From 37fbabaa92c8334de90d3cdd0bc6ce82403b3028 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Wed, 14 Oct 2015 23:07:01 +0100
Subject: [PATCH 01/40] fix `CellToolbar.utils.checkbox_ui_generator` and
 `CellToolbar.utils.checkbox_input_generator` to match
 `CellToolbar.utils.checkbox_select_generator`, adding the input/checkbox to
 the button container rather than the to the label.

---
 notebook/static/notebook/js/celltoolbar.js | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/notebook/static/notebook/js/celltoolbar.js b/notebook/static/notebook/js/celltoolbar.js
index 654bcc0e0..b0bb31a2b 100644
--- a/notebook/static/notebook/js/celltoolbar.js
+++ b/notebook/static/notebook/js/celltoolbar.js
@@ -354,7 +354,6 @@ define([
 
             var chkb = $('<input/>').attr('type', 'checkbox');
             var lbl = $('<label/>').append($('<span/>').text(name));
-            lbl.append(chkb);
             chkb.attr("checked", getter(cell));
 
             chkb.click(function(){
@@ -362,7 +361,7 @@ define([
                         setter(cell, !v);
                         chkb.attr("checked", !v);
             });
-            button_container.append($('<span/>').append(lbl));
+            button_container.append($('<span/>').append(lbl).append(chkb));
         };
     };
 
@@ -387,13 +386,12 @@ define([
 
             var text = $('<input/>').attr('type', 'text');
             var lbl = $('<label/>').append($('<span/>').text(name));
-            lbl.append(text);
             text.attr("value", getter(cell));
 
             text.keyup(function(){
                 setter(cell, text.val());
             });
-            button_container.append($('<span/>').append(lbl));
+            button_container.append($('<span/>').append(lbl).append(text));
             IPython.keyboard_manager.register_events(text);
         };
     };

From d81d6a8e39c3f0ceefc3858074d82e96665fe26c Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Thu, 5 Nov 2015 11:57:29 -0800
Subject: [PATCH 02/40] Work around #699

---
 notebook/static/notebook/js/notificationarea.js | 6 +++---
 notebook/static/notebook/js/textcell.js         | 3 +++
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/notebook/static/notebook/js/notificationarea.js b/notebook/static/notebook/js/notificationarea.js
index 4b615248a..8f010c9e5 100644
--- a/notebook/static/notebook/js/notificationarea.js
+++ b/notebook/static/notebook/js/notificationarea.js
@@ -35,7 +35,7 @@ define([
      */
     NotebookNotificationArea.prototype.init_kernel_notification_widget = function () {
         var that = this;
-        var knw = this.new_notification_widget('kernel');
+        var knw = this.widget('kernel');
         var $kernel_ind_icon = $("#kernel_indicator_icon");
         var $modal_ind_icon = $("#modal_indicator");
         var $readonly_ind_icon = $('#readonly-indicator');
@@ -284,7 +284,7 @@ define([
      * @method init_notebook_notification_widget
      */
     NotebookNotificationArea.prototype.init_notebook_notification_widget = function () {
-        var nnw = this.new_notification_widget('notebook');
+        var nnw = this.widget('notebook');
 
         // Notebook events
         this.events.on('notebook_loading.Notebook', function () {
@@ -346,7 +346,7 @@ define([
      * @method init_marked_cells_notification_widget
      */
     NotebookNotificationArea.prototype.init_marked_cells_notification_widget = function () {
-        var mcnw = this.new_notification_widget('marked_cells');
+        var mcnw = this.widget('marked_cells');
 
         this.events.on('marked_offscreen.Cell', function (evt, num) {
             if (num === 0) {
diff --git a/notebook/static/notebook/js/textcell.js b/notebook/static/notebook/js/textcell.js
index e5bde67be..0b0e4ea49 100644
--- a/notebook/static/notebook/js/textcell.js
+++ b/notebook/static/notebook/js/textcell.js
@@ -286,6 +286,9 @@ define([
                             .addClass('anchor-link')
                             .attr('href', '#' + hash)
                             .text('¶')
+                            .on('click',function(){
+                                setTimeout(function(){that.unrender(); that.render()}, 100)
+                            })
                     );
                 });
                 // links in markdown cells should open in new tabs

From cdd2ae7cc6f92c48759419e1ef8055be92072e99 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Tue, 17 Nov 2015 11:25:08 -0800
Subject: [PATCH 03/40] Add debug statements for #484

---
 notebook/static/notebook/js/notebook.js | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/notebook/static/notebook/js/notebook.js b/notebook/static/notebook/js/notebook.js
index 54a889b61..1844ce6c8 100644
--- a/notebook/static/notebook/js/notebook.js
+++ b/notebook/static/notebook/js/notebook.js
@@ -58,6 +58,8 @@ define(function (require) {
         this.ws_url = options.ws_url;
         this._session_starting = false;
         this.last_modified = null;
+        // debug 484
+        this._last_modified = 'init';
 
         //  Create default scroll manager.
         this.scroll_manager = new scrollmanager.ScrollManager(this);
@@ -2320,6 +2322,8 @@ define(function (require) {
                 function (data) {
                     var last_modified = new Date(data.last_modified);
                     if (last_modified > that.last_modified) {
+                        console.warn("Last saving was done on `"+that.last_modified+"`("+that._last_modified+"), "+
+                                    "while the current file seem to have been saved on `"+data.last_modified+"`")
                         dialog.modal({
                             notebook: that,
                             keyboard_manager: that.keyboard_manager,
@@ -2365,6 +2369,8 @@ define(function (require) {
     Notebook.prototype.save_notebook_success = function (start, data) {
         this.set_dirty(false);
         this.last_modified = new Date(data.last_modified);
+        // debug 484
+        this._last_modified = 'save-success:'+data.last_modified;
         if (data.message) {
             // save succeeded, but validation failed.
             var body = $("<div>");
@@ -2513,6 +2519,8 @@ define(function (require) {
                 that.notebook_name = json.name;
                 that.notebook_path = json.path;
                 that.last_modified = new Date(json.last_modified);
+                // debug 484
+                _that.last_modified = json.last_modified;
                 that.session.rename_notebook(json.path);
                 that.events.trigger('notebook_renamed.Notebook', json);
             }
@@ -2610,6 +2618,8 @@ define(function (require) {
         this.scroll_to_top();
         this.writable = data.writable || false;
         this.last_modified = new Date(data.last_modified);
+        // debug 484
+        this._last_modified = 'load-success:'+data.last_modified
         var nbmodel = data.content;
         var orig_nbformat = nbmodel.metadata.orig_nbformat;
         var orig_nbformat_minor = nbmodel.metadata.orig_nbformat_minor;

From 75a0585aecc39111679026678cf6ba8ee12c20b2 Mon Sep 17 00:00:00 2001
From: "Brian E. Granger" <ellisonbg@gmail.com>
Date: Fri, 20 Nov 2015 17:07:45 -0800
Subject: [PATCH 04/40] Work on the style and usability of find and replace...

---
 .../static/notebook/js/searchandreplace.js    | 78 +++++++++----------
 1 file changed, 37 insertions(+), 41 deletions(-)

diff --git a/notebook/static/notebook/js/searchandreplace.js b/notebook/static/notebook/js/searchandreplace.js
index 312810c3d..a9b1cbb58 100644
--- a/notebook/static/notebook/js/searchandreplace.js
+++ b/notebook/static/notebook/js/searchandreplace.js
@@ -68,7 +68,7 @@ define(function(require){
     if(aborted){
       body.append($('<p/>').addClass('bg-warning').text("Warning, too many matches ("+html.length+"+), some changes might not be shown or applied"));
     } else {
-      body.append($('<p/>').addClass('bg-info').text(html.length+" match"+(html.length==1?'':'es')));
+      body.append($('<p/>').text(html.length+" match"+(html.length==1?'':'es')));
     }
     for(var rindex=0; rindex<html.length; rindex++){
       var pre = $('<pre/>')
@@ -147,58 +147,54 @@ define(function(require){
    * Search N' Replace action handler.
    **/
   var snr = function(env, event) {
-    var search  = $("<input/>")
-      .addClass('form-control')
-      .attr('placeholder','Find');
+      
     var isRegExpButton = $('<button/>')
       .attr('type', 'button')
       .attr('id', 'isreg')
-      .addClass("btn btn-default")
+      .addClass("btn btn-default btn-sm")
       .attr('data-toggle','button')
+      .css('font-weight', 'bold')
       .attr('title', 'Use regex (JavaScript regex syntax)')
       .text('.*');
 
-    var onlySelectedButton = $('<button/>')
+    var onlySelectedButton = $('<button><i class="fa fa-align-left"/></button>')
       .attr('type', 'button')
-      .addClass("btn btn-default")
-      .append($('<i/>')
-        .addClass("fa fa-check-square-o")
-      )
+      .addClass("btn btn-default btn-sm")
       .attr('data-toggle','button')
-      .attr('title', 'Replace only in selected cells');
+      .attr('title', 'Find in selected cells');
 
     var isCaseSensitiveButton = $('<button/>')
       .attr('type', 'button')
-      .addClass("btn btn-default")
+      .addClass("btn btn-default btn-sm")
       .attr('data-toggle','button')
       .attr('tabindex', '0')
-      .attr('title', 'Case sensitive')
-      .text('a≠A');
-
-    var repl = $("<input/>")
-      .addClass('form-control')
-      .attr('placeholder','Replace');
-    var body = $('<div/>')
-      .attr('id', 'replace-preview');
-    var form = $('<form/>')
-      .attr('id', 'find-and-replace')
-      .append($('<div/>').addClass('form-group')
+      .attr('title', 'Match case')
+      .css('font-weight', 'bold')
+      .text('Aa');
+     
+    var search  = $("<input/>").addClass('form-control input-sm').attr('placeholder','Find');
+    var findFormGroup = $('<div/>').addClass('form-group');
+    findFormGroup.append(
+        $('<div/>').addClass('input-group')
         .append(
-          $('<div/>').addClass('input-group')
-          .append(
             $('<div/>').addClass('input-group-btn')
                 .append(isCaseSensitiveButton)
                 .append(isRegExpButton)
                 .append(onlySelectedButton)
-          )
-          .append(search)
         )
-      )
-      .append($('<div/>').addClass('form-group')
-        .append(repl)
-      )
-      .append(body);
+        .append(search)
+    )
 
+    var replace = $("<input/>").addClass('form-control input-sm').attr('placeholder','Replace');
+    var replaceFormGroup = $('<div/>').addClass('form-group');
+    replaceFormGroup.append(replace);
+
+    var body = $('<div/>').attr('id', 'replace-preview');
+     
+    var form = $('<form/>').attr('id', 'find-and-replace')
+    form.append(findFormGroup);
+    form.append(replaceFormGroup);
+    form.append(body);
 
     // return whether the search is case sensitive
     var isCaseSensitive = function(){
@@ -272,14 +268,14 @@ define(function(require){
       }
 
       // might want to warn if replace is empty
-      var replace = repl.val();
+      var replaceValue = replace.val();
       var lines = get_all_text(get_cells(env));
 
-      var _hb = compute_preview_model(sre, lines, isCaseSensitive(), RegExpOrNot, replace);
+      var _hb = compute_preview_model(sre, lines, isCaseSensitive(), RegExpOrNot, replaceValue);
       var html = _hb[0];
       var aborted = _hb[1];
 
-      build_preview(body, aborted, html, replace);
+      build_preview(body, aborted, html, replaceValue);
 
       // done on type return false not to submit form
       return false;
@@ -287,7 +283,7 @@ define(function(require){
 
     var onsubmit = function(event) {
       var sre = search.val();
-      var replace = repl.val();
+      var replaceValue = replace.val();
       if (!sre) {
         return false;
       }
@@ -300,7 +296,7 @@ define(function(require){
       for (var c = 0; c < cells.length; c++) {
         var cell = cells[c];
         var oldvalue = cell.code_mirror.getValue();
-        var newvalue = oldvalue.replace(reg , replace);
+        var newvalue = oldvalue.replace(reg , replaceValue);
         cell.code_mirror.setValue(newvalue);
         if (cell.cell_type === 'markdown') {
           cell.rendered = false;
@@ -322,19 +318,19 @@ define(function(require){
     });
 
     onlySelectedButton.click(function(){
-      repl.focus();
+      replace.focus();
       setTimeout(function(){onChange();}, 100);
     });
 
 
     search.keypress(function (e) {
       if (e.which == 13) {//enter
-        repl.focus();
+        replace.focus();
       }
     });
 
     search.on('input', onChange);
-    repl.on('input',  onChange);
+    replace.on('input',  onChange);
 
 
     var mod = dialog.modal({
@@ -352,7 +348,7 @@ define(function(require){
       }
     });
 
-    repl.keypress(function (e) {
+    replace.keypress(function (e) {
       if (e.which == 13) {//enter
         onsubmit();
         mod.modal('hide');

From ed812735cf05adf5d51fa4451d2cd1381ec4ebc7 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 24 Nov 2015 21:27:06 +0100
Subject: [PATCH 05/40] allow specifying default dialog button

rather than always focusing rightmost button

use:

    default_button: "label"

to explicitly request a button be the default.
---
 notebook/static/base/js/dialog.js | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/notebook/static/base/js/dialog.js b/notebook/static/base/js/dialog.js
index 14212bfa5..769817410 100644
--- a/notebook/static/base/js/dialog.js
+++ b/notebook/static/base/js/dialog.js
@@ -75,6 +75,8 @@ define(function(require) {
         
         var footer = $("<div/>").addClass("modal-footer");
         
+        var default_button;
+        
         for (var label in options.buttons) {
             var btn_opts = options.buttons[label];
             var button = $("<button/>")
@@ -88,12 +90,18 @@ define(function(require) {
                 button.addClass(btn_opts.class);
             }
             footer.append(button);
+            if (options.default_button && label === options.default_button) {
+                default_button = button;
+            }
+        }
+        if (!options.default_button) {
+            default_button = footer.find("button").last();
         }
         dialog_content.append(footer);
         // hook up on-open event
-        modal.on("shown.bs.modal", function() {
-            setTimeout(function() {
-                footer.find("button").last().focus();
+        modal.on("shown.bs.modal", function () {
+            setTimeout(function () {
+                default_button.focus();
                 if (options.open) {
                     $.proxy(options.open, modal)();
                 }

From 0576363be42860bf68012bedb76a1b08ac333291 Mon Sep 17 00:00:00 2001
From: "Brian E. Granger" <ellisonbg@gmail.com>
Date: Tue, 24 Nov 2015 17:38:08 -0800
Subject: [PATCH 06/40] Better jQuery style...

---
 notebook/static/notebook/js/searchandreplace.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/notebook/static/notebook/js/searchandreplace.js b/notebook/static/notebook/js/searchandreplace.js
index a9b1cbb58..7cf0d99bf 100644
--- a/notebook/static/notebook/js/searchandreplace.js
+++ b/notebook/static/notebook/js/searchandreplace.js
@@ -157,7 +157,8 @@ define(function(require){
       .attr('title', 'Use regex (JavaScript regex syntax)')
       .text('.*');
 
-    var onlySelectedButton = $('<button><i class="fa fa-align-left"/></button>')
+      var onlySelectedButton = $('<button/>')
+      .append($('<i/>').addClass('fa fa-align-left'))
       .attr('type', 'button')
       .addClass("btn btn-default btn-sm")
       .attr('data-toggle','button')

From e31fc195e2345d51ba750011ee6be0569abd5719 Mon Sep 17 00:00:00 2001
From: "Brian E. Granger" <ellisonbg@gmail.com>
Date: Tue, 24 Nov 2015 17:57:52 -0800
Subject: [PATCH 07/40] Addressing review comments...

