@graphty/layout 1.2.6 → 1.2.8

package/README.md

@@ -4,9 +4,9 @@
 [![Coverage Status](https://coveralls.io/repos/github/graphty-org/layout/badge.svg?branch=main)](https://coveralls.io/github/graphty-org/layout?branch=main)
 [![npm version](https://badge.fury.io/js/%40graphty%2Flayout.svg)](https://badge.fury.io/js/%40graphty%2Flayout)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![GitHub Pages](https://img.shields.io/badge/demo-github%20pages-blue)](https://graphty-org.github.io/layout/)
+[![GitHub Pages](https://img.shields.io/badge/demo-github%20pages-blue)](https://graphty-org.github.io/layout/examples/index.html)
 
-**[View Interactive Examples →](https://graphty-org.github.io/layout/index.html)**
+**[View Interactive Examples →](https://graphty-org.github.io/layout/examples/index.html)**
 
 Layout is a TypeScript library for positioning nodes in graphs. It's a TypeScript port of the [layout algorithms](https://networkx.org/documentation/stable/reference/drawing.html) from the Python [NetworkX](https://networkx.org/documentation/stable/) library.
 
@@ -51,6 +51,12 @@ Additionally, the library includes:
 - **combineLayouts** - Blend multiple layout algorithms
 - **interpolateLayouts** - Smooth animation between layouts
 
+## Installation
+
+```bash
+npm install @graphty/layout
+```
+
 ## How to Use
 
 Import the library in your TypeScript/JavaScript project:
@@ -91,7 +97,7 @@ import {
   layoutQuality,
   combineLayouts,
   interpolateLayouts
-} from './layout.js'
+} from '@graphty/layout'
 ```
 
 ## Quick Start
@@ -476,12 +482,30 @@ if (detected) {
 }
 ```
 
+## 3D Support
+
+All layout algorithms support 3D positioning by setting the `dim` parameter to 3:
+
+```typescript
+// Any layout algorithm in 3D
+const positions3D = springLayout(graph, null, null, null, 50, 1, [0, 0, 0], 3)
+// Returns: { node1: [x, y, z], node2: [x, y, z], ... }
+
+// ForceAtlas2 in 3D
+const fa3D = forceatlas2Layout(graph, null, 100, 1, 2, 1, false, false, null, null, null, false, false, 42, 3)
+
+// Circular layout in 3D (creates a sphere)
+const circular3D = circularLayout(graph, 1, [0, 0, 0], 3)
+```
+
+When using 3D layouts, positions will have three coordinates `[x, y, z]` instead of two.
+
 ## Common Parameters
 
 Most layout functions share these parameters:
 
 - **scale** (number): Scale factor for positions (default: 1)
-- **center** (number[]): Center coordinates around which to center the layout (default: [0, 0])
+- **center** (number[]): Center coordinates around which to center the layout (default: [0, 0] for 2D, [0, 0, 0] for 3D)
 - **dim** (number): Layout dimension - 2D or 3D (default: 2)
 - **seed** (number): Seed for random generation (for reproducible layouts)
 
