push(w);
+                }
+            }
+        }
+    }
+    return queue;
+}
+// Build a coarse graph where each community becomes a single node.
+// Self-loops (g.selfLoop[]) don't need separate handling here because they
+// are already present in g.outEdges (directed path keeps them in both arrays).
+// When the coarse graph is fed back to makeGraphAdapter at the next level,
+// the adapter re-detects cu===cu edges as self-loops and populates selfLoop[].
+function buildCoarseGraph(g, p) {
+    const coarse = new CodeGraph({ directed: g.directed });
+    for (let c = 0; c < p.communityCount; c++) {
+        coarse.addNode(String(c), { size: p.communityTotalSize[c] });
+    }
+    const acc = new Map();
+    for (let i = 0; i < g.n; i++) {
+        const cu = p.nodeCommunity[i];
+        const list = g.outEdges[i];
+        for (let k = 0; k < list.length; k++) {
+            const j = list[k].to;
+            const w = list[k].w;
+            const cv = p.nodeCommunity[j];
+            // Undirected: each non-self edge (i,j) appears in both outEdges[i] and
+            // outEdges[j]. For intra-community edges (cu===cv), skip the reverse to
+            // avoid inflating the coarse self-loop weight by 2x.
+            if (!g.directed && cu === cv && j < i)
+                continue;
+            const key = `${cu}:${cv}`;
+            acc.set(key, (acc.get(key) || 0) + w);
+        }
+    }
+    for (const [key, w] of acc.entries()) {
+        const parts = key.split(':');
+        coarse.addEdge(parts[0], parts[1], { weight: w });
+    }
+    return coarse;
+}
+/**
+ * Collect eligible candidate communities for node `v` during refinement.
+ * A candidate must: (a) be in the same macro-community, (b) respect the size
+ * limit, and (c) produce a positive quality gain above GAIN_EPSILON.
+ * Returns the number of collected candidates written into `scratch`.
+ */
+function collectRefinementCandidates(p, g, v, touchedCount, macroV, commMacro, maxSize, opts, scratch) {
+    let candLen = 0;
+    for (let t = 0; t < touchedCount; t++) {
+        const c = p.getCandidateCommunityAt(t);
+        if (c === p.nodeCommunity[v])
+            continue;
+        if (commMacro[c] !== macroV)
+            continue;
+        if (maxSize < Infinity) {
+            const nextSize = p.getCommunityTotalSize(c) + g.size[v];
+            if (nextSize > maxSize)
+                continue;
+        }
+        const gain = computeQualityGain(p, v, c, opts);
+        if (gain > GAIN_EPSILON) {
+            scratch.candC[candLen] = c;
+            scratch.candGain[candLen] = gain;
+            candLen++;
+        }
+    }
+    return candLen;
+}
+/**
+ * Boltzmann probabilistic selection from collected candidates (Algorithm 3).
+ * Returns the chosen community ID, or -1 if the node should stay as singleton.
+ *
+ * p(v, C) is proportional to exp(deltaH / theta), with the "stay as singleton"
+ * option (deltaH = 0) included. For numerical stability, the max gain is
+ * subtracted before exponentiation.
+ */
+function boltzmannSelectCandidate(candLen, theta, rng, scratch) {
+    let maxGain = 0;
+    for (let i = 0; i < candLen; i++) {
+        if (scratch.candGain[i] > maxGain)
+            maxGain = scratch.candGain[i];
+    }
+    // "Stay as singleton" weight: exp((0 - maxGain) / theta)
+    const stayWeight = Math.exp((0 - maxGain) / theta);
+    let totalWeight = stayWeight;
+    for (let i = 0; i < candLen; i++) {
+        scratch.candWeight[i] = Math.exp((scratch.candGain[i] - maxGain) / theta);
+        totalWeight += scratch.candWeight[i];
+    }
+    const r = rng() * totalWeight;
+    if (r < stayWeight)
+        return -1; // node stays as singleton
+    let cumulative = stayWeight;
+    for (let i = 0; i < candLen; i++) {
+        cumulative += scratch.candWeight[i];
+        if (r < cumulative)
+            return scratch.candC[i];
+    }
+    return scratch.candC[candLen - 1]; // fallback
+}
+/**
+ * True Leiden refinement phase (Algorithm 3, Traag et al. 2019).
+ *
+ * Key properties that distinguish this from Louvain-style refinement:
+ *
+ * 1. Singleton start — each node begins in its own community.
+ * 2. Singleton guard — only nodes still in singleton communities are
+ *    considered for merging. Once a node joins a non-singleton community
+ *    it is locked for the remainder of the pass. This prevents oscillation
+ *    and is essential for the gamma-connectedness guarantee.
+ * 3. Single pass — one randomized sweep through all nodes, not an
+ *    iterative loop until convergence (that would be Louvain behavior).
+ * 4. Probabilistic selection — candidate communities are sampled from
+ *    a Boltzmann distribution p(v, C) proportional to exp(deltaH / theta),
+ *    with the "stay as singleton" option (deltaH = 0) included in the
+ *    distribution. This means a node may probabilistically choose to remain
+ *    alone even when positive-gain merges exist.
+ *
+ * theta (refinementTheta) controls temperature: lower = more deterministic
+ * (approaches greedy), higher = more exploratory. Determinism is preserved
+ * via the seeded PRNG — same seed produces the same assignments.
+ */
+function refineWithinCoarseCommunities(g, basePart, rng, opts, fixedMask0) {
+    const p = makePartition(g);
+    p.initializeAggregates();
+    p.graph = g;
+    const macro = basePart.nodeCommunity;
+    const commMacro = new Int32Array(p.communityCount);
+    for (let i = 0; i < p.communityCount; i++)
+        commMacro[i] = macro[i];
+    const theta = typeof opts.refinementTheta === 'number' ? opts.refinementTheta : 1.0;
+    if (theta <= 0)
+        throw new RangeError(`refinementTheta must be > 0 (got ${theta})`);
+    // Single pass in random order (Algorithm 3, step 2).
+    const order = new Int32Array(g.n);
+    for (let i = 0; i < g.n; i++)
+        order[i] = i;
+    shuffleArrayInPlace(order, rng);
+    // Pre-allocate flat arrays for candidate collection to avoid per-node GC pressure.
+    const scratch = {
+        candC: new Int32Array(g.n),
+        candGain: new Float64Array(g.n),
+        candWeight: new Float64Array(g.n),
+    };