---
 notebook/static/notebook/js/searchandreplace.js     | 11 ++++++++---
 notebook/static/notebook/less/searchandreplace.less | 12 ++++++++----
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/notebook/static/notebook/js/searchandreplace.js b/notebook/static/notebook/js/searchandreplace.js
index 7cf0d99bf..c1118d6b2 100644
--- a/notebook/static/notebook/js/searchandreplace.js
+++ b/notebook/static/notebook/js/searchandreplace.js
@@ -162,7 +162,7 @@ define(function(require){
       .attr('type', 'button')
       .addClass("btn btn-default btn-sm")
       .attr('data-toggle','button')
-      .attr('title', 'Find in selected cells');
+      .attr('title', 'Replace in selected cells');
 
     var isCaseSensitiveButton = $('<button/>')
       .attr('type', 'button')
@@ -173,7 +173,10 @@ define(function(require){
       .css('font-weight', 'bold')
       .text('Aa');
      
-    var search  = $("<input/>").addClass('form-control input-sm').attr('placeholder','Find');
+    var search  = $("<input/>")
+      .addClass('form-control input-sm')
+      .attr('placeholder','Find');
+
     var findFormGroup = $('<div/>').addClass('form-group');
     findFormGroup.append(
         $('<div/>').addClass('input-group')
@@ -186,7 +189,9 @@ define(function(require){
         .append(search)
     )
 
-    var replace = $("<input/>").addClass('form-control input-sm').attr('placeholder','Replace');
+    var replace = $("<input/>")
+      .addClass('form-control input-sm')
+      .attr('placeholder','Replace');
     var replaceFormGroup = $('<div/>').addClass('form-group');
     replaceFormGroup.append(replace);
 
diff --git a/notebook/static/notebook/less/searchandreplace.less b/notebook/static/notebook/less/searchandreplace.less
index 9b99b1102..c09f7a75a 100644
--- a/notebook/static/notebook/less/searchandreplace.less
+++ b/notebook/static/notebook/less/searchandreplace.less
@@ -1,6 +1,7 @@
 
 #find-and-replace {
-  #replace-preview .match, #replace-preview .insert{
+
+  #replace-preview .match, #replace-preview .insert {
     background-color:lightblue;
     border-color: darken(lightblue, 20%);
     border-style: solid;
@@ -10,22 +11,25 @@
     
   #replace-preview .replace {
     
-    & .match{
+    & .match {
       //display: none;
       background-color:salmon;
       text-decoration: line-through;
       border-color: darken(salmon, 20%);
     }
     
-    & .insert{
+    & .insert {
       background-color: green;
       background-color:lightGreen;
       border-color: darken(lightGreen, 20%);
     }
   }
 
-  & #replace-preview {
+  #replace-preview {
     max-height: 60vh;
     overflow: auto;
+    pre {
+        padding: 5px 10px;
+    }
   }
 }

From b9280d50e37633781172f5f0a994cbcb2777e051 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Wed, 25 Nov 2015 09:15:07 +0100
Subject: [PATCH 08/40] Create tool to auto generate secure settings.

---
 tools/secure_notebook.py | 101 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 tools/secure_notebook.py

diff --git a/tools/secure_notebook.py b/tools/secure_notebook.py
new file mode 100644
index 000000000..a6134980c
--- /dev/null
+++ b/tools/secure_notebook.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+from notebook.auth import passwd
+from traitlets.config.loader import JSONFileConfigLoader, ConfigFileNotFound
+import six
+from jupyter_core.paths import jupyter_config_dir
+from traitlets.config import Config
+
+
+
+from OpenSSL import crypto, SSL
+from socket import gethostname
+from pprint import pprint
+from time import gmtime, mktime
+from os.path import exists, join
+
+import io
+import os
+import json
+
+
+def create_self_signed_cert(cert_dir, keyfile, certfiile):
+    """
+    If datacard.crt and datacard.key don't exist in cert_dir, create a new
+    self-signed cert and keypair and write them into that directory.
+    """
+
+    if not exists(join(cert_dir, certfiile)) \
+            or not exists(join(cert_dir, keyfile)):
+
+        # create a key pair
+        k = crypto.PKey()
+        k.generate_key(crypto.TYPE_RSA, 1024)
+
+        # create a self-signed cert
+        cert = crypto.X509()
+        cert.get_subject().C = "US"
+        cert.get_subject().ST = "Jupyter notebook self-signed certificat"
+        cert.get_subject().L = "Jupyter notebook self-signed certificat"
+        cert.get_subject().O = "Jupyter notebook self-signed certificat"
+        cert.get_subject().OU = "my organization"
+        cert.get_subject().CN = "Jupyter notebook self-signed certificat"
+        cert.set_serial_number(1000)
+        cert.gmtime_adj_notBefore(0)
+        cert.gmtime_adj_notAfter(365*24*60*60)
+        cert.set_issuer(cert.get_subject())
+        cert.set_pubkey(k)
+        cert.sign(k, 'sha256')
+
+        with io.open(join(cert_dir, certfile), "wt") as f:
+            f.write(crypto.dump_certificate(crypto.FILETYPE_PEM, cert).decode('utf8'))
+        with io.open(join(cert_dir, keyfile), "wt") as f:
+            f.write(crypto.dump_privatekey(crypto.FILETYPE_PEM, k).decode('utf8'))
+
+
+if __name__ == '__main__':
+    print("This guide you into securing your notebook server")
+    print("fist choose a password.")
+    pw = passwd()
+    print("We will sore you password encrypted in the notebook configuration file: ")
+    print(pw)
+
+    loader = JSONFileConfigLoader('jupyter_notebook_config.json', jupyter_config_dir())
+    try:
+        config = loader.load_config()
+    except ConfigFileNotFound:
+        config = Config()
+
+    config.NotebookApp.password = pw
+
+    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w+') as f:
+        f.write(six.u(json.dumps(config, indent=2)))
+
+    print('... done')
+    print()
+
+    print("Now let's generate self signed https certificats to secure your connexion.")
+    print("where should the certificate live ?")
+    location = input('path [~/.ssh]: ')
+    if not location.strip():
+        location = os.path.expanduser('~/.ssh')
+    keyfile = input('keyfile name [jupyter_server.key]: ')
+    if not keyfile.strip():
+        keyfile = 'jupyter_server.key'
+    certfile = input('certfile name [jupyter_server.crt]: ')
+    if not certfile.strip():
+        certfile = 'jupyter_server.crt'
+
+    create_self_signed_cert(location, keyfile, certfile)
+
+    fullkey = os.path.join(location, keyfile)
+    fullcrt = os.path.join(location, certfile)
+
+    config.NotebookApp.certfile = fullcrt
+    config.NotebookApp.keyfile = fullkey
+
+    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w+') as f:
+        f.write(six.u(json.dumps(config, indent=2)))
+
+
+

From 5a7a41a83e93f515716ec415d70df98f0dc2c36e Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Wed, 25 Nov 2015 13:39:04 +0100
Subject: [PATCH 09/40] don't write english before breakfast

---
 tools/secure_notebook.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/tools/secure_notebook.py b/tools/secure_notebook.py
index a6134980c..ebdc22a54 100644
--- a/tools/secure_notebook.py
+++ b/tools/secure_notebook.py
@@ -35,11 +35,11 @@ def create_self_signed_cert(cert_dir, keyfile, certfiile):
         # create a self-signed cert
         cert = crypto.X509()
         cert.get_subject().C = "US"
-        cert.get_subject().ST = "Jupyter notebook self-signed certificat"
-        cert.get_subject().L = "Jupyter notebook self-signed certificat"
-        cert.get_subject().O = "Jupyter notebook self-signed certificat"
+        cert.get_subject().ST = "Jupyter notebook self-signed certificate"
+        cert.get_subject().L = "Jupyter notebook self-signed certificate"
+        cert.get_subject().O = "Jupyter notebook self-signed certificate"
         cert.get_subject().OU = "my organization"
-        cert.get_subject().CN = "Jupyter notebook self-signed certificat"
+        cert.get_subject().CN = "Jupyter notebook self-signed certificate"
         cert.set_serial_number(1000)
         cert.gmtime_adj_notBefore(0)
         cert.gmtime_adj_notAfter(365*24*60*60)
@@ -55,9 +55,9 @@ def create_self_signed_cert(cert_dir, keyfile, certfiile):
 
 if __name__ == '__main__':
     print("This guide you into securing your notebook server")
-    print("fist choose a password.")
+    print("first choose a password.")
     pw = passwd()
-    print("We will sore you password encrypted in the notebook configuration file: ")
+    print("We will store your password encrypted in the notebook configuration file: ")
     print(pw)
 
     loader = JSONFileConfigLoader('jupyter_notebook_config.json', jupyter_config_dir())
@@ -68,14 +68,14 @@ if __name__ == '__main__':
 
     config.NotebookApp.password = pw
 
-    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w+') as f:
+    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w') as f:
         f.write(six.u(json.dumps(config, indent=2)))
 
     print('... done')
     print()
 
-    print("Now let's generate self signed https certificats to secure your connexion.")
-    print("where should the certificate live ?")
+    print("Now let's generate self-signed certificates to secure your connexion.")
+    print("where should the certificate live?")
     location = input('path [~/.ssh]: ')
     if not location.strip():
         location = os.path.expanduser('~/.ssh')
@@ -94,7 +94,7 @@ if __name__ == '__main__':
     config.NotebookApp.certfile = fullcrt
     config.NotebookApp.keyfile = fullkey
 
-    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w+') as f:
+    with io.open(os.path.join(jupyter_config_dir(), 'jupyter_notebook_config.json'), 'w') as f:
         f.write(six.u(json.dumps(config, indent=2)))
 
 

From a9626ce3d1fa291763a50416d6fc0378262832d0 Mon Sep 17 00:00:00 2001
From: "Brian E. Granger" <ellisonbg@gmail.com>
Date: Wed, 25 Nov 2015 08:55:32 -0800
Subject: [PATCH 10/40] Changing colors on find and replace matches.

---
 .../notebook/less/searchandreplace.less       | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/notebook/static/notebook/less/searchandreplace.less b/notebook/static/notebook/less/searchandreplace.less
index c09f7a75a..01cedeef3 100644
--- a/notebook/static/notebook/less/searchandreplace.less
+++ b/notebook/static/notebook/less/searchandreplace.less
@@ -2,26 +2,28 @@
 #find-and-replace {
 
   #replace-preview .match, #replace-preview .insert {
-    background-color:lightblue;
-    border-color: darken(lightblue, 20%);
+    background-color: #BBDEFB; // MD Blue 100
+    border-color: #90CAF9; // MD Blue 200
     border-style: solid;
     border-width: 1px;
-    border-radius: @border-radius-base
+    border-radius: 0px;
   }
     
   #replace-preview .replace {
     
     & .match {
-      //display: none;
-      background-color:salmon;
-      text-decoration: line-through;
-      border-color: darken(salmon, 20%);
+     // text-decoration: line-through;
+      background-color: #FFCDD2; // MD Red 100
+      border-color: #EF9A9A; // MD Red 200
+      border-radius: 0px;
+      
     }
     
     & .insert {
-      background-color: green;
-      background-color:lightGreen;
-      border-color: darken(lightGreen, 20%);
+      background-color: #C8E6C9; // MD Green 100
+      border-color: #A5D6A7; // MD Green 200
+      border-radius: 0px;
+      
     }
   }
 

From 1feb3960d8b14b91b38bb5426799e015b8e6278b Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Wed, 25 Nov 2015 19:22:10 +0100
Subject: [PATCH 11/40] Start documenting how to write font end extension

This if course require more work, but the request for custom key binding
is too high, and the process of writing extensions too widespread on the
internet.
---
 docs/source/extending/frontend_extensions.rst | 145 ++++++++++++++++++
 1 file changed, 145 insertions(+)
 create mode 100644 docs/source/extending/frontend_extensions.rst

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
new file mode 100644
index 000000000..c16c7624b
--- /dev/null
+++ b/docs/source/extending/frontend_extensions.rst
@@ -0,0 +1,145 @@
+Custom front-end extesions
+==========================
+
+This describe the basic steps to write a JavaScript extension for the Jupyter
+notebook front-end. This allows you to customize the behavior of the various
+pages like the dashboard, the notebook, the text editor. 
+
+The structure of an extension
+-----------------------------
+
+.. note::
+
+    The notebook fontend and Javascript API are not stable, and are subject to
+    lot of changes. Any extension written for the current notebook is almost
+    guarantied to break in the next release.
+
+A front-end extension is a JavaScript file that define an AMD module which
+expose at least a function called `load_ipython_extension` which takes no
+arguments. We will not get into details about what each of these term are, 
+but here is the minimal code needed for a working extension:
+
+.. code:: javascript
+
+    //file myext/main.js
+
+    define(function(){
+
+        function load_ipython_extension(){
+            console.info('this is my first extension')
+        }
+
+        return {load_ipython_extension: load_ipython_extension };
+    })
+
+.. note::
+    
+    for historical reason the function is called `load_ipython_extension`,
+    though it does apply to the Jupyter notebook as well and will work
+    regardless of the kernel you use. 
+
+If you are familiar with JavaScript, you can use this template to require any
+Jupyter module and modify their configuration.  Your extension will be loaded
+at the right time during the notebook page initialisation for you to hook
+listener for the various even that the page can trigger. 
+
+You might want to access to the current instances of the various component on
+the page, these a re exposed by a module name `base/js/namespace`.  If you plan
+on accessing instances on the page, be careful to require this module and not
+access the global variable `Jupyter`.
+
+Here is how to do that:
+
+
+.. code:: javascript
+
+    //file myext/main.js
+
+    define(['base/js/namespace'],function(Jupyter){
+
+        function load_ipython_extension(){
+            console.log('This is the current notebook application instance', Jupyter.notebook);
+        }
+
+        return {load_ipython_extension: load_ipython_extension };
+    })
+
+
+
+Modify key bindings
+-------------------
+
+One of the ability of extensions is to modify key bindings, once again this is
+a API which is not guarantied to be stable. Though the request for custom key
+bindings is often require and helpful to increase accessibility, so in the
+following we show how to access theses.
+
+Here is an example of extension that will unbind `0,0` in command mode to
+restart the kernel, and bind `0,0,0` in it's place.
+
+.. code:: javascript
+
+    //file myext/main.js
+
+    define(['base/js/namespace'],function(Jupyter){
+
+        function load_ipython_extension(){
+            Jupyter.keyboard_manager.command_shortcuts.remove_shortcut('0,0')
+            Jupyter.keyboard_manager.command_shortcuts.add_shortcut('0,0,0', 'jupyter-notebook:restart-kernel')
+        }
+
+        return {load_ipython_extension: load_ipython_extension };
+    })
+
+.. note::
+    
+    We are awre the keybindings might not work correctly on non US keyboard,
+    unfortunately it is a limitation of browser implmentation and teh status of
+    the keyboard handling on the web. We appreciate you input if you have issue
+    binding some keys, or help to improve the situation. 
+
+You can see that I have used the **command name**
+`jupyter-notebook:restart-kernel` to bind the new shortcut. There is no API yet
+to access the list of all available *commands*, though the following in the
+JavaScript console of your browser on a notebook page should give you an idea
+of what of available. 
+
+
+
+.. code:: javascript
+
+    Object.keys(IPython.actions._actions)
+
+I'm also binding keyboard shortcut on the **command mode** you can also bind
+them on the edit mode. Keep in mind though the most keyboard shortcuts on the
+edit mode are handled by CodeMirror which also support custom key bindings, but
+not using the system describe here. 
+
+You can also define and register your own action to be used, but the
+documentation for it has not been written yet. If you need to do it, 
+please ask us, we can give you the necessary information, and we would appreciate
+if you could format them in a detailed way in place of this paragraph.
+
+
+
+installation and activation of extension
+----------------------------------------
+
+You can install your extension in the Jupyter configuration directory, under
+the `nbextensions` subdirectory. On Unix system this will likely be
+`~/.jupyter/nbextensions/`. 
+
+You thus will likely end up with the file
+`~/.jupyter/nbextensions/myextension/main.js` that now need to be loaded by the
+notebook. You can configure you Jupyter Notebook to do so using the Jupyter
+front-end configuration system described later in these docs. 
+
+A 1 line to activate you extension would be to issue the following **once** in
+a notebook JavaScript console:
+
+.. code:: javascript
+
+    Jupyter.notebook.config.update({
+      "load_extensions": {"myextension/main": true}
+    }) 
+

From 6f5e7cae97fc38efb5383bc6a2cc07f39fe44863 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Thu, 26 Nov 2015 23:11:20 +0100
Subject: [PATCH 12/40] fix typo

---
 notebook/static/notebook/js/notebook.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/notebook/static/notebook/js/notebook.js b/notebook/static/notebook/js/notebook.js
index 1844ce6c8..5de9f14ba 100644
--- a/notebook/static/notebook/js/notebook.js
+++ b/notebook/static/notebook/js/notebook.js
@@ -2520,7 +2520,7 @@ define(function (require) {
                 that.notebook_path = json.path;
                 that.last_modified = new Date(json.last_modified);
                 // debug 484
-                _that.last_modified = json.last_modified;
+                that._last_modified = json.last_modified;
                 that.session.rename_notebook(json.path);
                 that.events.trigger('notebook_renamed.Notebook', json);
             }

From a0929ab8c1436f032e26a416c9cdf4479dadc436 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Fri, 27 Nov 2015 13:29:03 +0100
Subject: [PATCH 13/40] Timeout is an option of `waitFor`, not `then`