@@ -722,7 +746,26 @@ const positions = forceatlas2Layout(
   true, // dissuadeHubs: good for scale-free
   false, // linlog: logarithmic attraction
   42, // seed
-  2 // dim
+  2 // dim: 2 for 2D, 3 for 3D
+)
+
+// 3D layout example
+const positions3D = forceatlas2Layout(
+  graph,
+  null,
+  100,
+  1.0,
+  2.0,
+  1.0,
+  false,
+  false,
+  null,
+  null,
+  null,
+  false,
+  false,
+  42,
+  3 // 3D mode - returns [x, y, z] coordinates
 )
 ```
 
@@ -1098,6 +1141,13 @@ To deploy to GitHub Pages, see `gh-pages/DEPLOY.md` after building.
 4. **Build for production** with `npm run build:all`
 5. **Deploy examples** with `npm run build:gh-pages`
 
+## Recent Updates
+
+### Version 1.2.7 (Latest)
+- **Fixed**: ForceAtlas2 now correctly returns numeric Z coordinates in 3D mode (previously returned NaN)
+- **Fixed**: NPM package now uses the correct bundled entry point (`dist/layout.js`)
+- **Added**: Full 3D support documentation and examples
+
 ## Contributing
 
 This project is a TypeScript port of the NetworkX Python library. For contributions and issues, visit the [GitHub repository](https://github.com/graphty-org/layout).

package/dist/layout.d.ts

@@ -0,0 +1,17 @@
+/**
+ * TypeScript declarations for @graphty/layout
+ * 
+ * This file provides type information for the bundled dist/layout.js module.
+ */
+
+// Re-export all types
+export * from './src/types/index';
+
+// Re-export utilities that are part of the public API  
+export { rescaleLayout, rescaleLayoutDict } from './src/utils/rescale';
+
+// Re-export all layout algorithms
+export * from './src/layouts/index';
+
+// Re-export all graph generation functions
+export * from './src/generators/index';

package/dist/src/algorithms/index.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Re-export all algorithm utilities
+ */
+export * from './planarity';
+export * from './optimization';

package/dist/src/algorithms/index.js

@@ -0,0 +1,6 @@
+/**
+ * Re-export all algorithm utilities
+ */
+export * from './planarity';
+export * from './optimization';
+//# sourceMappingURL=index.js.map

package/dist/src/algorithms/index.js.map

@@ -0,0 +1 @@
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package/dist/src/algorithms/optimization/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Re-export all optimization algorithms
+ */
+export type { DistanceMap } from './types';
+export { _computeShortestPathDistances, _kamadaKawaiSolve, _kamadaKawaiCostfn } from './kamada-kawai-solver';
+export { _lbfgsDirection } from './lbfgs';
+export { _backtrackingLineSearch } from './line-search';

package/dist/src/algorithms/optimization/index.js

@@ -0,0 +1,7 @@
+/**
+ * Re-export all optimization algorithms
+ */
+export { _computeShortestPathDistances, _kamadaKawaiSolve, _kamadaKawaiCostfn } from './kamada-kawai-solver';
+export { _lbfgsDirection } from './lbfgs';
+export { _backtrackingLineSearch } from './line-search';
+//# sourceMappingURL=index.js.map

package/dist/src/algorithms/optimization/index.js.map

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package/dist/src/algorithms/optimization/kamada-kawai-solver.d.ts

@@ -0,0 +1,32 @@
+/**
+ * Kamada-Kawai layout algorithm optimization functions
+ */
+import { Graph } from '../../types';
+import { DistanceMap } from './types';
+/**
+ * Compute all-pairs shortest path distances for the graph
+ *
+ * @param G - NetworkX graph
+ * @param weight - Edge attribute for weight
+ * @returns Dictionary of dictionaries of shortest path distances
+ */
+export declare function _computeShortestPathDistances(G: Graph, weight: string): DistanceMap;
+/**
+ * Solve the Kamada-Kawai layout optimization problem
+ *
+ * @param distMatrix - Matrix of desired distances between nodes
+ * @param positions - Initial node positions
+ * @param dim - Dimension of layout
+ * @returns Optimized node positions
+ */
+export declare function _kamadaKawaiSolve(distMatrix: number[][], positions: number[][], dim: number): number[][];
+/**
