logical-tree: Make it mutate to improve performance

The clone we were doing to save ourselves from mutation proved to be
excessively slow. While lodash is being updated to not have the
same scaling issues, it was determined that we weren't gaining
anything from not mutating here, so there was no reason to pay
even a lesser price.

PR-URL: #9803
Fixes: #8826

Author: iarna

lib/install/logical-tree.js renamed to lib/install/mutate-into-logical-tree.js

@@ -1,5 +1,4 @@
 'use strict'
-var clone = require('lodash.clonedeep')
 var union = require('lodash.union')
 var without = require('lodash.without')
 var validate = require('aproba')
@@ -8,17 +7,15 @@ var isExtraneous = require('./is-extraneous.js')
 var validateAllPeerDeps = require('./deps.js').validateAllPeerDeps
 var getPackageId = require('./get-package-id.js')
 
-var logicalTree = module.exports = function (tree) {
+var mutateIntoLogicalTree = module.exports = function (tree) {
   validate('O', arguments)
 
-  var newTree = clone(tree)
-
-  validateAllPeerDeps(newTree, function (tree, pkgname, version) {
+  validateAllPeerDeps(tree, function (tree, pkgname, version) {
     if (!tree.missingPeers) tree.missingPeers = {}
     tree.missingPeers[pkgname] = version
   })
 
-  var flat = flattenTree(newTree)
+  var flat = flattenTree(tree)
 
   function getNode (flatname) {
     return flatname.substr(0, 5) === '#DEV:' ?
@@ -47,14 +44,15 @@ var logicalTree = module.exports = function (tree) {
       parentNode.children = union(parentNode.children, [node])
     })
     if (node.package._requiredBy.some(function (nodename) { return nodename[0] === '#' })) {
-      newTree.children = union(newTree.children, [node])
+      tree.children = union(tree.children, [node])
     }
   })
-  return newTree
+  return tree
 }
 
 module.exports.asReadInstalled = function (tree) {
-  return translateTree(logicalTree(tree))
+  mutateIntoLogicalTree(tree)
+  return translateTree(tree)
 }
 
 function translateTree (tree) {

lib/ls.js

@@ -16,7 +16,7 @@ var color = require('ansicolors')
 var npa = require('npm-package-arg')
 var iferr = require('iferr')
 var npm = require('./npm.js')
-var logicalTree = require('./install/logical-tree.js')
+var mutateIntoLogicalTree = require('./install/mutate-into-logical-tree.js')
 var recalculateMetadata = require('./install/deps.js').recalculateMetadata
 var getPackageId = require('./install/get-package-id.js')
 
@@ -61,7 +61,8 @@ var lsFromTree = ls.fromTree = function (dir, physicalTree, args, silent, cb) {
     })
   }
 
-  var data = logicalTree.asReadInstalled(physicalTree)
+  var data = mutateIntoLogicalTree.asReadInstalled(physicalTree)
+
   pruneNestedExtraneous(data)
   filterByEnv(data)
   var bfs = filterFound(bfsify(data), args)

lib/outdated.js

@@ -32,7 +32,7 @@ var styles = require('ansistyles')
 var table = require('text-table')
 var semver = require('semver')
 var npa = require('npm-package-arg')
-var logicalTree = require('./install/logical-tree.js')
+var mutateIntoLogicalTree = require('./install/mutate-into-logical-tree.js')
 var cache = require('./cache.js')
 var npm = require('./npm.js')
 var long = npm.config.get('long')
@@ -73,8 +73,8 @@ function outdated (args, silent, cb) {
   // default depth for `outdated` is 0 (cf. `ls`)
   if (npm.config.get('depth') === Infinity) npm.config.set('depth', 0)
 
-  readPackageTree(dir, andRecalculateMetadata(function (er, physicalTree) {
-    var tree = logicalTree(physicalTree)
+  readPackageTree(dir, andRecalculateMetadata(function (er, tree) {
+    mutateIntoLogicalTree(tree)
     outdated_(args, '', tree, {}, 0, function (er, list) {
       list = uniq(list || []).sort(function (aa, bb) {
         return aa[0].path.localeCompare(bb[0].path) ||