---
 notebook/tests/util.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/notebook/tests/util.js b/notebook/tests/util.js
index aa0d995a5..4f5eb18aa 100644
--- a/notebook/tests/util.js
+++ b/notebook/tests/util.js
@@ -166,11 +166,11 @@ casper.wait_for_output = function (cell_num, out_num) {
             },
             // pass parameter from the test suite js to the browser code js
             {c : cell_num, o : out_num});
+        },
+        function then() { },
+        function timeout() {
+            this.echo("wait_for_output timed out!");
         });
-    },
-    function then() { },
-    function timeout() {
-        this.echo("wait_for_output timed out!");
     });
 };
 

From c54b4f0e1d5eb1b64201155e4dec9e9884af5cc5 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Fri, 27 Nov 2015 13:46:04 +0100
Subject: [PATCH 14/40] more info on timeout

---
 notebook/tests/util.js | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/notebook/tests/util.js b/notebook/tests/util.js
index 4f5eb18aa..950cbcbc7 100644
--- a/notebook/tests/util.js
+++ b/notebook/tests/util.js
@@ -169,7 +169,11 @@ casper.wait_for_output = function (cell_num, out_num) {
         },
         function then() { },
         function timeout() {
-            this.echo("wait_for_output timed out!");
+            this.echo("wait_for_output timed out on cell "+cell_num+", waiting for "+out_num+"outputs .");
+            pn = this.evaluate(function get_prompt(c) {
+                return IPython.notebook.get_cell(c).input_prompt_number;
+            });
+            this.echo("cell prompt was :'"+pn+"'.")
         });
     });
 };

From 6692ea73484862c7361daa1605812cd5bf80e7bb Mon Sep 17 00:00:00 2001
From: marcelo-ramires <marcelo.f.ramires@gmail.com>
Date: Fri, 27 Nov 2015 19:02:37 -0200
Subject: [PATCH 15/40] Fixing backspace on multiple selection bug

---
 notebook/static/notebook/js/codecell.js | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/notebook/static/notebook/js/codecell.js b/notebook/static/notebook/js/codecell.js
index 59d8b4729..42e693eed 100644
--- a/notebook/static/notebook/js/codecell.js
+++ b/notebook/static/notebook/js/codecell.js
@@ -50,7 +50,14 @@ define([
      */
     CodeMirror.commands.delSpaceToPrevTabStop = function(cm){
         var from = cm.getCursor(true), to = cm.getCursor(false), sel = !posEq(from, to);
-        if (!posEq(from, to)) { cm.replaceRange("", from, to); return; }
+         if (sel) { 
+            var ranges = cm.listSelections();
+            for (var i = ranges.length - 1; i >= 0; i--) {
+              var cur = ranges[i].head;
+              cm.replaceRange("", Pos(cur.line, cur.ch - 1), Pos(cur.line, cur.ch + 1));
+            }
+            return;
+        }
         var cur = cm.getCursor(), line = cm.getLine(cur.line);
         var tabsize = cm.getOption('tabSize');
         var chToPrevTabStop = cur.ch-(Math.ceil(cur.ch/tabsize)-1)*tabsize;

From 2cb85ab939e5728b444ac4651704330fdc674d04 Mon Sep 17 00:00:00 2001
From: Sylvain Corlay <sylvain.corlay@gmail.com>
Date: Fri, 27 Nov 2015 16:59:20 -0500
Subject: [PATCH 16/40] fix deprecation warning

---
 notebook/notebookapp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/notebook/notebookapp.py b/notebook/notebookapp.py
index c9badd0b8..2c1d392d7 100644
--- a/notebook/notebookapp.py
+++ b/notebook/notebookapp.py
@@ -120,7 +120,7 @@ class DeprecationHandler(IPythonHandler):
     def get(self, url_path):
         self.set_header("Content-Type", 'text/javascript')
         self.finish("""
-            console.warn('`/static/widgets/js` is deprecated.  Use `/nbextensions/widgets/widgets/js` instead.');
+            console.warn('`/static/widgets/js` is deprecated.  Use `nbextensions/widgets/widgets/js` instead.');
             define(['%s'], function(x) { return x; });
         """ % url_path_join('nbextensions', 'widgets', 'widgets', url_path.rstrip('.js')))
         self.log.warn('Deprecated widget Javascript path /static/widgets/js/*.js was used')

From 259be440b51bd802d4d840bd19f22baf3a8da4cd Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Sun, 29 Nov 2015 14:04:41 +0100
Subject: [PATCH 17/40] use var

---
 notebook/tests/util.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/notebook/tests/util.js b/notebook/tests/util.js
index 950cbcbc7..8a15b1d56 100644
--- a/notebook/tests/util.js
+++ b/notebook/tests/util.js
@@ -170,7 +170,7 @@ casper.wait_for_output = function (cell_num, out_num) {
         function then() { },
         function timeout() {
             this.echo("wait_for_output timed out on cell "+cell_num+", waiting for "+out_num+"outputs .");
-            pn = this.evaluate(function get_prompt(c) {
+            var pn = this.evaluate(function get_prompt(c) {
                 return IPython.notebook.get_cell(c).input_prompt_number;
             });
             this.echo("cell prompt was :'"+pn+"'.")

From 531b373eb8776593edf103e1c31fdd90295cb373 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Mon, 30 Nov 2015 01:05:44 +0000
Subject: [PATCH 18/40] fix bug in `notebook/js/quickhelp` whereby edit-mode
 shortcuts were duplicated on every rebuild

---
 notebook/static/notebook/js/quickhelp.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/notebook/static/notebook/js/quickhelp.js b/notebook/static/notebook/js/quickhelp.js
index 6c49d8519..735358b50 100644
--- a/notebook/static/notebook/js/quickhelp.js
+++ b/notebook/static/notebook/js/quickhelp.js
@@ -257,8 +257,8 @@ define([
     
     QuickHelp.prototype.build_edit_help = function (cm_shortcuts) {
         var edit_shortcuts = this.keyboard_manager.edit_shortcuts.help();
-        jQuery.merge(cm_shortcuts, edit_shortcuts);
-        return build_div('<h4>Edit Mode (press <kbd>Enter</kbd> to enable)</h4>', cm_shortcuts);
+        edit_shortcuts = jQuery.merge(jQuery.merge([], cm_shortcuts), edit_shortcuts);
+        return build_div('<h4>Edit Mode (press <kbd>Enter</kbd> to enable)</h4>', edit_shortcuts);
     };
 
     var build_one = function (s) {

From f32651e202e9cbc74a18f9e40c7ab1e243026435 Mon Sep 17 00:00:00 2001
From: Sylvain Corlay <sylvain.corlay@gmail.com>
Date: Fri, 27 Nov 2015 18:38:17 -0500
Subject: [PATCH 19/40] Use jquery-ui instead of jqueryui

---
 notebook/static/notebook/js/outputarea.js | 2 +-
 notebook/static/notebook/js/pager.js      | 2 +-
 notebook/static/tree/js/main.js           | 2 +-
 notebook/templates/page.html              | 9 +++++++--
 tools/build-main.js                       | 9 +++++++--
 5 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/notebook/static/notebook/js/outputarea.js b/notebook/static/notebook/js/outputarea.js
index 5a5e25d1b..600484ba3 100644
--- a/notebook/static/notebook/js/outputarea.js
+++ b/notebook/static/notebook/js/outputarea.js
@@ -2,7 +2,7 @@
 // Distributed under the terms of the Modified BSD License.
 
 define([
-    'jqueryui',
+    'jquery-ui',
     'base/js/utils',
     'base/js/security',
     'base/js/keyboard',
diff --git a/notebook/static/notebook/js/pager.js b/notebook/static/notebook/js/pager.js
index 0b423758b..260f7b471 100644
--- a/notebook/static/notebook/js/pager.js
+++ b/notebook/static/notebook/js/pager.js
@@ -2,7 +2,7 @@
 // Distributed under the terms of the Modified BSD License.
 
 define([
-    'jqueryui',
+    'jquery-ui',
     'base/js/utils',
 ], function($, utils) {
     "use strict";
diff --git a/notebook/static/tree/js/main.js b/notebook/static/tree/js/main.js
index 1cf61e248..fd12a4ae8 100644
--- a/notebook/static/tree/js/main.js
+++ b/notebook/static/tree/js/main.js
@@ -17,7 +17,7 @@ require([
     'tree/js/newnotebook',
     'auth/js/loginwidget',
     // only loaded, not used:
-    'jqueryui',
+    'jquery-ui',
     'bootstrap',
     'custom/custom',
 ], function(
diff --git a/notebook/templates/page.html b/notebook/templates/page.html
index 13402b92c..f9cd56a97 100644
--- a/notebook/templates/page.html
+++ b/notebook/templates/page.html
@@ -34,12 +34,17 @@
             jquery: 'components/jquery/jquery.min',
             bootstrap: 'components/bootstrap/js/bootstrap.min',
             bootstraptour: 'components/bootstrap-tour/build/js/bootstrap-tour.min',
-            jqueryui: 'components/jquery-ui/ui/minified/jquery-ui.min',
+            'jquery-ui': 'components/jquery-ui/ui/minified/jquery-ui.min',
             moment: 'components/moment/moment',
             codemirror: 'components/codemirror',
             termjs: 'components/term.js/src/term',
             typeahead: 'components/jquery-typeahead/dist/jquery.typeahead'
           },
+	  map: { // for backward compatibility
+	    "*": {
+		"jqueryui": "jquery-ui",
+	    }
+	  },
           shim: {
             typeahead: {
               deps: ["jquery"],
@@ -60,7 +65,7 @@
               deps: ["bootstrap"],
               exports: "Tour"
             },
-            jqueryui: {
+            "jquery-ui": {
               deps: ["jquery"],
               exports: "$"
             }
diff --git a/tools/build-main.js b/tools/build-main.js
index 00763b9b8..1ae0a64a1 100644
--- a/tools/build-main.js
+++ b/tools/build-main.js
@@ -18,13 +18,18 @@ var rjs_config = {
     jquery: 'components/jquery/jquery.min',
     bootstrap: 'components/bootstrap/js/bootstrap.min',
     bootstraptour: 'components/bootstrap-tour/build/js/bootstrap-tour.min',
-    jqueryui: 'components/jquery-ui/ui/minified/jquery-ui.min',
+    "jquery-ui": 'components/jquery-ui/ui/minified/jquery-ui.min',
     moment: 'components/moment/moment',
     codemirror: 'components/codemirror',
     termjs: 'components/term.js/src/term',
     typeahead: 'components/jquery-typeahead/dist/jquery.typeahead',
     contents: 'empty:'
   },
+  map: { // for backward compatibility
+    "*": {
+        "jqueryui": "jquery-ui",
+    }
+  },
   shim: {
     typeahead: {
             deps: ["jquery"],
@@ -45,7 +50,7 @@ var rjs_config = {
       deps: ["bootstrap"],
       exports: "Tour"
     },
-    jqueryui: {
+    "jquery-ui": {
       deps: ["jquery"],
       exports: "$"
     }

From 92caca5683f6cfb638aa3917340447bfc2f81b45 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Mon, 30 Nov 2015 18:26:25 +0000
Subject: [PATCH 20/40] English fixes and update description of installing and
 activating extensions

---
 docs/source/extending/frontend_extensions.rst | 105 ++++++++----------
 1 file changed, 49 insertions(+), 56 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index c16c7624b..7b7e72f82 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -1,22 +1,22 @@
 Custom front-end extesions
 ==========================
 
-This describe the basic steps to write a JavaScript extension for the Jupyter
-notebook front-end. This allows you to customize the behavior of the various
-pages like the dashboard, the notebook, the text editor. 
+This describes the basic steps to write a JavaScript extension for the Jupyter
+notebook front-end. This allows you to customize the behaviour of the various
+pages like the dashboard, the notebook, or the text editor.
 
 The structure of an extension
 -----------------------------
 
 .. note::
 
-    The notebook fontend and Javascript API are not stable, and are subject to
-    lot of changes. Any extension written for the current notebook is almost
-    guarantied to break in the next release.
+    The notebook frontend and Javascript API are not stable, and are subject to
+    a lot of changes. Any extension written for the current notebook is almost
+    guaranteed to break in the next release.
 
-A front-end extension is a JavaScript file that define an AMD module which
-expose at least a function called `load_ipython_extension` which takes no
-arguments. We will not get into details about what each of these term are, 
+A front-end extension is a JavaScript file that defines an AMD module
+exposing at least a function called `load_ipython_extension`, which takes no
+arguments. We will not get into the details of what each of these terms are,
 but here is the minimal code needed for a working extension:
 
 .. code:: javascript
@@ -34,22 +34,19 @@ but here is the minimal code needed for a working extension:
 
 .. note::
     
-    for historical reason the function is called `load_ipython_extension`,
-    though it does apply to the Jupyter notebook as well and will work
+    For historical reasons, the function is called `load_ipython_extension`,
+    but it does apply to the Jupyter notebook as well, and will work
     regardless of the kernel you use. 
 
 If you are familiar with JavaScript, you can use this template to require any
-Jupyter module and modify their configuration.  Your extension will be loaded
-at the right time during the notebook page initialisation for you to hook
-listener for the various even that the page can trigger. 
+Jupyter module and modify its configuration. Your extension will be loaded
+at the right time during the notebook page initialisation for you to set up a
+listener for the various events that the page can trigger.
 
 You might want to access to the current instances of the various component on
-the page, these a re exposed by a module name `base/js/namespace`.  If you plan
-on accessing instances on the page, be careful to require this module and not
-access the global variable `Jupyter`.
-
-Here is how to do that:
-
+the page, these are exposed by a module named `base/js/namespace`. If you plan
+on accessing instances on the page, you should require this module rather than
+accessing the global variable `Jupyter`. Here is how to do that:
 
 .. code:: javascript
 
@@ -66,16 +63,15 @@ Here is how to do that:
 
 
 
-Modify key bindings
--------------------
+Modifying key bindings
+----------------------
 
-One of the ability of extensions is to modify key bindings, once again this is
-a API which is not guarantied to be stable. Though the request for custom key
-bindings is often require and helpful to increase accessibility, so in the
-following we show how to access theses.
+Extensions have the ability to modify key bindings. Once again, this API
+is not guaranteed to be stable, but changing key bindings is a common request.
+This is how to do it in the current version of the notebook.
 
-Here is an example of extension that will unbind `0,0` in command mode to
-restart the kernel, and bind `0,0,0` in it's place.
+Here is an example of extension that will unbind `0,0` in command mode, which
+normally restarts the kernel, and bind `0,0,0` in it's place.
 
 .. code:: javascript
 
@@ -93,53 +89,50 @@ restart the kernel, and bind `0,0,0` in it's place.
 
 .. note::
     
-    We are awre the keybindings might not work correctly on non US keyboard,
-    unfortunately it is a limitation of browser implmentation and teh status of
-    the keyboard handling on the web. We appreciate you input if you have issue
-    binding some keys, or help to improve the situation. 
+    Keybindings might not work correctly on non-US keyboards.
+    Unfortunately, this is a limitation of browser implementations and the status of
+    keyboard event handling on the web. We appreciate your feedback if you have
+    issues binding keys, or ideas to help improve the situation.
 
 You can see that I have used the **command name**
 `jupyter-notebook:restart-kernel` to bind the new shortcut. There is no API yet
 to access the list of all available *commands*, though the following in the
 JavaScript console of your browser on a notebook page should give you an idea
-of what of available. 
-
-
+of what of available:
 
 .. code:: javascript
 
     Object.keys(IPython.actions._actions)
 
-I'm also binding keyboard shortcut on the **command mode** you can also bind
-them on the edit mode. Keep in mind though the most keyboard shortcuts on the
-edit mode are handled by CodeMirror which also support custom key bindings, but
-not using the system describe here. 
+In this example, we changed keyboard shortcuts in **command mode**; you can also
+customise keyboard shortcuts in edit mode.
+However, most of the keyboard shortcuts in edit mode are handled by CodeMirror,
+which supports custom key bindings via a completely different API.
 
 You can also define and register your own action to be used, but the
-documentation for it has not been written yet. If you need to do it, 
+documentation for this has not been written yet. If you need to do it,
 please ask us, we can give you the necessary information, and we would appreciate
 if you could format them in a detailed way in place of this paragraph.
 