+ * Cost function and gradient for Kamada-Kawai layout algorithm
+ *
+ * @param posVec - Flattened position array
+ * @param invDist - Inverse distance matrix
+ * @param meanWeight - Weight for centering positions
+ * @param dim - Dimension of layout
+ * @returns Array with [cost, gradient]
+ */
+export declare function _kamadaKawaiCostfn(posVec: number[], invDist: number[][], meanWeight: number, dim: number): [number, number[]];

package/dist/src/algorithms/optimization/kamada-kawai-solver.js

@@ -0,0 +1,176 @@
+/**
+ * Kamada-Kawai layout algorithm optimization functions
+ */
+import { _lbfgsDirection } from './lbfgs';
+import { _backtrackingLineSearch } from './line-search';
+import { getNodesFromGraph, getEdgesFromGraph } from '../../utils/graph';
+/**
+ * Compute all-pairs shortest path distances for the graph
+ *
+ * @param G - NetworkX graph
+ * @param weight - Edge attribute for weight
+ * @returns Dictionary of dictionaries of shortest path distances
+ */
+export function _computeShortestPathDistances(G, weight) {
+    const distances = {};
+    const nodes = getNodesFromGraph(G);
+    const edges = getEdgesFromGraph(G);
+    // Initialize distances with direct edges
+    for (const node of nodes) {
+        distances[node] = {};
+        distances[node][node] = 0;
+        for (const other of nodes) {
+            if (node !== other) {
+                distances[node][other] = Infinity;
+            }
+        }
+    }
+    // Add direct edges
+    for (const [source, target] of edges) {
+        // In a real implementation, we would get the weight from the graph
+        // For now, assume weight = 1 or use weight attribute if available
+        let edgeWeight = 1;
+        if (G.getEdgeData) {
+            edgeWeight = G.getEdgeData(source, target, weight) || 1;
+        }
+        distances[source][target] = edgeWeight;
+        distances[target][source] = edgeWeight; // Assuming undirected graph
+    }
+    // Floyd-Warshall algorithm for all-pairs shortest paths
+    for (const k of nodes) {
+        for (const i of nodes) {
+            for (const j of nodes) {
+                if (distances[i][k] + distances[k][j] < distances[i][j]) {
+                    distances[i][j] = distances[i][k] + distances[k][j];
+                }
+            }
+        }
+    }
+    return distances;
+}
+/**
+ * Solve the Kamada-Kawai layout optimization problem
+ *
+ * @param distMatrix - Matrix of desired distances between nodes
+ * @param positions - Initial node positions
+ * @param dim - Dimension of layout
+ * @returns Optimized node positions
+ */
+export function _kamadaKawaiSolve(distMatrix, positions, dim) {
+    // Implementation of L-BFGS optimization for Kamada-Kawai
+    const nNodes = positions.length;
+    const meanWeight = 1e-3;
+    // Convert distances to inverse distances (with protection against division by zero)
+    const invDistMatrix = distMatrix.map(row => row.map(d => d === 0 ? 0 : 1 / (d + 1e-3)));
+    // Flatten positions for optimization
+    let posVec = positions.flat();
+    // Optimization parameters
+    const maxIter = 500;
+    const gtol = 1e-5;
+    const m = 10; // L-BFGS memory size
+    // Implement a simplified L-BFGS-B algorithm
+    let alpha = 1.0;
+    const oldValues = [];
+    const oldGrads = [];
+    for (let iter = 0; iter < maxIter; iter++) {
+        // Calculate cost and gradient
+        const [cost, grad] = _kamadaKawaiCostfn(posVec, invDistMatrix, meanWeight, dim);
+        // Compute search direction using L-BFGS approximation
+        const direction = _lbfgsDirection(grad, oldValues, oldGrads, m);
+        // Simple line search for step size
+        alpha = _backtrackingLineSearch(posVec, direction, cost, grad, (x) => _kamadaKawaiCostfn(x, invDistMatrix, meanWeight, dim)[0], alpha);
+        // Save current position and gradient for next iteration
+        const oldPos = [...posVec];
+        // Update position
+        for (let i = 0; i < posVec.length; i++) {
