Fix position for nodes without adjacencies:

New nodes positions after graph.refresh() called all nodes with no adjacencies was placed outside the visible area or on the corner and it was difficult to work with this items.
This change makes visible area smaller and all the nodes becomes visible.
Also yuicompressor version updated to 2.4.7 from 2.4.2 and make.py cleaned for pep8.

Source/Layouts/Layouts.ForceDirected.js

@@ -34,6 +34,7 @@ Layouts.ForceDirected = new Class({
       width: w,
       height: h,
       tstart: w * 0.1,
+      ldist: l / 2,
       nodef: function(x) { return k2 / (x || 1); },
       edgef: function(x) { return /* x * x / k; */ k * (x - l); }
     };
@@ -127,7 +128,9 @@ Layouts.ForceDirected = new Class({
       node.visited = !T;
     });
     //arrange positions to fit the canvas
-    var t = opt.t, w2 = opt.width / 2, h2 = opt.height / 2;
+    var t = opt.t,
+        w2 = opt.width / 2 - opr.ldist,
+        h2 = opt.height / 2 - opt.ldist;
     graph.eachNode(function(u) {
       $.each(property, function(p) {
         var disp = u.disp[p];
@@ -140,4 +143,4 @@ Layouts.ForceDirected = new Class({
       });
     });
   }
-});
+});

make.py

@@ -1,15 +1,15 @@
-from os import system, walk, path, mkdir
-from shutil import copy
-import sys, re
+from os import system, path, mkdir
+import re
+import sys
 
 from tests import tests_model
 from serve import render
 from build import Build
 
-YC = 'yuicompressor-2.4.2.jar'
+YC = 'yuicompressor-2.4.7.jar'
 EXCLUDES = ['Source/Extras',
             'Source/Layouts',
-            'Source/Options/Options.js'
+            'Source/Options/Options.js',
             'Source/Core/Fx.js',
             'Source/Graph/Graph.Geom.js',
             'Source/Visualizations/ForceDirected3D.js']
@@ -18,31 +18,36 @@
 
 
 def main():
-    if 'docs' in sys.argv: make_docs()
-    if 'examples' in sys.argv: make_examples()
-    if 'examples-fancy' in sys.argv: make_examples(fancy=True)
-    if 'build' in sys.argv: make_build()
-    if 'build-fancy' in sys.argv: make_build(fancy=True)
+    if 'docs' in sys.argv:
+        make_docs()
+    if 'examples' in sys.argv:
+        make_examples()
+    if 'examples-fancy' in sys.argv:
+        make_examples(fancy=True)
+    if 'build' in sys.argv:
+        make_build()
+    if 'build-fancy' in sys.argv:
+        make_build(fancy=True)
 
 
 def make_docs():
     if not path.exists(NATURALDOCS):
         print "Requires NaturalDocs %s." % NATURALDOCS_VER
         print "http://www.naturaldocs.org/download.html"
         return
-    
+
     natural_docs_dir = path.join(NATURALDOCS, 'img')
     if not path.exists(natural_docs_dir):
         mkdir(natural_docs_dir)
-    
+
     if not path.exists('Docs'):
         mkdir('Docs')
-    
+
     # If we can't use 'docstyle' then fallback to 'Default'
     docstyle = 'docstyle'
     if not path.exists(NATURALDOCS + '/Styles/' + docstyle + '.css'):
         docstyle = 'Default'
-    
+
     system("perl "
         + NATURALDOCS + "/NaturalDocs -r "
         + " -i Source/"
@@ -56,16 +61,16 @@ def make_docs():
 def make_examples(fancy=False):
     if not path.exists('Examples'):
         mkdir('Examples')
-    
+
     #clean examples folders
     system("rm -rf Examples/*")
-    
+
     #copy css base files
     system('cp -r Tests/css Examples/css')
-    
+
     #iterate over the examples
     has_example = lambda x: 'Example' in x and x['Example']
-    
+
     for viz, tests in tests_model.items():
     #create example folder
         if filter(has_example, tests):
@@ -75,59 +80,62 @@ def make_examples(fancy=False):
                 if has_example(model):
                     make_example(viz, model, i, count, fancy)
                     count += 1
-    
+
     #copy some extra files
     if fancy:
         system('cp -r Extras/sh Examples/')
         system('cp Extras/code.css Examples/css/code.css')
 
 
 def make_example(viz, ex, i, count, fancy):
-
     name = viz
     stri = str(i + 1)
     model = ex
     title = model['Title']
     extras = model['Extras'][:]
     example = 'example' + str(count)
     strdir = 'Examples/' + viz + '/'
-    
+
     #insert the example js file
     fcommon = open('Tests/js/common.js', 'r')
     ftest = open('Tests/' + viz + '/test' + stri + '.js', 'r')
     fout = open(strdir + example + '.js', 'w')
-    fout.write('\n\n'.join([fcommon.read(), ftest.read().replace('/Tests/css', '../css')]))
+    fout.write('\n\n'.join([fcommon.read(), ftest.read().replace('/Tests/css',
+                                                                 '../css')]))
     fcommon.close()
     ftest.close()
     fout.close()
-    
+
     #render the html file
     includes = {
-        'left':  getattr(render['TestCases'], viz + '/' + 'left')(model, viz, 1, 1),
-        'right': getattr(render['TestCases'], viz + '/' + 'test' + stri)(model),
+        'left': getattr(render['TestCases'], viz + '/left')(model, viz, 1, 1),
+        'right': getattr(render['TestCases'], viz + '/test' + stri)(model),
     }
-    
+
     fhtml = open(strdir + example + '.html', 'w')
-    html = render['TestCases'].baseexamples(name, title, extras, example, '', includes, fancy).__body__
+    html = render['TestCases'].baseexamples(name, title, extras, example, '',
+                                            includes, fancy).__body__
     fhtml.write(html)
     fhtml.close()
-    
+
     #create syntax highlighted code page
     if fancy:
-        begin, end, res = re.compile("[\s]*//[\s]?init ([a-zA-Z0-9]+)[\s]*"), re.compile('[\s]*//[\s]?end[\s]*'), []
+        begin = re.compile("[\s]*//[\s]?init ([a-zA-Z0-9]+)[\s]*")
+        end = re.compile('[\s]*//[\s]?end[\s]*')
+        res = []
         ftest = open('Tests/' + viz + '/test' + stri + '.js', 'r')
         for l in ftest:
             if begin.match(l):
                 name, lines = begin.match(l).group(1), []
                 for blockline in ftest:
-                    if end.match(blockline): break
+                    if end.match(blockline):
+                        break
                     lines.append(blockline)
-                
+
                 res.append({
                     'name': name,
                     'code': ''.join(lines)
                 })
-
         fcode = open(strdir + example + '.code.html', 'w')
         html = render['TestCases'].basecode(name, title, res, example).__body__
         fcode.write(html)
@@ -157,7 +165,7 @@ def make_build(fancy=False):
     system('rm Jit.zip')
     system('zip -r Jit.zip Jit/')
     print "Done, I guess."
-    
+
 
 if __name__ == "__main__":
-    main()
+    main()