+Installing and enabling extensions
+----------------------------------
 
+You can install your nbextension with the command:
 
-installation and activation of extension
-----------------------------------------
-
-You can install your extension in the Jupyter configuration directory, under
-the `nbextensions` subdirectory. On Unix system this will likely be
-`~/.jupyter/nbextensions/`. 
+    jupyter nbextension install path/to/myext/
 
-You thus will likely end up with the file
-`~/.jupyter/nbextensions/myextension/main.js` that now need to be loaded by the
-notebook. You can configure you Jupyter Notebook to do so using the Jupyter
-front-end configuration system described later in these docs. 
+Where myext is the directory containing the Javascript files. This will copy
+it to a Jupyter data directory (the exact location is platform dependent - see
+:ref:`jupyter_path`).
 
-A 1 line to activate you extension would be to issue the following **once** in
-a notebook JavaScript console:
+For development, you can use the ``--symlink`` flag to symlink your extension
+rather than copying it, so there's no need to reinstall after changes.
 
-.. code:: javascript
+To use your extension, you'll also need to **enable** it, which tells the
+notebook interface to load it. You can do that with another command:
 
-    Jupyter.notebook.config.update({
-      "load_extensions": {"myextension/main": true}
-    }) 
+    jupyter nbextension enable myext/main
 
+The argument refers to the Javascript module containing your ``load_ipython_extension``
+function, which is ``myext/main.js`` in this example. There is a corresponding
+``disable`` command to stop using an extension without installing it.

From 1a855af8f276cc6bf9b8bac232a4bab43cbe3580 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Mon, 30 Nov 2015 21:17:28 +0000
Subject: [PATCH 21/40] give defined ordering to keyboard shortcuts with the
 same help_index

---
 notebook/static/base/js/keyboard.js | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/notebook/static/base/js/keyboard.js b/notebook/static/base/js/keyboard.js
index 2259cd126..ee2f46e2c 100644
--- a/notebook/static/base/js/keyboard.js
+++ b/notebook/static/base/js/keyboard.js
@@ -255,7 +255,13 @@ define([
         }
         help.sort(function (a, b) {
             if (a.help_index === b.help_index) {
-                return 0;
+                if (a.shortcut === b.shortcut) {
+                    return 0;
+                }
+                if (a.shortcut > b.shortcut) {
+                    return 1;
+                }
+                return -1;
             }
             if (a.help_index === undefined || a.help_index > b.help_index){
                 return 1;

From 8e0a8d1ea6f89015321f87917465381cd36aba1c Mon Sep 17 00:00:00 2001
From: Safia Abdalla <safia@safia.rocks>
Date: Mon, 30 Nov 2015 17:52:01 -0600
Subject: [PATCH 22/40] Added tests for directory renaming

---
 notebook/services/contents/tests/test_manager.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/notebook/services/contents/tests/test_manager.py b/notebook/services/contents/tests/test_manager.py
index 3ff2c805f..180a1d337 100644
--- a/notebook/services/contents/tests/test_manager.py
+++ b/notebook/services/contents/tests/test_manager.py
@@ -460,6 +460,19 @@ class TestContentsManager(TestCase):
         # Check that a 'get' on the deleted notebook raises and error
         self.assertRaises(HTTPError, cm.get, path)
 
+    def test_rename(self):
+        cm = self.contents_manager
+        # Create a new notebook
+        nb, name, path = self.new_notebook()
+
+        # Rename the notebook
+        cm.rename(path, "changed_path")
+
+        # Attempting to get the notebook under the old name raises an error
+        self.assertRaises(HTTPError, cm.get, path)
+        # Fetching the notebook under the new name is successful
+        assert isinstance(cm.get("changed_path"), dict)
+
     def test_delete_root(self):
         cm = self.contents_manager
         with self.assertRaises(HTTPError) as err:

From 66f7390f8d3cf289d28cbda010f9e8b37ff04b71 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Tue, 1 Dec 2015 10:27:36 +0100
Subject: [PATCH 23/40] missing N

---
 docs/source/extending/frontend_extensions.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index 7b7e72f82..5fbade66c 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -1,5 +1,5 @@
-Custom front-end extesions
-==========================
+Custom front-end extensions
+===========================
 
 This describes the basic steps to write a JavaScript extension for the Jupyter
 notebook front-end. This allows you to customize the behaviour of the various

From 6024f046988cfdf9243933ea80ba99734511c9fd Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Mon, 9 Nov 2015 14:40:21 +0100
Subject: [PATCH 24/40] allow some KernelManager methods to be async

Allows custom KernelManagers to do slower async operations as part of kernel startup/shutdown.
---
 notebook/services/kernels/handlers.py      | 10 +++++++---
 notebook/services/kernels/kernelmanager.py | 13 ++++++++-----
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/notebook/services/kernels/handlers.py b/notebook/services/kernels/handlers.py
index 19bc20315..0da36714f 100644
--- a/notebook/services/kernels/handlers.py
+++ b/notebook/services/kernels/handlers.py
@@ -25,12 +25,15 @@ class MainKernelHandler(APIHandler):
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def get(self):
         km = self.kernel_manager
-        self.finish(json.dumps(km.list_kernels()))
+        kernels = yield gen.maybe_future(km.list_kernels())
+        self.finish(json.dumps(kernels))
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def post(self):
         km = self.kernel_manager
         model = self.get_json_body()
@@ -41,7 +44,7 @@ class MainKernelHandler(APIHandler):
         else:
             model.setdefault('name', km.default_kernel_name)
 
-        kernel_id = km.start_kernel(kernel_name=model['name'])
+        kernel_id = yield gen.maybe_future(km.start_kernel(kernel_name=model['name']))
         model = km.kernel_model(kernel_id)
         location = url_path_join(self.base_url, 'api', 'kernels', url_escape(kernel_id))
         self.set_header('Location', location)
@@ -61,9 +64,10 @@ class KernelHandler(APIHandler):
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def delete(self, kernel_id):
         km = self.kernel_manager
-        km.shutdown_kernel(kernel_id)
+        yield gen.maybe_future(km.shutdown_kernel(kernel_id))
         self.set_status(204)
         self.finish()
 
diff --git a/notebook/services/kernels/kernelmanager.py b/notebook/services/kernels/kernelmanager.py
index d08d2ba8d..ccf2738a7 100644
--- a/notebook/services/kernels/kernelmanager.py
+++ b/notebook/services/kernels/kernelmanager.py
@@ -62,7 +62,8 @@ class MappingKernelManager(MultiKernelManager):
         while not os.path.isdir(os_path) and os_path != self.root_dir:
             os_path = os.path.dirname(os_path)
         return os_path
-
+    
+    @gen.coroutine
     def start_kernel(self, kernel_id=None, path=None, **kwargs):
         """Start a kernel for a session and return its kernel_id.
 
@@ -82,8 +83,9 @@ class MappingKernelManager(MultiKernelManager):
         if kernel_id is None:
             if path is not None:
                 kwargs['cwd'] = self.cwd_for_path(path)
-            kernel_id = super(MappingKernelManager, self).start_kernel(
-                                            **kwargs)
+            kernel_id = yield gen.maybe_future(
+                super(MappingKernelManager, self).start_kernel(**kwargs)
+            )
             self.log.info("Kernel started: %s" % kernel_id)
             self.log.debug("Kernel args: %r" % kwargs)
             # register callback for failed auto-restart
@@ -94,12 +96,13 @@ class MappingKernelManager(MultiKernelManager):
         else:
             self._check_kernel_id(kernel_id)
             self.log.info("Using existing kernel: %s" % kernel_id)
-        return kernel_id
+        # py2-compat
+        raise gen.Return(kernel_id)
 
     def shutdown_kernel(self, kernel_id, now=False):
         """Shutdown a kernel by kernel_id"""
         self._check_kernel_id(kernel_id)
-        super(MappingKernelManager, self).shutdown_kernel(kernel_id, now=now)
+        return super(MappingKernelManager, self).shutdown_kernel(kernel_id, now=now)
 
     def restart_kernel(self, kernel_id):
         """Restart a kernel by kernel_id"""

From 9043ae145c874b33be8fc60385fa4964f22b311c Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 10 Nov 2015 14:59:45 +0100
Subject: [PATCH 25/40] handle async in sessions

needed because sessions call kernel methods
---
 notebook/services/sessions/handlers.py        | 27 ++++---
 notebook/services/sessions/sessionmanager.py  | 19 +++--
 .../sessions/tests/test_sessionmanager.py     | 71 ++++++++++++-------
 3 files changed, 74 insertions(+), 43 deletions(-)

diff --git a/notebook/services/sessions/handlers.py b/notebook/services/sessions/handlers.py
index 4c46c45df..b7a7f11de 100644
--- a/notebook/services/sessions/handlers.py
+++ b/notebook/services/sessions/handlers.py
@@ -8,7 +8,7 @@ Preliminary documentation at https://github.com/ipython/ipython/wiki/IPEP-16%3A-
 
 import json
 
-from tornado import web
+from tornado import gen, web
 
 from ...base.handlers import APIHandler, json_errors
 from jupyter_client.jsonutil import date_default
@@ -20,20 +20,20 @@ class SessionRootHandler(APIHandler):
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def get(self):
         # Return a list of running sessions
         sm = self.session_manager
-        sessions = sm.list_sessions()
+        sessions = yield gen.maybe_future(sm.list_sessions())
         self.finish(json.dumps(sessions, default=date_default))
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def post(self):
         # Creates a new session
         #(unless a session already exists for the named nb)
         sm = self.session_manager
-        cm = self.contents_manager
-        km = self.kernel_manager
 
         model = self.get_json_body()
         if model is None:
@@ -49,11 +49,13 @@ class SessionRootHandler(APIHandler):
             kernel_name = None
 
         # Check to see if session exists
-        if sm.session_exists(path=path):
-            model = sm.get_session(path=path)
+        exists = yield gen.maybe_future(sm.session_exists(path=path))
+        if exists:
+            model = yield gen.maybe_future(sm.get_session(path=path))
         else:
             try:
-                model = sm.create_session(path=path, kernel_name=kernel_name)
+                model = yield gen.maybe_future(
+                    sm.create_session(path=path, kernel_name=kernel_name))
             except NoSuchKernel:
                 msg = ("The '%s' kernel is not available. Please pick another "
                        "suitable kernel instead, or install that kernel." % kernel_name)
@@ -73,14 +75,16 @@ class SessionHandler(APIHandler):
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def get(self, session_id):
         # Returns the JSON model for a single session
         sm = self.session_manager
-        model = sm.get_session(session_id=session_id)
+        model = yield gen.maybe_future(sm.get_session(session_id=session_id))
         self.finish(json.dumps(model, default=date_default))
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def patch(self, session_id):
         # Currently, this handler is strictly for renaming notebooks
         sm = self.session_manager
@@ -93,17 +97,18 @@ class SessionHandler(APIHandler):
             if 'path' in notebook:
                 changes['path'] = notebook['path']
 
-        sm.update_session(session_id, **changes)
-        model = sm.get_session(session_id=session_id)
+        yield gen.maybe_future(sm.update_session(session_id, **changes))
+        model = yield gen.maybe_future(sm.get_session(session_id=session_id))
         self.finish(json.dumps(model, default=date_default))
 
     @web.authenticated
     @json_errors
+    @gen.coroutine
     def delete(self, session_id):
         # Deletes the session with given session_id
         sm = self.session_manager
         try:
-            sm.delete_session(session_id)
+            yield gen.maybe_future(sm.delete_session(session_id))
         except KeyError:
             # the kernel was deleted but the session wasn't!
             raise web.HTTPError(410, "Kernel deleted before session")
diff --git a/notebook/services/sessions/sessionmanager.py b/notebook/services/sessions/sessionmanager.py
index b75732087..ffd0cc28a 100644
--- a/notebook/services/sessions/sessionmanager.py
+++ b/notebook/services/sessions/sessionmanager.py
@@ -6,7 +6,7 @@
 import uuid
 import sqlite3
 
-from tornado import web
+from tornado import gen, web
 
 from traitlets.config.configurable import LoggingConfigurable
 from ipython_genutils.py3compat import unicode_type
@@ -56,17 +56,22 @@ class SessionManager(LoggingConfigurable):
     def new_session_id(self):
         "Create a uuid for a new session"
         return unicode_type(uuid.uuid4())
-
+    
+    @gen.coroutine
     def create_session(self, path=None, kernel_name=None):
         """Creates a session and returns its model"""
         session_id = self.new_session_id()
         # allow nbm to specify kernels cwd
         kernel_path = self.contents_manager.get_kernel_path(path=path)
-        kernel_id = self.kernel_manager.start_kernel(path=kernel_path,
-                                                     kernel_name=kernel_name)
-        return self.save_session(session_id, path=path,
-                                 kernel_id=kernel_id)
-
+        kernel_id = yield gen.maybe_future(
+            self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
+        )
+        result = yield gen.maybe_future(
+            self.save_session(session_id, path=path, kernel_id=kernel_id)
+        )
+        # py2-compat
+        raise gen.Return(result)
+    
     def save_session(self, session_id, path=None, kernel_id=None):
         """Saves the items for the session with the given session_id
         
diff --git a/notebook/services/sessions/tests/test_sessionmanager.py b/notebook/services/sessions/tests/test_sessionmanager.py
index d1382ed1d..dbb4feb5e 100644
--- a/notebook/services/sessions/tests/test_sessionmanager.py
+++ b/notebook/services/sessions/tests/test_sessionmanager.py
@@ -2,7 +2,8 @@
 
 from unittest import TestCase
 
-from tornado import web
+from tornado import gen, web
+from tornado.ioloop import IOLoop
 
 from ..sessionmanager import SessionManager
 from notebook.services.kernels.kernelmanager import MappingKernelManager
@@ -37,12 +38,31 @@ class TestSessionManager(TestCase):
             kernel_manager=DummyMKM(),
             contents_manager=ContentsManager(),
         )
-
+        self.loop = IOLoop()
+    
+    def tearDown(self):
+        self.loop.close(all_fds=True)
+    
+    def create_sessions(self, *kwarg_list):
+        @gen.coroutine
+        def co_add():
+            sessions = []
+            for kwargs in kwarg_list:
+                session = yield self.sm.create_session(**kwargs)
+                sessions.append(session)
+            raise gen.Return(sessions)
+        return self.loop.run_sync(co_add)
+    
+    def create_session(self, **kwargs):
+        return self.create_sessions(kwargs)[0]
+    
+    def get_session(self, **kwargs):
+        return self.loop.run_sync(lambda : self.sm.get_session(**kwargs))
+    
     def test_get_session(self):
         sm = self.sm
-        session_id = sm.create_session(path='/path/to/test.ipynb',
-                                       kernel_name='bar')['id']
-        model = sm.get_session(session_id=session_id)
+        session_id = self.create_session(path='/path/to/test.ipynb', kernel_name='bar')['id']
+        model = self.get_session(session_id=session_id)
         expected = {'id':session_id,
                     'notebook':{'path': u'/path/to/test.ipynb'},
                     'kernel': {'id':u'A', 'name': 'bar'}}
@@ -51,13 +71,13 @@ class TestSessionManager(TestCase):
     def test_bad_get_session(self):
         # Should raise error if a bad key is passed to the database.
         sm = self.sm
-        session_id = sm.create_session(path='/path/to/test.ipynb',
+        session_id = self.create_session(path='/path/to/test.ipynb',
                                        kernel_name='foo')['id']
         self.assertRaises(TypeError, sm.get_session, bad_id=session_id) # Bad keyword
 
     def test_get_session_dead_kernel(self):
         sm = self.sm
-        session = sm.create_session(path='/path/to/1/test1.ipynb', kernel_name='python')
+        session = self.create_session(path='/path/to/1/test1.ipynb', kernel_name='python')
         # kill the kernel
         sm.kernel_manager.shutdown_kernel(session['kernel']['id'])
         with self.assertRaises(KeyError):
@@ -68,11 +88,12 @@ class TestSessionManager(TestCase):
 
     def test_list_sessions(self):
         sm = self.sm
-        sessions = [
-            sm.create_session(path='/path/to/1/test1.ipynb', kernel_name='python'),
-            sm.create_session(path='/path/to/2/test2.ipynb', kernel_name='python'),
-            sm.create_session(path='/path/to/3/test3.ipynb', kernel_name='python'),
-        ]
+        sessions = self.create_sessions(
+            dict(path='/path/to/1/test1.ipynb', kernel_name='python'),
+            dict(path='/path/to/2/test2.ipynb', kernel_name='python'),
+            dict(path='/path/to/3/test3.ipynb', kernel_name='python'),
+        )
+        
         sessions = sm.list_sessions()
         expected = [
             {
@@ -93,10 +114,10 @@ class TestSessionManager(TestCase):
 