+            posVec[i] += alpha * direction[i];
+        }
+        // Calculate new gradient
+        const [, newGrad] = _kamadaKawaiCostfn(posVec, invDistMatrix, meanWeight, dim);
+        // Update L-BFGS memory
+        oldValues.push(posVec.map((val, i) => val - oldPos[i]));
+        oldGrads.push(newGrad.map((val, i) => val - grad[i]));
+        // Keep only m most recent updates
+        if (oldValues.length > m) {
+            oldValues.shift();
+            oldGrads.shift();
+        }
+        // Check convergence
+        const gradNorm = Math.sqrt(newGrad.reduce((sum, g) => sum + g * g, 0));
+        if (gradNorm < gtol) {
+            break;
+        }
+    }
+    // Reshape result back into positions array
+    const result = [];
+    for (let i = 0; i < nNodes; i++) {
+        result.push(posVec.slice(i * dim, (i + 1) * dim));
+    }
+    return result;
+}
+/**
+ * Cost function and gradient for Kamada-Kawai layout algorithm
+ *
+ * @param posVec - Flattened position array
+ * @param invDist - Inverse distance matrix
+ * @param meanWeight - Weight for centering positions
+ * @param dim - Dimension of layout
+ * @returns Array with [cost, gradient]
+ */
+export function _kamadaKawaiCostfn(posVec, invDist, meanWeight, dim) {
+    const nNodes = invDist.length;
+    const positions = [];
+    // Reshape flat vector into positions array
+    for (let i = 0; i < nNodes; i++) {
+        positions.push(posVec.slice(i * dim, (i + 1) * dim));
+    }
+    // Calculate cost
+    let cost = 0;
+    // Add mean position penalty term
+    const sumPos = Array(dim).fill(0);
+    for (let i = 0; i < nNodes; i++) {
+        for (let d = 0; d < dim; d++) {
+            sumPos[d] += positions[i][d];
+        }
+    }
+    cost += 0.5 * meanWeight * sumPos.reduce((sum, val) => sum + val * val, 0);
+    // Add distance penalty terms
+    for (let i = 0; i < nNodes; i++) {
+        for (let j = i + 1; j < nNodes; j++) {
+            // Calculate actual distance
+            const diff = positions[i].map((val, d) => val - positions[j][d]);
+            const distance = Math.sqrt(diff.reduce((sum, d) => sum + d * d, 0));
+            // Add penalty for difference between actual and ideal distance
+            const idealInvDist = invDist[i][j];
+            const offset = distance * idealInvDist - 1.0;
+            cost += 0.5 * offset * offset;
+        }
+    }
+    // Calculate gradient
+    const grad = new Array(posVec.length).fill(0);
+    // Add gradient of mean position penalty
+    for (let i = 0; i < nNodes; i++) {
+        for (let d = 0; d < dim; d++) {
+            grad[i * dim + d] += meanWeight * sumPos[d];
+        }
+    }
+    // Add gradient of distance penalties
+    for (let i = 0; i < nNodes; i++) {
+        for (let j = i + 1; j < nNodes; j++) {
+            // Calculate actual distance and direction
+            const diff = positions[i].map((val, d) => val - positions[j][d]);
+            const distance = Math.sqrt(diff.reduce((sum, d) => sum + d * d, 0)) || 1e-10;
+            const direction = diff.map(d => d / distance);
+            // Calculate contribution to gradient
+            const idealInvDist = invDist[i][j];
+            const offset = distance * idealInvDist - 1.0;
+            for (let d = 0; d < dim; d++) {
+                const force = idealInvDist * offset * direction[d];
+                grad[i * dim + d] += force;
+                grad[j * dim + d] -= force;
+            }
+        }
+    }
+    return [cost, grad];
+}
+//# sourceMappingURL=kamada-kawai-solver.js.map

package/dist/src/algorithms/optimization/kamada-kawai-solver.js.map

@@ -0,0 +1 @@
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package/dist/src/algorithms/optimization/lbfgs.d.ts

@@ -0,0 +1,13 @@
+/**
+ * L-BFGS optimization utilities
+ */
+/**
+ * Compute the search direction using L-BFGS approximation
+ *
+ * @param grad - Current gradient
+ * @param sList - List of position differences (s_k)
