Migrate all remaining imports

src/covariance.js

@@ -22,7 +22,7 @@ export function variancecovariance(v) {
     }
     for (i = 0; i < o; i++) {
 	for (j = i; j < o; j++)
-	    cov[i][j] = cov[j][i] = reorder.covariancetranspose(v, i, j);
+	    cov[i][j] = cov[j][i] = covariancetranspose(v, i, j);
     }
     return cov;
 };

src/cuthill_mckee_order.js

@@ -42,7 +42,7 @@ export function cuthill_mckee(graph, comp) {
 };
 
 export function reverse_cuthill_mckee(graph, comp) {
-    return reorder.cuthill_mckee(graph, comp).reverse();
+    return cuthill_mckee(graph, comp).reverse();
 };
 
 export function cuthill_mckee_order(graph, comps) {
@@ -53,7 +53,7 @@ export function cuthill_mckee_order(graph, comps) {
     for (i = 0; i < comps.length; i++) {
 	comp = comps[i];
 	order = order.concat(
-	    reorder.cuthill_mckee(graph, comp));
+	    cuthill_mckee(graph, comp));
     }
     return order;
 };
@@ -66,7 +66,7 @@ export function reverse_cuthill_mckee_order(graph, comps) {
     for (i = 0; i < comps.length; i++) {
 	comp = comps[i];
 	order = order.concat(
-	    reorder.reverse_cuthill_mckee(graph, comp));
+	    reverse_cuthill_mckee(graph, comp));
     }
     return order;
 };

src/debug.js

@@ -12,7 +12,7 @@ export function displaymat(mat, rowperm, colperm) {
     }
 };
 
-export function printve(row, prec, colperm, line) {
+export function printvec(row, prec, colperm, line) {
     var j;
     if (! line)
 	line = "";
@@ -32,7 +32,7 @@ export function printmat(m, prec, rowperm, colperm) {
     if (! prec) prec=4;
     for (i = 0; i < m.length; i++) {
 	row = rowperm ? m[rowperm[i]] : m[i];
-	reorder.printvec(row, prec, colperm, i+": ");
+	printvec(row, prec, colperm, i+": ");
     }
 };
 
@@ -49,6 +49,6 @@ export function printhcluster(cluster,indent) {
 
     return Array(indent+1).join(' ')
 	+"id: "+cluster.id+", dist: "+cluster.dist+"\n"
-	+reorder.printhcluster(cluster.left, indent+1)+"\n"
-	+reorder.printhcluster(cluster.right, indent+1);
+	+printhcluster(cluster.left, indent+1)+"\n"
+	+printhcluster(cluster.right, indent+1);
 };

src/dist.js

@@ -1,5 +1,7 @@
+import { distance } from './distance';
+
 export function dist() {
-    var distance = reorder.distance.euclidean;
+    var distance = distance.euclidean;
 
     function dist(vectors) {
 	var n = vectors.length,

src/edgesum.js

@@ -1,6 +1,8 @@
+import { range } from './range';
+
 export function edgesum(graph, order) {
     if (! order)
-	order = reorder.range(graph.nodes().length);
+	order = range(graph.nodes().length);
 
     var inv = inverse_permutation(order),
 	links = graph.links(),

src/fiedler.js

@@ -1,4 +1,9 @@
-// Compute te Fiedler vector, the smallest non-null eigenvector of a matrix.
+import { debug } from './core';
+import { poweriteration, poweriteration_n } from './poweriteration';
+import { array1d } from './utils';
+import { random_array } from './random';
+
+// Compute the Fiedler vector, the smallest non-null eigenvector of a matrix.
 // See:
 // Yehuda Koren, Liran Carmel, David Harel
 // ACE: A Fast Multiscale Eigenvector Computation for Drawing Huge Graphs
@@ -21,7 +26,7 @@ function gershgorin_bound(B) {
 	if (t > max)
 	    max = t;
     }
-    if (reorder.debug) {
+    if (debug) {
 	console.log('gershgorin_bound=%d', max);
     }
     return max;
@@ -42,7 +47,7 @@ export function fiedler_vector(B, eps) {
 		row[j] = - row[j];
 	}
     }
-    var init = [ reorder.array1d(n, 1), reorder.random_array(n) ],
-	eig = reorder.poweriteration_n(Bhat, 2, init, eps, 1);
+    var init = [ array1d(n, 1), random_array(n) ],
+	eig = poweriteration_n(Bhat, 2, init, eps, 1);
     return eig[0][1];
 }

src/graph.js

@@ -1,3 +1,6 @@
+import { debug } from './core';
+import { cmp_number } from './utils';
+
 export function graph(nodes, links, directed) {
     var graph = {},
         linkDistance = 1,
@@ -108,7 +111,7 @@ export function graph(nodes, links, directed) {
     graph.edges = function(node) { 
 	if (typeof node != "number") {
 	    node = node.index;
-	    if (reorder.debug) {
+	    if (debug) {
 		console.log('received node %d', node);
 	    }
 	}
@@ -229,7 +232,7 @@ export function graph(nodes, links, directed) {
 		}
 	    }
 	    if (ccomp.length) {
-		ccomp.sort(reorder.cmp_number);
+		ccomp.sort(cmp_number);
 		comps.push(ccomp);
 	    }
 	}

src/graph2distmat.js

@@ -1,11 +1,17 @@
+import { zeroes } from './aliases';
+import { distmax } from './dist';
+import { all_pairs_distance } from './all_pairs_distance';
+import { permute } from './permute';
+import { flatten } from './utils';
+
 // Converts a graph with weighted edges (weight in l.value)
 // into a distance matrix suitable for reordering with e.g.
 // Optimal Leaf Ordering.
 