     def test_list_sessions_dead_kernel(self):
         sm = self.sm
-        sessions = [
-            sm.create_session(path='/path/to/1/test1.ipynb', kernel_name='python'),
-            sm.create_session(path='/path/to/2/test2.ipynb', kernel_name='python'),
-        ]
+        sessions = self.create_sessions(
+            dict(path='/path/to/1/test1.ipynb', kernel_name='python'),
+            dict(path='/path/to/2/test2.ipynb', kernel_name='python'),
+        )
         # kill one of the kernels
         sm.kernel_manager.shutdown_kernel(sessions[0]['kernel']['id'])
         listed = sm.list_sessions()
@@ -116,10 +137,10 @@ class TestSessionManager(TestCase):
 
     def test_update_session(self):
         sm = self.sm
-        session_id = sm.create_session(path='/path/to/test.ipynb',
+        session_id = self.create_session(path='/path/to/test.ipynb',
                                        kernel_name='julia')['id']
         sm.update_session(session_id, path='/path/to/new_name.ipynb')
-        model = sm.get_session(session_id=session_id)
+        model = self.loop.run_sync(lambda : sm.get_session(session_id=session_id))
         expected = {'id':session_id,
                     'notebook':{'path': u'/path/to/new_name.ipynb'},
                     'kernel':{'id':u'A', 'name':'julia'}}
@@ -128,17 +149,17 @@ class TestSessionManager(TestCase):
     def test_bad_update_session(self):
         # try to update a session with a bad keyword ~ raise error
         sm = self.sm
-        session_id = sm.create_session(path='/path/to/test.ipynb',
+        session_id = self.create_session(path='/path/to/test.ipynb',
                                        kernel_name='ir')['id']
         self.assertRaises(TypeError, sm.update_session, session_id=session_id, bad_kw='test.ipynb') # Bad keyword
 
     def test_delete_session(self):
         sm = self.sm
-        sessions = [
-            sm.create_session(path='/path/to/1/test1.ipynb', kernel_name='python'),
-            sm.create_session(path='/path/to/2/test2.ipynb', kernel_name='python'),
-            sm.create_session(path='/path/to/3/test3.ipynb', kernel_name='python'),
-        ]
+        sessions = self.create_sessions(
+            dict(path='/path/to/1/test1.ipynb', kernel_name='python'),
+            dict(path='/path/to/2/test2.ipynb', kernel_name='python'),
+            dict(path='/path/to/3/test3.ipynb', kernel_name='python'),
+        )
         sm.delete_session(sessions[1]['id'])
         new_sessions = sm.list_sessions()
         expected = [{
@@ -156,7 +177,7 @@ class TestSessionManager(TestCase):
     def test_bad_delete_session(self):
         # try to delete a session that doesn't exist ~ raise error
         sm = self.sm
-        sm.create_session(path='/path/to/test.ipynb', kernel_name='python')
+        self.create_session(path='/path/to/test.ipynb', kernel_name='python')
         self.assertRaises(TypeError, sm.delete_session, bad_kwarg='23424') # Bad keyword
         self.assertRaises(web.HTTPError, sm.delete_session, session_id='23424') # nonexistant
 

From cfa64552b26372e5b7109759d61d875b0c3ca931 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 10 Nov 2015 15:00:52 +0100
Subject: [PATCH 26/40] initialize Application in background thread

rather than initializing in main and starting in background, which seemed to cause occasional issues.

Also fix checking for dead notebook, which is no longer a subprocess.
---
 .../sessions/tests/test_sessionmanager.py     |  7 +--
 notebook/tests/launchnotebook.py              | 50 +++++++++++--------
 2 files changed, 30 insertions(+), 27 deletions(-)

diff --git a/notebook/services/sessions/tests/test_sessionmanager.py b/notebook/services/sessions/tests/test_sessionmanager.py
index dbb4feb5e..0b31d97a4 100644
--- a/notebook/services/sessions/tests/test_sessionmanager.py
+++ b/notebook/services/sessions/tests/test_sessionmanager.py
@@ -56,13 +56,10 @@ class TestSessionManager(TestCase):
     def create_session(self, **kwargs):
         return self.create_sessions(kwargs)[0]
     
-    def get_session(self, **kwargs):
-        return self.loop.run_sync(lambda : self.sm.get_session(**kwargs))
-    
     def test_get_session(self):
         sm = self.sm
         session_id = self.create_session(path='/path/to/test.ipynb', kernel_name='bar')['id']
-        model = self.get_session(session_id=session_id)
+        model = sm.get_session(session_id=session_id)
         expected = {'id':session_id,
                     'notebook':{'path': u'/path/to/test.ipynb'},
                     'kernel': {'id':u'A', 'name': 'bar'}}
@@ -140,7 +137,7 @@ class TestSessionManager(TestCase):
         session_id = self.create_session(path='/path/to/test.ipynb',
                                        kernel_name='julia')['id']
         sm.update_session(session_id, path='/path/to/new_name.ipynb')
-        model = self.loop.run_sync(lambda : sm.get_session(session_id=session_id))
+        model = sm.get_session(session_id=session_id)
         expected = {'id':session_id,
                     'notebook':{'path': u'/path/to/new_name.ipynb'},
                     'kernel':{'id':u'A', 'name':'julia'}}
diff --git a/notebook/tests/launchnotebook.py b/notebook/tests/launchnotebook.py
index b957cdf4d..e9842ca43 100644
--- a/notebook/tests/launchnotebook.py
+++ b/notebook/tests/launchnotebook.py
@@ -19,6 +19,7 @@ except ImportError:
 
 from tornado.ioloop import IOLoop
 
+import jupyter_core.paths
 from ..notebookapp import NotebookApp
 from ipython_genutils.tempdir import TemporaryDirectory
 
@@ -51,9 +52,8 @@ class NotebookTestBase(TestCase):
             try:
                 requests.get(url)
             except Exception as e:
-                if cls.notebook.poll() is not None:
-                    raise RuntimeError("The notebook server exited with status %s" \
-                                        % cls.notebook.poll())
+                if not cls.notebook_thread.is_alive():
+                    raise RuntimeError("The notebook server failed to start")
                 time.sleep(POLL_INTERVAL)
             else:
                 return
@@ -77,31 +77,35 @@ class NotebookTestBase(TestCase):
             'JUPYTER_DATA_DIR' : data_dir.name
         })
         cls.env_patch.start()
+        cls.path_patch = patch.object(jupyter_core.paths, 'SYSTEM_JUPYTER_PATH', [])
+        cls.path_patch.start()
         cls.config_dir = TemporaryDirectory()
         cls.data_dir = data_dir
         cls.runtime_dir = TemporaryDirectory()
         cls.notebook_dir = TemporaryDirectory()
-        app = cls.notebook = NotebookApp(
-            port=cls.port,
-            port_retries=0,
-            open_browser=False,
-            config_dir=cls.config_dir.name,
-            data_dir=cls.data_dir.name,
-            runtime_dir=cls.runtime_dir.name,
-            notebook_dir=cls.notebook_dir.name,
-            base_url=cls.url_prefix,
-            config=cls.config,
-        )
         
-        # clear log handlers and propagate to root for nose to capture it
-        # needs to be redone after initialize, which reconfigures logging
-        app.log.propagate = True
-        app.log.handlers = []
-        app.initialize(argv=[])
-        app.log.propagate = True
-        app.log.handlers = []
         started = Event()
         def start_thread():
+            app = cls.notebook = NotebookApp(
+                port=cls.port,
+                port_retries=0,
+                open_browser=False,
+                config_dir=cls.config_dir.name,
+                data_dir=cls.data_dir.name,
+                runtime_dir=cls.runtime_dir.name,
+                notebook_dir=cls.notebook_dir.name,
+                base_url=cls.url_prefix,
+                config=cls.config,
+            )
+            # don't register signal handler during tests
+            app.init_signal = lambda : None
+            # clear log handlers and propagate to root for nose to capture it
+            # needs to be redone after initialize, which reconfigures logging
+            app.log.propagate = True
+            app.log.handlers = []
+            app.initialize(argv=[])
+            app.log.propagate = True
+            app.log.handlers = []
             loop = IOLoop.current()
             loop.add_callback(started.set)
             try:
@@ -109,6 +113,7 @@ class NotebookTestBase(TestCase):
             finally:
                 # set the event, so failure to start doesn't cause a hang
                 started.set()
+                app.session_manager.close()
         cls.notebook_thread = Thread(target=start_thread)
         cls.notebook_thread.start()
         started.wait()
@@ -118,12 +123,13 @@ class NotebookTestBase(TestCase):
     def teardown_class(cls):
         cls.notebook.stop()
         cls.wait_until_dead()
-        cls.env_patch.start()
         cls.home_dir.cleanup()
         cls.config_dir.cleanup()
         cls.data_dir.cleanup()
         cls.runtime_dir.cleanup()
         cls.notebook_dir.cleanup()
+        cls.env_patch.stop()
+        cls.path_patch.stop()
 
     @classmethod
     def base_url(cls):

From ba344843eb57bd93df8363ffdb384e6bf4c74fdd Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 1 Dec 2015 11:36:22 +0100
Subject: [PATCH 27/40] add SessionManager.close

allows explicit closing, rather than relying on implicit del,
which can run in the wrong thread.
---
 notebook/services/sessions/sessionmanager.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/notebook/services/sessions/sessionmanager.py b/notebook/services/sessions/sessionmanager.py
index ffd0cc28a..125940408 100644
--- a/notebook/services/sessions/sessionmanager.py
+++ b/notebook/services/sessions/sessionmanager.py
@@ -39,10 +39,16 @@ class SessionManager(LoggingConfigurable):
             self._connection = sqlite3.connect(':memory:')
             self._connection.row_factory = sqlite3.Row
         return self._connection
-        
+    
+    def close(self):
+        """Close the sqlite connection"""
+        if self._cursor is not None:
+            self._cursor.close()
+            self._cursor = None
+
     def __del__(self):
         """Close connection once SessionManager closes"""
-        self.cursor.close()
+        self.close()
 
     def session_exists(self, path):
         """Check to see if the session for a given notebook exists"""

From 67c6aaafaee3783672521eb58b66a00d69d4a752 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Fri, 27 Nov 2015 17:44:22 +0000
Subject: [PATCH 28/40] in docs/extending/frontend_extensions: * fix some typos
 & misspellings * some improvements to phrasing

---
 docs/source/extending/frontend_extensions.rst | 86 ++++++++++---------
 1 file changed, 47 insertions(+), 39 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index 5fbade66c..ff92258c8 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -5,19 +5,20 @@ This describes the basic steps to write a JavaScript extension for the Jupyter
 notebook front-end. This allows you to customize the behaviour of the various
 pages like the dashboard, the notebook, or the text editor.
 
-The structure of an extension
------------------------------
+The structure of a front-end extension
+--------------------------------------
 
 .. note::
 
-    The notebook frontend and Javascript API are not stable, and are subject to
-    a lot of changes. Any extension written for the current notebook is almost
-    guaranteed to break in the next release.
+    The notebook front-end and Javascript API are not stable, and are subject
+    to a lot of changes. Any extension written for the current notebook is
+    almost guaranteed to break in the next release.
 
-A front-end extension is a JavaScript file that defines an AMD module
-exposing at least a function called `load_ipython_extension`, which takes no
-arguments. We will not get into the details of what each of these terms are,
-but here is the minimal code needed for a working extension:
+A front-end extension is a JavaScript file that defines an
+[AMD module](https://en.wikipedia.org/wiki/Asynchronous_module_definition)
+which exposes at least a function called `load_ipython_extension`, which takes
+no arguments. We will not get into the details of what each of these terms
+consists of yet, but here is the minimal code needed for a working extension:
 
 .. code:: javascript
 
@@ -34,19 +35,23 @@ but here is the minimal code needed for a working extension:
 
 .. note::
     
-    For historical reasons, the function is called `load_ipython_extension`,
-    but it does apply to the Jupyter notebook as well, and will work
-    regardless of the kernel you use. 
+    Although for historical reasons the function is called
+    `load_ipython_extension`, it does apply to the Jupyter notebook in general,
+    and will work regardless of the kernel in use.
 
 If you are familiar with JavaScript, you can use this template to require any
-Jupyter module and modify its configuration. Your extension will be loaded
-at the right time during the notebook page initialisation for you to set up a
-listener for the various events that the page can trigger.
-
-You might want to access to the current instances of the various component on
-the page, these are exposed by a module named `base/js/namespace`. If you plan
-on accessing instances on the page, you should require this module rather than
-accessing the global variable `Jupyter`. Here is how to do that:
+Jupyter module and modify its configuration, or do anything else in client-side
+Javascript. Your extension will be loaded at the right time during the notebook
+page initialisation for you to set up a listener for the various events that
+the page can trigger.
+
+You might want access to the current instances of the various Jupyter notebook
+components on the page, as opposed to the classes defined in the modules.
+The current instances are exposed by a module named `base/js/namespace`.
+If you plan
+on accessing instances on the page, you should ``require`` this module rather
+than accessing the global variable `Jupyter`, which will be removed in future.
+The following example demonstrates how to access the current notebook instance:
 
 .. code:: javascript
 
@@ -66,12 +71,14 @@ accessing the global variable `Jupyter`. Here is how to do that:
 Modifying key bindings
 ----------------------
 
-Extensions have the ability to modify key bindings. Once again, this API
-is not guaranteed to be stable, but changing key bindings is a common request.
-This is how to do it in the current version of the notebook.
+One of the abilities of extensions is to modify key bindings, although once
+again this is an API which is not guaranteed to be stable. However, custom key
+bindings are frequently requested, and are helpful to increase accessibility,
+so in the following we show how to access them.
 
-Here is an example of extension that will unbind `0,0` in command mode, which
-normally restarts the kernel, and bind `0,0,0` in it's place.
+Here is an example of an extension that will unbind the shortcut `0,0` in
+command mode, which normally restarts the kernel, and bind `0,0,0` in its
+place:
 
 .. code:: javascript
 
@@ -89,30 +96,31 @@ normally restarts the kernel, and bind `0,0,0` in it's place.
 
 .. note::
     
-    Keybindings might not work correctly on non-US keyboards.
-    Unfortunately, this is a limitation of browser implementations and the status of
-    keyboard event handling on the web. We appreciate your feedback if you have
-    issues binding keys, or ideas to help improve the situation.
+    The standard keybindings might not work correctly on non-US keyboards.
+    Unfortunately, this is a limitation of browser implementations and the
+    status of keyboard event handling on the web in general. We appreciate your
+    feedback if you have issues binding keys, or have any ideas to help improve
+    the situation.
 
-You can see that I have used the **command name**
+You can see that I have used the **action name**
 `jupyter-notebook:restart-kernel` to bind the new shortcut. There is no API yet
-to access the list of all available *commands*, though the following in the
+to access the list of all available *actions*, though the following in the
 JavaScript console of your browser on a notebook page should give you an idea
-of what of available:
+of what is available:
 
 .. code:: javascript
 
     Object.keys(IPython.actions._actions)
 
-In this example, we changed keyboard shortcuts in **command mode**; you can also
-customise keyboard shortcuts in edit mode.
+In this example, we changed the keyboard shortcut in the **command mode**; you
+can also customize keyboard shortcuts in **edit mode**.
 However, most of the keyboard shortcuts in edit mode are handled by CodeMirror,
 which supports custom key bindings via a completely different API.
 
-You can also define and register your own action to be used, but the
-documentation for this has not been written yet. If you need to do it,
-please ask us, we can give you the necessary information, and we would appreciate
-if you could format them in a detailed way in place of this paragraph.
+You can also define and register your own **actions** to be used, but the
+documentation for this has not been written yet. If you need to do it, please
+ask us, we can give you the necessary information, and we would appreciate if
+you could format them in a detailed way in place of this paragraph.
 
 Installing and enabling extensions
 ----------------------------------
@@ -135,4 +143,4 @@ notebook interface to load it. You can do that with another command:
 
 The argument refers to the Javascript module containing your ``load_ipython_extension``
 function, which is ``myext/main.js`` in this example. There is a corresponding
-``disable`` command to stop using an extension without installing it.
+``disable`` command to stop using an extension without uninstalling it.