+ * @param yList - List of gradient differences (y_k)
+ * @param m - Memory size
+ * @returns Direction vector
+ */
+export declare function _lbfgsDirection(grad: number[], sList: number[][], yList: number[][], m: number): number[];

package/dist/src/algorithms/optimization/lbfgs.js

@@ -0,0 +1,56 @@
+/**
+ * L-BFGS optimization utilities
+ */
+/**
+ * Compute the search direction using L-BFGS approximation
+ *
+ * @param grad - Current gradient
+ * @param sList - List of position differences (s_k)
+ * @param yList - List of gradient differences (y_k)
+ * @param m - Memory size
+ * @returns Direction vector
+ */
+export function _lbfgsDirection(grad, sList, yList, m) {
+    if (sList.length === 0) {
+        // First iteration - use negative gradient
+        return grad.map(g => -g);
+    }
+    const q = grad.slice();
+    const alpha = Array(sList.length).fill(0);
+    const rho = [];
+    // Compute rho values
+    for (let i = 0; i < sList.length; i++) {
+        const s = sList[i];
+        const y = yList[i];
+        rho.push(1 / y.reduce((sum, val, j) => sum + val * s[j], 0));
+    }
+    // Forward pass
+    for (let i = sList.length - 1; i >= 0; i--) {
+        const s = sList[i];
+        alpha[i] = rho[i] * s.reduce((sum, val, j) => sum + val * q[j], 0);
+        for (let j = 0; j < q.length; j++) {
+            q[j] -= alpha[i] * yList[i][j];
+        }
+    }
+    // Scale initial Hessian approximation
+    let gamma = 1;
+    if (sList.length > 0 && yList.length > 0) {
+        const y = yList[yList.length - 1];
+        const s = sList[sList.length - 1];
+        gamma = s.reduce((sum, val, i) => sum + val * y[i], 0) /
+            y.reduce((sum, val) => sum + val * val, 0);
+    }
+    // Initialize direction with scaled negative gradient
+    const direction = q.map(val => -gamma * val);
+    // Backward pass
+    for (let i = 0; i < sList.length; i++) {
+        const s = sList[i];
+        const y = yList[i];
+        const beta = rho[i] * y.reduce((sum, val, j) => sum + val * direction[j], 0);
+        for (let j = 0; j < direction.length; j++) {
+            direction[j] += s[j] * (alpha[i] - beta);
+        }
+    }
+    return direction;
+}
+//# sourceMappingURL=lbfgs.js.map

package/dist/src/algorithms/optimization/lbfgs.js.map

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package/dist/src/algorithms/optimization/line-search.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Line search optimization utilities
+ */
+/**
+ * Backtracking line search to find step size
+ *
+ * @param x - Current position
+ * @param direction - Search direction
+ * @param f - Function value at current position
+ * @param grad - Gradient at current position
+ * @param func - Function to evaluate cost
+ * @param alpha0 - Initial step size
+ * @returns Optimal step size
+ */
+export declare function _backtrackingLineSearch(x: number[], direction: number[], f: number, grad: number[], func: (x: number[]) => number, alpha0: number): number;

package/dist/src/algorithms/optimization/line-search.js

@@ -0,0 +1,37 @@
+/**
+ * Line search optimization utilities
+ */
+/**
+ * Backtracking line search to find step size
+ *
+ * @param x - Current position
+ * @param direction - Search direction
+ * @param f - Function value at current position
+ * @param grad - Gradient at current position
+ * @param func - Function to evaluate cost
+ * @param alpha0 - Initial step size
+ * @returns Optimal step size
+ */
+export function _backtrackingLineSearch(x, direction, f, grad, func, alpha0) {
+    const c1 = 1e-4;
+    const c2 = 0.9;
+    const initialSlope = grad.reduce((sum, g, i) => sum + g * direction[i], 0);
+    if (initialSlope >= 0) {
+        return 1e-8; // Direction is not a descent direction
+    }
+    let alpha = alpha0;
+    const maxIter = 20;
+    for (let i = 0; i < maxIter; i++) {
+        // Try step
+        const newX = x.map((val, i) => val + alpha * direction[i]);
+        const newF = func(newX);