 export function distmat2valuemat(distmat) {
     var n = distmat.length,
-	valuemat = reorder.zeroes(n, n),
-	max_dist = reorder.distmax(distmat),
+	valuemat = zeroes(n, n),
+	max_dist = distmax(distmat),
 	i, j;
 
     for (i = 0; i < n; i++) {
@@ -20,7 +26,7 @@ export function graph2valuemats(graph, comps) {
     if (! comps)
 	comps = graph.components();
 
-    var	dists = reorder.all_pairs_distance(graph, comps);
+    var	dists = all_pairs_distance(graph, comps);
     return dists.map(distmat2valuemat);
 };
 
@@ -29,8 +35,8 @@ export function valuemats_reorder(valuemats, leaforder, comps) {
 
     if (comps) {
 	orders = orders.map(function(d, i) {
-	    return reorder.permute(comps[i], d);
+	    return permute(comps[i], d);
 	});
     }
-    return orders.reduce(reorder.flatten);
+    return orders.reduce(flatten);
 };

src/graph2mat.js

@@ -1,3 +1,5 @@
+import { zeroes } from './aliases';
+
 export function graph2mat(graph, directed) {
     var nodes = graph.nodes(),
 	links = graph.links(),
@@ -23,15 +25,15 @@ export function graph2mat(graph, directed) {
 		cols--;
 	}
 	//console.log("Rows: "+rows+" Cols: "+cols);
-	mat = reorder.zeroes(rows, cols);
+	mat = zeroes(rows, cols);
 
 	for (i = 0; i < links.length; i++) {
 	    l = links[i];
 	    mat[l.source.index][l.target.index] = l.value ? l.value : 1;
 	}
     }
     else {
-	mat = reorder.zeroes(n, n);
+	mat = zeroes(n, n);
 
 	for (i = 0; i < links.length; i++) {
 	    l = links[i];

src/graph_complete.js

@@ -1,3 +1,5 @@
+import { graph } from './graph';
+
 export function complete_graph(n, directed) {
     var nodes = graph_empty_nodes(n),
 	links = [],
@@ -17,5 +19,5 @@ export function complete_graph(n, directed) {
 		links.push({source: i, target: j });
 	}
     }
-    return reorder.graph(nodes, links, directed).init();
+    return graph(nodes, links, directed).init();
 };

src/graph_random.js

@@ -1,8 +1,12 @@
+import { graph_empty } from './graph_empty';
+import { complete_graph } from './graph_complete';
+import { graph } from './graph';
+
 export function graph_random_erdos_renyi(n, p, directed) {
     if (p <= 0)
-	return reorder.graph_empty(n, directed);
+	return graph_empty(n, directed);
     else if (p >= 1)
-	return reorder.graph_complete(n, directed);
+	return complete_graph(n, directed);
 
     var nodes = graph_empty_nodes(n),
 	links = [],
@@ -39,7 +43,7 @@ export function graph_random_erdos_renyi(n, p, directed) {
 		links.push({source: v, target: w});
 	}
     }
-    return reorder.graph(nodes, links, directed).init();
+    return graph(nodes, links, directed).init();
 };
 
 export const graph_random = graph_random_erdos_renyi;

src/hcluster.js

@@ -1,7 +1,9 @@
+import { distance } from './distance';
+
 // This is a modified implementation of hcluster derived from:
 // https://github.com/jasondavies/science.js/blob/master/src/stats/hcluster.js
 export function hcluster() {
-  var distance = reorder.distance.euclidean,
+  var distance = distance.euclidean,
       linkage = "single", // single, complete or average
       distMatrix = null;
 

src/index.js

@@ -27,7 +27,7 @@ export {
 } from './cuthill_mckee_order';
 export {
   displaymat,
-  printve,
+  printvec,
   printmat,
   assert,
   printhcluster

src/random.js

@@ -1,3 +1,6 @@
+import { permutation } from './permutation';
+import { zeroes } from './aliases';
+
 /* Fisher-Yates shuffle.
    See http://bost.ocks.org/mike/shuffle/
  */
@@ -19,7 +22,7 @@ export function randomPermute(array, i, j) {
 };
 
 export function randomPermutation(n) {
-    return reorder.randomPermute(reorder.permutation(n));
+    return randomPermute(permutation(n));
 };
 
 export function random_array(n, min, max) {
@@ -43,7 +46,7 @@ export function random_matrix(p, n, m, sym) {
 	sym = false;
     else if (! sym)
 	sym = true;
-    var mat = reorder.zeroes(n, m), i, j, cnt;
+    var mat = zeroes(n, m), i, j, cnt;
 
     if (sym) {
 	for (i = 0; i < n; i++) {