From ad7e657e5c830ea17f08dc11990187b03d7155f2 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Fri, 27 Nov 2015 17:45:49 +0000
Subject: [PATCH 29/40] in docs/extending/frontend_extensions: * beautify
 javascript examples * make one-liners fit on one line

---
 docs/source/extending/frontend_extensions.rst | 74 +++++++++++--------
 1 file changed, 45 insertions(+), 29 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index ff92258c8..5fab3dd06 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -22,16 +22,18 @@ consists of yet, but here is the minimal code needed for a working extension:
 
 .. code:: javascript
 
-    //file myext/main.js
+    // file my_extension/main.js
 
     define(function(){
 
         function load_ipython_extension(){
-            console.info('this is my first extension')
+            console.info('this is my first extension');
         }
 
-        return {load_ipython_extension: load_ipython_extension };
-    })
+        return {
+            load_ipython_extension: load_ipython_extension
+        };
+    });
 
 .. note::
     
@@ -55,17 +57,24 @@ The following example demonstrates how to access the current notebook instance:
 
 .. code:: javascript
 
-    //file myext/main.js
-
-    define(['base/js/namespace'],function(Jupyter){
-
-        function load_ipython_extension(){
-            console.log('This is the current notebook application instance', Jupyter.notebook);
+    // file my_extension/main.js
+
+    define([
+        'base/js/namespace'
+    ], function(
+        Jupyter
+    ) {
+        function load_ipython_extension() {
+            console.log(
+                'This is the current notebook application instance:',
+                Jupyter.notebook
+            );
         }
 
-        return {load_ipython_extension: load_ipython_extension };
-    })
-
+        return {
+            load_ipython_extension: load_ipython_extension
+        };
+    });
 
 
 Modifying key bindings
@@ -82,17 +91,23 @@ place:
 
 .. code:: javascript
 
-    //file myext/main.js
+    // file my_extension/main.js
 
-    define(['base/js/namespace'],function(Jupyter){
+    define([
+        'base/js/namespace'
+    ], function(
+        Jupyter
+    ) {
 
-        function load_ipython_extension(){
-            Jupyter.keyboard_manager.command_shortcuts.remove_shortcut('0,0')
-            Jupyter.keyboard_manager.command_shortcuts.add_shortcut('0,0,0', 'jupyter-notebook:restart-kernel')
+        function load_ipython_extension() {
+            Jupyter.keyboard_manager.command_shortcuts.remove_shortcut('0,0');
+            Jupyter.keyboard_manager.command_shortcuts.add_shortcut('0,0,0', 'jupyter-notebook:restart-kernel');
         }
 
-        return {load_ipython_extension: load_ipython_extension };
-    })
+        return {
+            load_ipython_extension: load_ipython_extension
+        };
+    });
 
 .. note::
     
@@ -110,7 +125,7 @@ of what is available:
 
 .. code:: javascript
 
-    Object.keys(IPython.actions._actions)
+    Object.keys(require('base/js/namespace').actions._actions);
 
 In this example, we changed the keyboard shortcut in the **command mode**; you
 can also customize keyboard shortcuts in **edit mode**.
@@ -127,11 +142,11 @@ Installing and enabling extensions
 
 You can install your nbextension with the command:
 
-    jupyter nbextension install path/to/myext/
+    jupyter nbextension install path/to/my_extension/
 
-Where myext is the directory containing the Javascript files. This will copy
-it to a Jupyter data directory (the exact location is platform dependent - see
-:ref:`jupyter_path`).
+Where my_extension is the directory containing the Javascript files.
+This will copy it to a Jupyter data directory (the exact location is platform
+dependent - see :ref:`jupyter_path`).
 
 For development, you can use the ``--symlink`` flag to symlink your extension
 rather than copying it, so there's no need to reinstall after changes.
@@ -139,8 +154,9 @@ rather than copying it, so there's no need to reinstall after changes.
 To use your extension, you'll also need to **enable** it, which tells the
 notebook interface to load it. You can do that with another command:
 
-    jupyter nbextension enable myext/main
+    jupyter nbextension enable my_extension/main
 
-The argument refers to the Javascript module containing your ``load_ipython_extension``
-function, which is ``myext/main.js`` in this example. There is a corresponding
-``disable`` command to stop using an extension without uninstalling it.
+The argument refers to the Javascript module containing your
+``load_ipython_extension`` function, which is ``my_extension/main.js`` in this
+example. There is a corresponding ``disable`` command to stop using an
+extension without uninstalling it.

From bf44aace546d3923a4f68f24be581914720cbe1c Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Fri, 27 Nov 2015 18:26:47 +0000
Subject: [PATCH 30/40] in docs/extending/frontend_extensions: * fix inline
 literals, which in RST start and end with ``, not just `

---
 docs/source/extending/frontend_extensions.rst | 31 ++++++++++---------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index 5fab3dd06..ef84b8e96 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -16,9 +16,10 @@ The structure of a front-end extension
 
 A front-end extension is a JavaScript file that defines an
 [AMD module](https://en.wikipedia.org/wiki/Asynchronous_module_definition)
-which exposes at least a function called `load_ipython_extension`, which takes
-no arguments. We will not get into the details of what each of these terms
-consists of yet, but here is the minimal code needed for a working extension:
+which exposes at least a function called ``load_ipython_extension``, which
+takes no arguments. We will not get into the details of what each of these
+terms consists of yet, but here is the minimal code needed for a working
+extension:
 
 .. code:: javascript
 
@@ -38,8 +39,8 @@ consists of yet, but here is the minimal code needed for a working extension:
 .. note::
     
     Although for historical reasons the function is called
-    `load_ipython_extension`, it does apply to the Jupyter notebook in general,
-    and will work regardless of the kernel in use.
+    ``load_ipython_extension``, it does apply to the Jupyter notebook in
+    general, and will work regardless of the kernel in use.
 
 If you are familiar with JavaScript, you can use this template to require any
 Jupyter module and modify its configuration, or do anything else in client-side
@@ -48,12 +49,12 @@ page initialisation for you to set up a listener for the various events that
 the page can trigger.
 
 You might want access to the current instances of the various Jupyter notebook
-components on the page, as opposed to the classes defined in the modules.
-The current instances are exposed by a module named `base/js/namespace`.
-If you plan
-on accessing instances on the page, you should ``require`` this module rather
-than accessing the global variable `Jupyter`, which will be removed in future.
-The following example demonstrates how to access the current notebook instance:
+components on the page, as opposed to the classes defined in the modules. The
+current instances are exposed by a module named ``base/js/namespace``. If you
+plan on accessing instances on the page, you should ``require`` this module
+rather than accessing the global variable ``Jupyter``, which will be removed in
+future. The following example demonstrates how to access the current notebook
+instance:
 
 .. code:: javascript
 
@@ -85,8 +86,8 @@ again this is an API which is not guaranteed to be stable. However, custom key
 bindings are frequently requested, and are helpful to increase accessibility,
 so in the following we show how to access them.
 
-Here is an example of an extension that will unbind the shortcut `0,0` in
-command mode, which normally restarts the kernel, and bind `0,0,0` in its
+Here is an example of an extension that will unbind the shortcut ``0,0`` in
+command mode, which normally restarts the kernel, and bind ``0,0,0`` in its
 place:
 
 .. code:: javascript
@@ -118,8 +119,8 @@ place:
     the situation.
 
 You can see that I have used the **action name**
-`jupyter-notebook:restart-kernel` to bind the new shortcut. There is no API yet
-to access the list of all available *actions*, though the following in the
+``jupyter-notebook:restart-kernel`` to bind the new shortcut. There is no API
+yet to access the list of all available *actions*, though the following in the
 JavaScript console of your browser on a notebook page should give you an idea
 of what is available:
 

From 71f5a1969ecb26b21c30a2e1bfc2578113d8d0ab Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Fri, 27 Nov 2015 18:40:02 +0000
Subject: [PATCH 31/40] in docs/extending/frontend_extensions: * fix AMD link
 to use RST syntax (mistakenly used markdown previously)

---
 docs/source/extending/frontend_extensions.rst | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index ef84b8e96..6d32ce02b 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -14,8 +14,9 @@ The structure of a front-end extension
     to a lot of changes. Any extension written for the current notebook is
     almost guaranteed to break in the next release.
 
-A front-end extension is a JavaScript file that defines an
-[AMD module](https://en.wikipedia.org/wiki/Asynchronous_module_definition)
+.. _AMD module: https://en.wikipedia.org/wiki/Asynchronous_module_definition
+
+A front-end extension is a JavaScript file that defines an `AMD module`_
 which exposes at least a function called ``load_ipython_extension``, which
 takes no arguments. We will not get into the details of what each of these
 terms consists of yet, but here is the minimal code needed for a working

From 99f6379f146b439cbd550db15cba45f4c207ca8c Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Tue, 1 Dec 2015 13:53:16 +0000
Subject: [PATCH 32/40] in docs/extending/frontend_extensions: * Add some
 description of actions

---
 docs/source/extending/frontend_extensions.rst | 68 +++++++++++++++++--
 1 file changed, 64 insertions(+), 4 deletions(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index 6d32ce02b..46a5e888d 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -134,10 +134,70 @@ can also customize keyboard shortcuts in **edit mode**.
 However, most of the keyboard shortcuts in edit mode are handled by CodeMirror,
 which supports custom key bindings via a completely different API.
 
-You can also define and register your own **actions** to be used, but the
-documentation for this has not been written yet. If you need to do it, please
-ask us, we can give you the necessary information, and we would appreciate if
-you could format them in a detailed way in place of this paragraph.
+
+Defining and registering your own actions
+-----------------------------------------
+
+As part of your front-end extension, you may wish to define actions, which can
+be attached to toolbar buttons, or called from the command palette. Here is an
+example of an extension that defines a (not very useful!) action to show an
+alert, and adds a toolabr button using the full action name:
+
+.. code:: javascript
+
+    // file my_extension/main.js
+
+    define([
+        'base/js/namespace'
+    ], function(
+        Jupyter
+    ) {
+        function load_ipython_extension() {
+
+            var handler = function () {
+                alert('this is an alert from my_extension!');
+            };
+
+            var action = {
+                icon: 'fa-comment-o', // a font-awesome class used on buttons, etc
+                help    : 'Show an alert',
+                help_index : 'zz',
+                handler : handler
+            };
+            var prefix = 'my_extension';
+            var action_name = 'show-alert';
+
+            var full_action_name = Jupyter.actions.register(action, name, prefix); // returns 'my_extension:show-alert'
+            Jupyter.toolbar.add_buttons_group([full_action_name]);
+        }
+
+        return {
+            load_ipython_extension: load_ipython_extension
+        };
+    });
+
+Every action needs a name, which, when joined with its prefix to make the full
+action name, should be unique. Built-in actions, like the
+``jupyter-notebook:restart-kernel`` we bound in the earlier
+`Modifying key bindings`_ example, use the prefix ``jupyter-notebook``. For
+actions defined in an extension, it makes sense to use the extension name as
+the prefix. For the action name, the following guidelines should be considered:
+
+.. adapted from notebook/static/notebook/js/actions.js
+* First pick a noun and a verb for the action. For example, if the action is
+  "restart kernel," the verb is "restart" and the noun is "kernel".
+* Omit terms like "selected" and "active" by default, so "delete-cell", rather
+  than "delete-selected-cell". Only provide a scope like "-all-" if it is other
+  than the default "selected" or "active" scope.
+* If an action has a secondary action, separate the secondary action with
+  "-and-", so "restart-kernel-and-clear-output".
+* Use above/below or previous/next to indicate spatial and sequential
+  relationships.
+* Don't ever use before/after as they have a temporal connotation that is
+  confusing when used in a spatial context.
+* For dialogs, use a verb that indicates what the dialog will accomplish, such
+  as "confirm-restart-kernel".
+
 
 Installing and enabling extensions
 ----------------------------------

From 9bcac1d6293b376d4dedea94c36c7ad338c75771 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas@kluyver.me.uk>
Date: Tue, 1 Dec 2015 15:00:37 +0000
Subject: [PATCH 33/40] Remove explicit Python 3.3 classifier

If we're going to explicitly list 3.3, we should also be listing 3.4 and
3.5. But really we're compatible with any fairly recent Python 3
version, and will probably be compatible with future versions, so I
think it's best to just use the overall Python 3 classifier.
---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index d8c21d740..cf3178637 100755
--- a/setup.py
+++ b/setup.py
@@ -93,7 +93,6 @@ for more information.
         'Programming Language :: Python',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.3',
     ],
 )
 

From 9e9828f62447f215c8dbf3a578e05d543d837a98 Mon Sep 17 00:00:00 2001
From: Josh Barnes <joshuacookebarnes@gmail.com>
Date: Tue, 1 Dec 2015 15:57:54 +0000
Subject: [PATCH 34/40] in docs/extending/frontend_extensions: * fix 'the' typo

---
 docs/source/extending/frontend_extensions.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/extending/frontend_extensions.rst b/docs/source/extending/frontend_extensions.rst
index 46a5e888d..e23dfdd53 100644
--- a/docs/source/extending/frontend_extensions.rst
+++ b/docs/source/extending/frontend_extensions.rst
@@ -129,7 +129,7 @@ of what is available:
 
     Object.keys(require('base/js/namespace').actions._actions);
 
-In this example, we changed the keyboard shortcut in the **command mode**; you
+In this example, we changed a keyboard shortcut in **command mode**; you
 can also customize keyboard shortcuts in **edit mode**.
 However, most of the keyboard shortcuts in edit mode are handled by CodeMirror,
 which supports custom key bindings via a completely different API.

From 89b7d96ccd87d03226b7977b469e69172c39ef0e Mon Sep 17 00:00:00 2001
From: marcelo-ramires <marcelo.f.ramires@gmail.com>
Date: Wed, 2 Dec 2015 00:18:33 -0200
Subject: [PATCH 35/40] Fixing way in which selection ranges are deleted

---
 notebook/static/notebook/js/codecell.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/notebook/static/notebook/js/codecell.js b/notebook/static/notebook/js/codecell.js
index 42e693eed..c75ebd9e0 100644
--- a/notebook/static/notebook/js/codecell.js
+++ b/notebook/static/notebook/js/codecell.js
@@ -53,8 +53,9 @@ define([
          if (sel) { 
             var ranges = cm.listSelections();
             for (var i = ranges.length - 1; i >= 0; i--) {
-              var cur = ranges[i].head;
-              cm.replaceRange("", Pos(cur.line, cur.ch - 1), Pos(cur.line, cur.ch + 1));
+              var head = ranges[i].head;
+              var anchor = ranges[i].anchor;
+              cm.replaceRange("", Pos(head.line, head.ch), CodeMirror.Pos(anchor.line, anchor.ch));
             }
             return;
         }

From 4e8344831c73c6bb10da6886f8bce49acc8ea65c Mon Sep 17 00:00:00 2001
From: Safia Abdalla <safia@safia.rocks>
Date: Tue, 1 Dec 2015 22:08:42 -0600
Subject: [PATCH 36/40] Updated tests on rename in ContentsManager

---
 .../services/contents/tests/test_manager.py   | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)

diff --git a/notebook/services/contents/tests/test_manager.py b/notebook/services/contents/tests/test_manager.py
index 180a1d337..326280219 100644
--- a/notebook/services/contents/tests/test_manager.py
+++ b/notebook/services/contents/tests/test_manager.py
@@ -6,6 +6,7 @@ import os
 import sys
 import time
 from contextlib import contextmanager
+from itertools import combinations
 
 from nose import SkipTest
 from tornado.web import HTTPError
@@ -188,6 +189,41 @@ class TestFileContentsManager(TestCase):
 
 
 class TestContentsManager(TestCase):
+    @contextmanager
+    def assertRaisesHTTPError(self, status, msg=None):
+        msg = msg or "Should have raised HTTPError(%i)" % status
+        try:
+            yield
+        except HTTPError as e:
+            self.assertEqual(e.status_code, status)
+        else:
+            self.fail(msg)
+
+    def make_populated_dir(self, api_path):
+        cm = self.contents_manager
+
+        self.make_dir(api_path)
+
+        cm.new(path="/".join([api_path, "nb.ipynb"]))
+        cm.new(path="/".join([api_path, "file.txt"]))
+
+    def check_populated_dir_files(self, api_path):
+        dir_model = self.contents_manager.get(api_path)
+
+        self.assertEqual(dir_model['path'], api_path)
+        self.assertEqual(dir_model['type'], "directory")
+
+        for entry in dir_model['content']:
+            if entry['type'] == "directory":
+                continue
+            elif entry['type'] == "file":
+                self.assertEqual(entry['name'], "file.txt")
+                complete_path = "/".join([api_path, "file.txt"])
+                self.assertEqual(entry["path"], complete_path)
+            elif entry['type'] == "notebook":
+                self.assertEqual(entry['name'], "nb.ipynb")
+                complete_path = "/".join([api_path, "nb.ipynb"])
+                self.assertEqual(entry["path"], complete_path)
     
     def setUp(self):
         self._temp_dir = TemporaryDirectory()
@@ -473,6 +509,42 @@ class TestContentsManager(TestCase):
         # Fetching the notebook under the new name is successful
         assert isinstance(cm.get("changed_path"), dict)
 
+        # Ported tests on nested directory renaming from pgcontents
+        all_dirs = ['foo', 'bar', 'foo/bar', 'foo/bar/foo', 'foo/bar/foo/bar']
+        unchanged_dirs = all_dirs[:2]
+        changed_dirs = all_dirs[2:]
+
+        for _dir in all_dirs:
+            self.make_populated_dir(_dir)
+            self.check_populated_dir_files(_dir)
+
+        # Renaming to an existing directory should fail
+        for src, dest in combinations(all_dirs, 2):
+            with self.assertRaisesHTTPError(409):
+                cm.rename(src, dest)
+
+        # Creating a notebook in a non_existant directory should fail
+        with self.assertRaisesHTTPError(404):
+            cm.new_untitled("foo/bar_diff", ext=".ipynb")
+
+        cm.rename("foo/bar", "foo/bar_diff")
+
+        # Assert that unchanged directories remain so
+        for unchanged in unchanged_dirs:
+            self.check_populated_dir_files(unchanged)
+
+        # Assert changed directories can no longer be accessed under old names
+        for changed_dirname in changed_dirs:
+            with self.assertRaisesHTTPError(404):
+                cm.get(changed_dirname)
+
+            new_dirname = changed_dirname.replace("foo/bar", "foo/bar_diff", 1)
+
+            self.check_populated_dir_files(new_dirname)
+
+        # Created a notebook in the renamed directory should work
+        cm.new_untitled("foo/bar_diff", ext=".ipynb")
+
     def test_delete_root(self):
         cm = self.contents_manager
         with self.assertRaises(HTTPError) as err:

From f05dfae0f3b2368bead6e374779ac21f7948e245 Mon Sep 17 00:00:00 2001
From: Matthias Bussonnier <bussonniermatthias@gmail.com>
Date: Thu, 5 Nov 2015 15:05:34 -0800
Subject: [PATCH 37/40] Rework multiple selections to be continuous

It use the notion of Head/Anchor moving the selection normally move both
the head and the anchor. It is possible to mot move the anchor, for
example by pressing Shift.