+        // Check sufficient decrease condition (Armijo condition)
+        if (newF <= f + c1 * alpha * initialSlope) {
+            return alpha;
+        }
+        // Reduce step size
+        alpha *= c2;
+    }
+    return alpha; // Return last alpha even if not optimal
+}
+//# sourceMappingURL=line-search.js.map

package/dist/src/algorithms/optimization/line-search.js.map

@@ -0,0 +1 @@
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package/dist/src/algorithms/optimization/types.d.ts

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+/**
+ * Type definitions for optimization algorithms
+ */
+import { Node } from '../../types';
+export type DistanceMap = Record<Node, Record<Node, number>>;

package/dist/src/algorithms/optimization/types.js

@@ -0,0 +1,5 @@
+/**
+ * Type definitions for optimization algorithms
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/src/algorithms/optimization/types.js.map

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package/dist/src/algorithms/planarity/check.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Main planarity checking function
+ */
+import { Graph, Node, Edge, Embedding } from '../../types';
+/**
+ * Check if graph is planar using a simplified version of Boyer-Myrvold algorithm.
+ * Returns planarity and embedding information.
+ *
+ * @param G - Graph
+ * @param nodes - List of nodes
+ * @param edges - List of edges
+ * @returns Object containing isPlanar flag and embedding
+ */
+export declare function checkPlanarity(G: Graph, nodes: Node[], edges: Edge[]): {
+    isPlanar: boolean;
+    embedding: Embedding | null;
+};

package/dist/src/algorithms/planarity/check.js

@@ -0,0 +1,30 @@
+/**
+ * Main planarity checking function
+ */
+import { isK5, isK33 } from './special-graphs';
+import { lrPlanarityTest } from './lr-test';
+import { createTriangulationEmbedding } from './embedding';
+/**
+ * Check if graph is planar using a simplified version of Boyer-Myrvold algorithm.
+ * Returns planarity and embedding information.
+ *
+ * @param G - Graph
+ * @param nodes - List of nodes
+ * @param edges - List of edges
+ * @returns Object containing isPlanar flag and embedding
+ */
+export function checkPlanarity(G, nodes, edges) {
+    // For small graphs (n <= 4), all are planar
+    if (nodes.length <= 4) {
+        return { isPlanar: true, embedding: createTriangulationEmbedding(nodes, edges) };
+    }
+    // For K5 (complete graph with 5 nodes) and K3,3 (complete bipartite with 3,3 nodes)
+    // these are not planar by Kuratowski's theorem
+    if (isK5(nodes, edges) || isK33(nodes, edges)) {
+        return { isPlanar: false, embedding: null };
+    }
+    // For other graphs, use LR algorithm (Left-Right Planarity Test)
+    const result = lrPlanarityTest(nodes, edges);
+    return result;
+}
+//# sourceMappingURL=check.js.map

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package/dist/src/algorithms/planarity/embedding.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Embedding functions for planar graphs
+ */
+import { Node, Edge, Embedding, PositionMap } from '../../types';
+/**
+ * Create a triangulation-based embedding for a planar graph
+ *
+ * @param nodes - List of nodes
+ * @param edges - List of edges
+ * @returns Embedding object
+ */
+export declare function createTriangulationEmbedding(nodes: Node[], edges: Edge[]): Embedding;
+/**
+ * Find a simple cycle in the graph (for outer face)
+ *
+ * @param nodes - List of nodes
+ * @param edges - List of edges
+ * @param adjMap - Adjacency map
+ * @returns Cycle as array of nodes, or null if none found
+ */
+export declare function findCycle(nodes: Node[], edges: Edge[], adjMap: Record<Node, Set<Node>>): Node[] | null;
+/**
+ * Convert a combinatorial embedding to node positions
+ *
+ * @param embedding - The embedding object
+ * @param nodes - List of nodes
+ * @returns Dictionary mapping nodes to positions
+ */
+export declare function combinatorialEmbeddingToPos(embedding: Embedding, nodes: Node[]): PositionMap;