+    const maxSize = Number.isFinite(opts.maxCommunitySize) ? opts.maxCommunitySize : Infinity;
+    for (let idx = 0; idx < order.length; idx++) {
+        const v = order[idx];
+        if (fixedMask0?.[v])
+            continue;
+        // Singleton guard: only move nodes still alone in their community.
+        if (p.getCommunityNodeCount(p.nodeCommunity[v]) > 1)
+            continue;
+        const macroV = macro[v];
+        const touchedCount = p.accumulateNeighborCommunityEdgeWeights(v);
+        const candLen = collectRefinementCandidates(p, g, v, touchedCount, macroV, commMacro, maxSize, opts, scratch);
+        if (candLen === 0)
+            continue;
+        const chosenC = boltzmannSelectCandidate(candLen, theta, rng, scratch);
+        if (chosenC >= 0)
+            p.moveNodeToCommunity(v, chosenC);
+    }
+    return p;
+}
+/**
+ * Post-refinement connectivity check. For each community, run a BFS on
+ * the subgraph induced by its members (using the adapter's outEdges).
+ * If a community has multiple connected components, assign secondary
+ * components to new community IDs, then reinitialize aggregates once.
+ *
+ * O(V+E) total since communities partition V.
+ *
+ * This replaces the per-candidate gamma-connectedness check from the paper
+ * with a cheaper post-step that catches the most important violation
+ * (disconnected subcommunities).
+ */
+function splitDisconnectedCommunities(g, partition) {
+    const n = g.n;
+    const nc = partition.nodeCommunity;
+    const members = partition.getCommunityMembers();
+    let nextC = partition.communityCount;
+    let didSplit = false;
+    const visited = new Uint8Array(n);
+    const inCommunity = new Uint8Array(n);
+    for (let c = 0; c < members.length; c++) {
+        const nodes = members[c];
+        if (nodes.length <= 1)
+            continue;
+        for (let i = 0; i < nodes.length; i++)
+            inCommunity[nodes[i]] = 1;
+        let componentCount = 0;
+        for (let i = 0; i < nodes.length; i++) {
+            const start = nodes[i];
+            if (visited[start])
+                continue;
+            componentCount++;
+            const component = bfsComponent(g, start, inCommunity, visited);
+            if (componentCount > 1) {
+                // Secondary component — assign new community ID directly.
+                const newC = nextC++;
+                for (let q = 0; q < component.length; q++)
+                    nc[component[q]] = newC;
+                didSplit = true;
+            }
+        }
+        for (let i = 0; i < nodes.length; i++) {
+            inCommunity[nodes[i]] = 0;
+            visited[nodes[i]] = 0;
+        }
+    }
+    if (didSplit) {
+        // Grow the partition's typed arrays to accommodate new community IDs,
+        // then recompute all aggregates from the updated nodeCommunity array.
+        partition.resizeCommunities(nextC);
+        partition.initializeAggregates();
+    }
+}
+function computeQualityGain(partition, v, c, opts) {
+    if (!partition.graph) {
+        throw new Error('partition.graph must be set before computeQualityGain');
+    }
+    const quality = (opts.quality || 'modularity').toLowerCase();
+    const gamma = typeof opts.resolution === 'number' ? opts.resolution : 1.0;
+    if (quality === 'cpm') {
+        return diffCPM(partition, partition.graph, v, c, gamma);
+    }
+    // diffModularity dispatches to diffModularityDirected internally when g.directed is true
+    return diffModularity(partition, partition.graph, v, c, gamma);
+}
+function shuffleArrayInPlace(arr, rng = Math.random) {
+    for (let i = arr.length - 1; i > 0; i--) {
+        const j = Math.floor(rng() * (i + 1));
+        const t = arr[i];
+        arr[i] = arr[j];
+        arr[j] = t;
+    }
+    return arr;
+}
+function resolveCandidateStrategy(options) {
+    const val = options.candidateStrategy;
+    if (typeof val !== 'string')
+        return CandidateStrategy.Neighbors;
+    switch (val) {
+        case 'neighbors':
+            return CandidateStrategy.Neighbors;
+        case 'all':
+            return CandidateStrategy.All;
+        case 'random':
+            return CandidateStrategy.RandomAny;
+        case 'random-neighbor':
+            return CandidateStrategy.RandomNeighbor;
+        default:
+            return CandidateStrategy.Neighbors;
+    }
+}
+function normalizeOptions(options = {}) {
+    const directed = !!options.directed;
+    const randomSeed = Number.isFinite(options.randomSeed)
+        ? options.randomSeed
+        : 42;
+    const maxLevels = Number.isFinite(options.maxLevels)
+        ? options.maxLevels
+        : DEFAULT_MAX_LEVELS;
+    const maxLocalPasses = Number.isFinite(options.maxLocalPasses)
+        ? options.maxLocalPasses
+        : DEFAULT_MAX_LOCAL_PASSES;
+    const allowNewCommunity = !!options.allowNewCommunity;
+    const candidateStrategyCode = resolveCandidateStrategy(options);
+    const quality = (options.quality || 'modularity').toLowerCase();
+    const resolution = typeof options.resolution === 'number' ? options.resolution : 1.0;
+    const refine = options.refine !== false;
+    const preserveLabels = options.preserveLabels;
+    const maxCommunitySize = Number.isFinite(options.maxCommunitySize)
+        ? options.maxCommunitySize
+        : Infinity;
+    const refinementTheta = typeof options.refinementTheta === 'number' ? options.refinementTheta : 1.0;
+    return {
+        directed,
+        randomSeed,
+        maxLevels,
+        maxLocalPasses,
+        allowNewCommunity,
+        candidateStrategyCode,
+        quality,
+        resolution,
+        refine,
+        preserveLabels,
+        maxCommunitySize,
+        refinementTheta,
+        fixedNodes: options.fixedNodes,
+    };
+}
+function renumberCommunities(partition, preserveLabels) {
+    if (preserveLabels && preserveLabels instanceof Map) {
+        partition.compactCommunityIds({ preserveMap: preserveLabels });
+    }
+    else if (preserveLabels === true) {
+        partition.compactCommunityIds({ keepOldOrder: true });
+    }
+    else {
+        partition.compactCommunityIds();
+    }
+}
+//# sourceMappingURL=optimiser.js.map