Everything in between the head and the anchor (head and anchor included)
is in a "soft-selection" marked with the 'jupyter-soft-selection' class
in CSS.

This then remove completely the notion of marked cell, and thus disallow
discontinuous selection.

Unlike previous implementation the used a thick left border, this use
background gradient with 2 stops at the same position to archived the
same visual effect without the gap in between left border in between
contiguous cells.

For compatibility with previous versions, a few choices have been made.
An extra multi-selected class is added to the body when multiple
cells are selected. This allow to toggle the background to a soft blue
indicating selection. And the Head of the selection is still called the
"selected" cell.

The on_focus event have been reworked as a
click-let-click-release-outside of codemirror was putting the notebook
in undefined state with multiple selected cells, and the head in edit
mode.

Finally Travis now test on edge group, to get faster, which can be
removed in a few weeks as the all infrastructure of Travis will move on
Google Cloud.
---
 .travis.yml                                   |   1 +
 notebook/static/base/js/keyboard.js           |   2 +-
 notebook/static/notebook/js/actions.js        |  69 ++---
 notebook/static/notebook/js/cell.js           |  82 +++---
 notebook/static/notebook/js/codecell.js       |   8 +-
 .../static/notebook/js/keyboardmanager.js     |  10 +-
 notebook/static/notebook/js/menubar.js        |   2 +-
 notebook/static/notebook/js/notebook.js       | 244 +++++++-----------
 notebook/static/notebook/js/textcell.js       |   2 +-
 notebook/static/notebook/less/cell.less       |  54 ++--
 notebook/static/notebook/less/variables.less  |  17 +-
 notebook/tests/notebook/dualmode_merge.js     |   2 +-
 ...ked_cells.js => execute_selected_cells.js} |  69 ++---
 notebook/tests/notebook/marks.js              |  73 ------
 notebook/tests/notebook/multiselect.js        |  49 ++++
 notebook/tests/notebook/undelete.js           |  14 +-
 notebook/tests/util.js                        |  28 +-
 17 files changed, 302 insertions(+), 424 deletions(-)
 rename notebook/tests/notebook/{execute_marked_cells.js => execute_selected_cells.js} (61%)
 delete mode 100644 notebook/tests/notebook/marks.js
 create mode 100644 notebook/tests/notebook/multiselect.js

diff --git a/.travis.yml b/.travis.yml
index 99ae90699..7463d827e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,6 @@
 # http://travis-ci.org/#!/ipython/ipython
 language: python
+group: edge
 cache:
     directories:
         - ~/.cache/bower
diff --git a/notebook/static/base/js/keyboard.js b/notebook/static/base/js/keyboard.js
index 2259cd126..628ff99e4 100644
--- a/notebook/static/base/js/keyboard.js
+++ b/notebook/static/base/js/keyboard.js
@@ -362,7 +362,7 @@ define([
          **/
         var action_name = this.actions.get_name(data);
         if (! action_name){
-          throw new Error('does not know how to deal with', data);
+          throw new Error('does not know how to deal with : ' + data);
         }
         shortcut = normalize_shortcut(shortcut);
         this.set_shortcut(shortcut, action_name);
diff --git a/notebook/static/notebook/js/actions.js b/notebook/static/notebook/js/actions.js
index 2b05f7603..b39a68902 100644
--- a/notebook/static/notebook/js/actions.js
+++ b/notebook/static/notebook/js/actions.js
@@ -107,10 +107,10 @@ define(function(require){
             }
         },
         'run-cell':{
-            help    : 'run marked cells',
+            help    : 'run selected cells',
             help_index : 'bb',
             handler : function (env) {
-                env.notebook.execute_marked_cells();
+                env.notebook.execute_selected_cells();
             }
         },
         'run-cell-and-insert-below':{
@@ -163,7 +163,7 @@ define(function(require){
             handler : function (env) {
                 var index = env.notebook.get_selected_index();
                 if (index !== 0 && index !== null) {
-                    env.notebook.select_prev();
+                    env.notebook.select_prev(true);
                     env.notebook.focus_cell();
                 }
             }
@@ -174,23 +174,23 @@ define(function(require){
             handler : function (env) {
                 var index = env.notebook.get_selected_index();
                 if (index !== (env.notebook.ncells()-1) && index !== null) {
-                    env.notebook.select_next();
+                    env.notebook.select_next(true);
                     env.notebook.focus_cell();
                 }
             }
         },
-        'extend-marked-cells-above' : {
-            help: 'extend marked cells above',
+        'extend-selection-above' : {
+            help: 'extend selected cells above',
             help_index : 'dc',
             handler : function (env) {
-                env.notebook.extend_marked(-1);
+                env.notebook.extend_selection_by(-1)
             }
         },
-        'extend-marked-cells-below' : {
-            help: 'extend marked cells below',
+        'extend-selection-below' : {
+            help: 'extend selected cells below',
             help_index : 'dd',
             handler : function (env) {
-                env.notebook.extend_marked(1);
+                env.notebook.extend_selection_by(1)
             }
         },
         'cut-cell' : {
@@ -229,7 +229,7 @@ define(function(require){
             help_index : 'ec',
             handler : function (env) {
                 env.notebook.insert_cell_above();
-                env.notebook.select_prev();
+                env.notebook.select_prev(true);
                 env.notebook.focus_cell();
             }
         },
@@ -239,7 +239,7 @@ define(function(require){
             help_index : 'ed',
             handler : function (env) {
                 env.notebook.insert_cell_below();
-                env.notebook.select_next();
+                env.notebook.select_next(true);
                 env.notebook.focus_cell();
             }
         },
@@ -380,16 +380,10 @@ define(function(require){
             }
         },
         'merge-cells' : {
-            help : 'merge marked cells',
+            help : 'merge selected cells',
             help_index: 'el',
             handler: function(env) {
-                env.notebook.merge_marked_cells();
-            }
-        },
-        'close-pager' : {
-            help_index : 'gd',
-            handler : function (env) {
-                env.pager.collapse();
+                env.notebook.merge_selected_cells();
             }
         },
         'show-command-palette': {
@@ -400,29 +394,6 @@ define(function(require){
                 env.notebook.show_command_palette();
             }
         },
-        'toggle-cell-marked': {
-            help_index : 'cj',
-            help: 'toggle marks',
-            icon: 'fa-check',
-            handler : function(env){
-                // Use bitwise logic to toggle the marked state.
-                env.notebook.get_selected_cell().marked ^= true;
-            }
-        },
-        'unmark-all-cells': {
-            help_index : 'ck',
-            help : 'unmark all cells',
-            handler : function(env) {
-                env.notebook.unmark_all_cells();
-            }
-        },
-        'mark-all-cells': {
-            help_index : 'cl',
-            help : 'mark all cells',
-            handler : function(env) {
-                env.notebook.mark_all_cells();
-            }
-        },
         'toggle-toolbar':{
             help: 'hide/show the toolbar',
             handler : function(env){
@@ -438,14 +409,12 @@ define(function(require){
                 events.trigger('resize-header.Page');
             }
         },
-        'close-pager-or-unmark-all-cells': {
-            help : 'close the pager or unmark all cells',
+        'close-pager': {
+            help : 'close the pager',
             handler : function(env) {
-                // Collapse the page if it is open, otherwise unmark all.
+                // Collapse the page if it is open
                 if (env.pager && env.pager.expanded) {
                     env.pager.collapse();
-                } else {
-                    env.notebook.unmark_all_cells();
                 }
             }
         },
@@ -481,7 +450,7 @@ define(function(require){
                         event.preventDefault();
                     }
                     env.notebook.command_mode();
-                    env.notebook.select_prev();
+                    env.notebook.select_prev(true);
                     env.notebook.edit_mode();
                     cm = env.notebook.get_selected_cell().code_mirror;
                     cm.setCursor(cm.lastLine(), 0);
@@ -498,7 +467,7 @@ define(function(require){
                         event.preventDefault();
                     }
                     env.notebook.command_mode();
-                    env.notebook.select_next();
+                    env.notebook.select_next(true);
                     env.notebook.edit_mode();
                     var cm = env.notebook.get_selected_cell().code_mirror;
                     cm.setCursor(0, 0);
diff --git a/notebook/static/notebook/js/cell.js b/notebook/static/notebook/js/cell.js
index 8594816e3..fc67293fd 100644
--- a/notebook/static/notebook/js/cell.js
+++ b/notebook/static/notebook/js/cell.js
@@ -1,4 +1,3 @@
-// Copyright (c) Jupyter Development Team.
 // Distributed under the terms of the Modified BSD License.
 
 /**
@@ -21,7 +20,7 @@ define([
     "use strict";
     
     var overlayHack = CodeMirror.scrollbarModel.native.prototype.overlayHack;
-    
+
     CodeMirror.scrollbarModel.native.prototype.overlayHack = function () {
         overlayHack.apply(this, arguments);
         // Reverse `min-height: 18px` scrollbar hack on OS X
@@ -55,6 +54,7 @@ define([
         
         this.placeholder = config.placeholder || '';
         this.selected = false;
+        this.anchor = false;
         this.rendered = false;
         this.mode = 'command';
 
@@ -154,30 +154,29 @@ define([
         }
     };
 
+    /**
+     * trigger on focus and on click to bubble up to the notebook and
+     * potentially extend the selection if shift-click, contract the selection
+     * if just codemirror focus (so edit mode).
+     * We **might** be able to move that to notebook `handle_edit_mode`.
+     */
+    Cell.prototype._on_click = function(event){
+        if (!this.selected) {
+            this.events.trigger('select.Cell', {'cell':this, 'extendSelection':event.shiftKey});
+        }
+    }
+
     /**
      * Subclasses can implement override bind_events.
-     * Be carefull to call the parent method when overwriting as it fires event.
-     * this will be triggerd after create_element in constructor.
+     * Be careful to call the parent method when overwriting as it fires event.
+     * this will be triggered after create_element in constructor.
      * @method bind_events
      */
     Cell.prototype.bind_events = function () {
         var that = this;
         // We trigger events so that Cell doesn't have to depend on Notebook.
         that.element.click(function (event) {
-            if (!that.selected) {
-                that.events.trigger('select.Cell', {'cell':that});
-            }
-            
-            // Cmdtrl-click should mark the cell.
-            var isMac = navigator.platform.slice(0, 3).toLowerCase() === 'mac';
-            if ((!isMac && event.ctrlKey) || (isMac && event.metaKey)) {
-                that.marked = !that.marked;
-            }
-        });
-        that.element.focusin(function (event) {
-            if (!that.selected) {
-                that.events.trigger('select.Cell', {'cell':that});
-            }
+            that._on_click(event)
         });
         if (this.code_mirror) {
             this.code_mirror.on("change", function(cm, change) {
@@ -186,6 +185,9 @@ define([
         }
         if (this.code_mirror) {
             this.code_mirror.on('focus', function(cm, change) {
+                if (!that.selected) {
+                    that.events.trigger('select.Cell', {'cell':that});
+                }
                 that.events.trigger('edit_mode.Cell', {cell: that});
             });
         }
@@ -239,7 +241,7 @@ define([
 
 
     /**
-     * Triger typsetting of math by mathjax on current cell element
+     * Triger typesetting of math by mathjax on current cell element
      * @method typeset
      */
     Cell.prototype.typeset = function () {
@@ -251,7 +253,13 @@ define([
      * @method select
      * @return is the action being taken
      */
-    Cell.prototype.select = function () {
+    Cell.prototype.select = function (moveanchor) {
+        // if anchor is true, set the move the anchor
+        moveanchor = (moveanchor === undefined)? true:moveanchor;
+        if(moveanchor){
+            this.anchor=true;
+        }
+
         if (!this.selected) {
             this.element.addClass('selected');
             this.element.removeClass('unselected');
@@ -265,10 +273,14 @@ define([
     /**
      * handle cell level logic when the cell is unselected
      * @method unselect
-     * @param {bool} leave_selected - true to move cursor away and extend selection
      * @return is the action being taken
      */
-    Cell.prototype.unselect = function (leave_selected) {
+    Cell.prototype.unselect = function (moveanchor) {
+        // if anchor is true, remove also the anchor
+        moveanchor = (moveanchor === undefined)? true:moveanchor;
+        if (moveanchor){
+            this.anchor = false
+        }
         if (this.selected) {
             this.element.addClass('unselected');
             this.element.removeClass('selected');
@@ -279,32 +291,9 @@ define([
         }
     };
     
-    /**
-     * Whether or not the cell is marked.
-     * @return {boolean}
-     */
-    Object.defineProperty(Cell.prototype, 'marked', {
-        get: function() {
-            return this.element.hasClass('marked');
-        },
-        set: function(value) {
-            var isMarked = this.element.hasClass('marked');
-            // Use a casting comparison.  Allows for the caller to assign 0 or
-            // 1 instead of a boolean value, which in return means the caller
-            // can do cell.marked ^= true to toggle the mark.
-            if (isMarked != value) {
-                if (value) {
-                    this.element.addClass('marked');
-                } else {
-                    this.element.removeClass('marked');
-                }
-                this.events.trigger('marked_changed.Cell', {cell: this, value: value});
-            }
-        }
-    });
 
     /**
-     * should be overritten by subclass
+     * should be overwritten by subclass
      * @method execute
      */
     Cell.prototype.execute = function () {
@@ -426,6 +415,7 @@ define([
      */
     Cell.prototype.focus_cell = function () {
         this.element.focus();
+        this._on_click({});
     };
 
     /**
diff --git a/notebook/static/notebook/js/codecell.js b/notebook/static/notebook/js/codecell.js
index 59d8b4729..ecda8341b 100644
--- a/notebook/static/notebook/js/codecell.js
+++ b/notebook/static/notebook/js/codecell.js
@@ -188,7 +188,7 @@ define([
 
     /** @method bind_events */
     CodeCell.prototype.bind_events = function () {
-        Cell.prototype.bind_events.apply(this);
+        Cell.prototype.bind_events.apply(this, arguments);
         var that = this;
 
         this.element.focusout(
@@ -393,7 +393,7 @@ define([
     // Basic cell manipulation.
 