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

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

@@ -0,0 +1,44 @@
+/**
+ * Mutable community assignment with per-community aggregates.
+ * Vendored from ngraph.leiden (MIT) — no external dependencies.
+ *
+ * Maintains per-community totals and per-move scratch accumulators so we can
+ * compute modularity/CPM gains in O(neighborhood) time without rescanning the
+ * whole graph after each move.
+ */
+import type { GraphAdapter } from './adapter.js';
+export interface CompactOptions {
+    keepOldOrder?: boolean;
+    preserveMap?: Map<number, number>;
+}
+export interface Partition {
+    n: number;
+    readonly communityCount: number;
+    nodeCommunity: Int32Array;
+    readonly communityTotalSize: Float64Array;
+    readonly communityNodeCount: Int32Array;
+    readonly communityInternalEdgeWeight: Float64Array;
+    readonly communityTotalStrength: Float64Array;
+    readonly communityTotalOutStrength: Float64Array;
+    readonly communityTotalInStrength: Float64Array;
+    resizeCommunities(newCount: number): void;
+    initializeAggregates(): void;
+    accumulateNeighborCommunityEdgeWeights(v: number): number;
+    getCandidateCommunityCount(): number;
+    getCandidateCommunityAt(i: number): number;
+    getNeighborEdgeWeightToCommunity(c: number): number;
+    getOutEdgeWeightToCommunity(c: number): number;
+    getInEdgeWeightFromCommunity(c: number): number;
+    deltaModularityUndirected(v: number, newC: number, gamma?: number): number;
+    deltaModularityDirected(v: number, newC: number, gamma?: number): number;
+    deltaCPM(v: number, newC: number, gamma?: number): number;
+    moveNodeToCommunity(v: number, newC: number): boolean;
+    compactCommunityIds(opts?: CompactOptions): void;
+    getCommunityMembers(): number[][];
+    getCommunityTotalSize(c: number): number;
+    getCommunityNodeCount(c: number): number;
+    /** Attached by optimiser after creation — undefined until set. */
+    graph?: GraphAdapter;
+}
+export declare function makePartition(graph: GraphAdapter): Partition;
+//# sourceMappingURL=partition.d.ts.map

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

@@ -0,0 +1 @@
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