     CodeCell.prototype.select = function () {
-        var cont = Cell.prototype.select.apply(this);
+        var cont = Cell.prototype.select.apply(this, arguments);
         if (cont) {
             this.code_mirror.refresh();
             this.auto_highlight();
@@ -402,7 +402,7 @@ define([
     };
 
     CodeCell.prototype.render = function () {
-        var cont = Cell.prototype.render.apply(this);
+        var cont = Cell.prototype.render.apply(this, arguments);
         // Always execute, even if we are already in the rendered state
         return cont;
     };
@@ -540,7 +540,7 @@ define([
      * @return is the action being taken
      */
     CodeCell.prototype.unselect = function() {
-        var cont = Cell.prototype.unselect.call(this);
+        var cont = Cell.prototype.unselect.apply(this, arguments);
         if (cont) {
             // When a code cell is unselected, make sure that the corresponding
             // tooltip and completer to that cell is closed.
diff --git a/notebook/static/notebook/js/keyboardmanager.js b/notebook/static/notebook/js/keyboardmanager.js
index 9955923df..21138b4ee 100644
--- a/notebook/static/notebook/js/keyboardmanager.js
+++ b/notebook/static/notebook/js/keyboardmanager.js
@@ -96,14 +96,14 @@ define([
             'i,i' : 'jupyter-notebook:interrupt-kernel',
             '0,0' : 'jupyter-notebook:confirm-restart-kernel',
             'd,d' : 'jupyter-notebook:delete-cell',
-            'esc': 'jupyter-notebook:close-pager-or-unmark-all-cells',
+            'esc': 'jupyter-notebook:close-pager',
             'up' : 'jupyter-notebook:select-previous-cell',
             'k' : 'jupyter-notebook:select-previous-cell',
             'j' : 'jupyter-notebook:select-next-cell',
-            'shift-k': 'jupyter-notebook:extend-marked-cells-above',
-            'shift-j': 'jupyter-notebook:extend-marked-cells-below',
-            'shift-up': 'jupyter-notebook:extend-marked-cells-above',
-            'shift-down': 'jupyter-notebook:extend-marked-cells-below',
+            'shift-k': 'jupyter-notebook:extend-selection-above',
+            'shift-j': 'jupyter-notebook:extend-selection-below',
+            'shift-up': 'jupyter-notebook:extend-selection-above',
+            'shift-down': 'jupyter-notebook:extend-selection-below',
             'x' : 'jupyter-notebook:cut-cell',
             'c' : 'jupyter-notebook:copy-cell',
             'v' : 'jupyter-notebook:paste-cell-below',
diff --git a/notebook/static/notebook/js/menubar.js b/notebook/static/notebook/js/menubar.js
index 61207ff31..6ae6fc785 100644
--- a/notebook/static/notebook/js/menubar.js
+++ b/notebook/static/notebook/js/menubar.js
@@ -63,7 +63,7 @@ define([
                 // The selected cell loses focus when the menu is entered, so we
                 // re-select it upon selection.
                 var i = that.notebook.get_selected_index();
-                that.notebook.select(i);
+                that.notebook.select(i, false);
             }
         );
     };
diff --git a/notebook/static/notebook/js/notebook.js b/notebook/static/notebook/js/notebook.js
index 5de9f14ba..14c8b42aa 100644
--- a/notebook/static/notebook/js/notebook.js
+++ b/notebook/static/notebook/js/notebook.js
@@ -29,6 +29,12 @@ define(function (require) {
     var scrollmanager = require('notebook/js/scrollmanager');
     var commandpalette = require('notebook/js/commandpalette');
 
+    var _SOFT_SELECTION_CLASS = 'jupyter-soft-selected';
+
+    function soft_selected(cell){
+        return cell.element.hasClass(_SOFT_SELECTION_CLASS);
+    }
+
     /**
      * Contains and manages cells.
      * @class Notebook
@@ -187,9 +193,6 @@ define(function (require) {
     Notebook.prototype.bind_events = function () {
         var that = this;
 
-        this.events.on('marked_changed.Cell', function() {
-            that.update_marked_status();
-        });
 
         this.events.on('set_next_input.Notebook', function (event, data) {
             if (data.replace) {
@@ -221,7 +224,7 @@ define(function (require) {
 
         this.events.on('select.Cell', function (event, data) {
             var index = that.find_cell_index(data.cell);
-            that.select(index);
+            that.select(index, !data.extendSelection);
         });
 
         this.events.on('edit_mode.Cell', function (event, data) {
@@ -298,9 +301,6 @@ define(function (require) {
             expand_time(time);
         });
 
-        this.scroll_manager.onScroll(function () {
-            that.update_marked_status();
-        }, 100);
 
         // Firefox 22 broke $(window).on("beforeunload")
         // I'm not sure why or how.
@@ -584,13 +584,30 @@ define(function (require) {
         return i;
     };
 
+
+    Notebook.prototype.get_selected_cells = function () {
+        return this.get_cells().filter(function(cell, index){ return cell.selected || soft_selected(cell) || cell.anchor})
+    };
+
+    Notebook.prototype.get_selected_cells_indices = function () {
+
+        var result = [];
+        this.get_cells().filter(function (cell, index) {
+            if (cell.selected || soft_selected(cell) || cell.anchor) {
+                result.push(index);
+            }
+        });
+        return result;
+    };
+
+
     /**
      * Get the currently selected cell.
      * 
      * @return {Cell} The selected cell
      */
     Notebook.prototype.get_selected_cell = function () {
-        var index = this.get_selected_index();
+        var index = this.get_selected_cells_indices();
         return this.get_cell(index);
     };
 
@@ -608,6 +625,15 @@ define(function (require) {
         }
     };
 
+    Notebook.prototype.get_anchor_index = function () {
+        var result = null;
+        this.get_cell_elements().filter(function (index) {
+            if ($(this).data("cell").anchor === true) {
+                result = index;
+            }
+        });
+        return result;
+    };
     /**
      * Get the index of the currently selected cell.
      *
@@ -622,144 +648,52 @@ define(function (require) {
         });
         return result;
     };
-    
-    /**
-     * Toggles the marks on the cells
-     * @param  {Cell[]} [cells] - optionally specify what cells should be toggled
-     */
-    Notebook.prototype.toggle_cells_marked = function(cells) {
-        cells = cells || this.get_cells();
-        cells.forEach(function(cell) { cell.marked = !cell.marked; });
-    };
-    
-    /**
-     * Mark all of the cells
-     * @param  {Cell[]} [cells] - optionally specify what cells should be marked
-     */
-    Notebook.prototype.mark_all_cells = function(cells) {
-        cells = cells || this.get_cells();
-        cells.forEach(function(cell) { cell.marked = true; });
-    };
-    
-    /**
-     * Unmark all of the cells
-     * @param  {Cell[]} [cells] - optionally specify what cells should be unmarked
-     */
-    Notebook.prototype.unmark_all_cells = function(cells) {
-        this.get_marked_cells(cells).forEach(function(cell) { cell.marked = false; });
-    };
-    
-    /**
-     * Set the cells that should be marked, exclusively
-     * @param  {Cell[]} cells
-     */
-    Notebook.prototype.set_marked_cells = function(cells) {
-        this.unmark_all_cells();
-        this.mark_all_cells(cells);
-    };
-    
-    /**
-     * Gets the cells that are marked
-     * @param  {Cell[]} [cells] - optionally provide the cells to search through
-     * @return {Cell[]} marked cells
-     */
-    Notebook.prototype.get_marked_cells = function(cells) {
-        cells = cells || this.get_cells();
-        return cells.filter(function(cell) { return (cell.marked || cell.selected); });
-    };
-    
-    /**
-     * Sets the cells that are marked by indices
-     * @param  {number[]} indices
-     * @param  {Cell[]} [cells] - optionally provide the cells to search through
-     */
-    Notebook.prototype.set_marked_indices = function(indices, cells) {
-        cells = cells || this.get_cells();
-        this.unmark_all_cells(cells);
-        this.mark_all_cells(cells.filter(function(cell, index) { return indices.indexOf(index) !== -1; }));
-    };
-    
-    /**
-     * Gets the indices of the cells that are marked
-     * @param  {Cell[]} [cells] - optionally provide the cells to search through
-     * @return {number[]} marked cell indices
-     */
-    Notebook.prototype.get_marked_indices = function(cells) {
-        cells = cells || this.get_cells();
-        var markedCells = this.get_marked_cells(cells);
-        return markedCells.map(function(cell) { return cells.indexOf(cell); });
-    };
-    
-    /**
-     * Checks if the marked cells are contiguous
-     * @param  {Cell[]} [cells] - optionally provide the cells to search through
-     * @return {boolean}
-     */
-    Notebook.prototype.are_marked_cells_contiguous = function(cells) {
-        // Get a numerically sorted list of the marked indices.
-        var markedIndices = this.get_marked_indices(cells).sort(
-            function(a,b) { return a-b; });
 
-        // Check for contiguousness
-        for (var i = 0; i < markedIndices.length - 1; i++) {
-            if (markedIndices[i+1] - markedIndices[i] !== 1) {
-                return false;
-            }
-        }
-        return true;
-    };
-    
-    /**
-     * Checks if the marked cells specified by their indices are contiguous
-     * @param  {number[]} indices - the cell indices to search through
-     * @param  {Cell[]} [cells] - the cells to search through
-     * @return {boolean}
-     */
-    Notebook.prototype.are_marked_indices_contiguous = function(indices, cells) {
-        cells = cells || this.get_cells();
-        return this.are_marked_cells_contiguous(cells.filter(function(cell, index) {
-            return indices.indexOf(index) !== -1;
-        }));
-    };
 
-    /**
-     * Extend the selected range
-     *
-     * @param {number} offset
-     */
-    Notebook.prototype.extend_marked = function(offset) {
-        // Mark currently selected cell
-        this.get_selected_cell().marked = true;
+    // Cell selection.
 
-        // Select the cell in the offset direction.  Bound index between 0 and
-        // the number of cells -1.
-        var selectedIndex = Math.min(Math.max(this.get_selected_index() + offset, 0), this.ncells()-1);
-        this.select(selectedIndex);
-        this.ensure_focused();
+    Notebook.prototype.extend_selection_by = function(delta) {
+        var index = this.get_selected_index();
+        // do not move anchor
+        return this.select(index+delta, false);
     };
 
-    Notebook.prototype.update_marked_status = function() {
-        var marked_cells = this.get_marked_cells();
-        var num_offscreen = 0;
-        var i;
-        for (i = 0; i < marked_cells.length; i++) {
-            if (!this.scroll_manager.is_cell_visible(marked_cells[i])) {
-                num_offscreen += 1;
-            }
-        }
 
-        this.events.trigger('marked_offscreen.Cell', num_offscreen);
-    };
+    Notebook.prototype.update_soft_selection = function(){
+        var i1 = this.get_selected_index();
+        var i2 = this.get_anchor_index();
+        var low  = Math.min(i1, i2);
+        var high = Math.max(i1, i2);
+        if (low !== high){
+            $('body').addClass('jupyter-multi-select');
+        } else {
+            $('body').removeClass('jupyter-multi-select');
+        }
+        this.get_cells().map(function(cell, index, all){
+            if( low <= index && index <= high ){
+                cell.element.addClass(_SOFT_SELECTION_CLASS);
+            } else {
+                cell.element.removeClass(_SOFT_SELECTION_CLASS);
+            }
+        })
+    }
 
-    // Cell selection.
+    Notebook.prototype._contract_selection = function(){
+        var i = this.get_selected_index();
+        this.select(i, true);
+    }
 
     /**
      * Programmatically select a cell.
      * 
      * @param {integer} index - A cell's index
+     * @param {bool} moveanchor – whether to move the selection
+     *               anchor, default to true.
      * @return {Notebook} This notebook
      */
-    Notebook.prototype.select = function (index) {
+    Notebook.prototype.select = function (index, moveanchor) {
+        moveanchor = (moveanchor===undefined)? true : moveanchor;
+
         if (this.is_valid_cell_index(index)) {
             var sindex = this.get_selected_index();
             if (sindex !== null && index !== sindex) {
@@ -768,11 +702,13 @@ define(function (require) {
                 if (this.mode !== 'command') {
                     this.command_mode();
                 }
-                this.get_cell(sindex).unselect();
+                this.get_cell(sindex).unselect(moveanchor);
+            }
+            if(moveanchor){
+                this.get_cell(this.get_anchor_index()).unselect(true);
             }
             var cell = this.get_cell(index);
-            cell.select();
-            this.update_marked_status();
+            cell.select(moveanchor);
             if (cell.cell_type === 'heading') {
                 this.events.trigger('selected_cell_type_changed.Notebook',
                     {'cell_type':cell.cell_type,level:cell.level}
@@ -783,17 +719,20 @@ define(function (require) {
                 );
             }
         }
+        this.update_soft_selection();
         return this;
     };
 
     /**
      * Programmatically select the next cell.
      *
+     * @param {bool} moveanchor – whether to move the selection
+     *               anchor, default to true.
      * @return {Notebook} This notebook
      */
-    Notebook.prototype.select_next = function () {
+    Notebook.prototype.select_next = function (moveanchor) {
         var index = this.get_selected_index();
-        this.select(index+1);
+        this.select(index+1, moveanchor);
         return this;
     };
 
@@ -802,9 +741,9 @@ define(function (require) {
      *
      * @return {Notebook} This notebook
      */
-    Notebook.prototype.select_prev = function () {
+    Notebook.prototype.select_prev = function (moveanchor) {
         var index = this.get_selected_index();
-        this.select(index-1);
+        this.select(index-1, moveanchor);
         return this;
     };
 
@@ -858,6 +797,7 @@ define(function (require) {
      * @param {Cell} [cell] Cell to enter edit mode on.
      */
     Notebook.prototype.handle_edit_mode = function (cell) {
+        this._contract_selection();
         if (cell && this.mode !== 'edit') {
             cell.edit_mode();
             this.mode = 'edit';
@@ -870,6 +810,7 @@ define(function (require) {
      * Make a cell enter edit mode.
      */
     Notebook.prototype.edit_mode = function () {
+        this._contract_selection();
         var cell = this.get_selected_cell();
         if (cell && this.mode !== 'edit') {
             cell.unrender();
@@ -978,7 +919,7 @@ define(function (require) {
      */
     Notebook.prototype.delete_cells = function(indices) {
         if (indices === undefined) {
-            indices = this.get_marked_indices();
+            indices = this.get_selected_cells_indices();
         }
 
         this.undelete_backup = [];
@@ -1418,7 +1359,7 @@ define(function (require) {
      * Copy cells.
      */
     Notebook.prototype.copy_cell = function () {
-        var cells = this.get_marked_cells();
+        var cells = this.get_selected_cells();
         if (cells.length === 0) {
             cells = [this.get_selected_cell()];
         }
@@ -1507,7 +1448,6 @@ define(function (require) {
             // Unrender the new cell so we can call set_text.
             new_cell.unrender();
             new_cell.set_text(texta);
-            new_cell.marked = cell.marked;
         }
     };
 
@@ -1564,14 +1504,13 @@ define(function (require) {
         this.delete_cells(indices);
 
         this.select(this.find_cell_index(target));
-        this.unmark_all_cells();
     };
 
     /**
      * Merge the selected range of cells
      */
-    Notebook.prototype.merge_marked_cells = function() {
-        this.merge_cells(this.get_marked_indices());
+    Notebook.prototype.merge_selected_cells = function() {
+        this.merge_cells(this.get_selected_cells_indices());
     };
 
     /**
@@ -2009,27 +1948,27 @@ define(function (require) {
     /**
      * Execute or render cell outputs and go into command mode.
      */
-    Notebook.prototype.execute_marked_cells = function () {
-        this.execute_cells(this.get_marked_indices());
+    Notebook.prototype.execute_selected_cells = function () {
+        this.execute_cells(this.get_selected_cells_indices());
     };
 
+    
     /**
-     * Alias for execute_marked_cells, for backwards compatibility --
+     * Alias for execute_selected_cells, for backwards compatibility --
      * previously, doing "Run Cell" would only ever run a single cell (hence
      * `execute_cell`), but now it runs all marked cells, so that's the
      * preferable function to use. But it is good to keep this function to avoid
      * breaking existing extensions, etc.
      */
     Notebook.prototype.execute_cell = function () {
-        this.execute_marked_cells();
+        this.execute_selected_cells();
     };
 
     /**
      * Execute or render cell outputs and insert a new cell below.
      */
     Notebook.prototype.execute_cell_and_insert_below = function () {
-        // execute the marked cells, and don't insert anything
-        var indices = this.get_marked_indices();
+        var indices = this.get_selected_cells_indices();
         if (indices.length > 1) {
             this.execute_cells(indices);
             return;
@@ -2061,8 +2000,7 @@ define(function (require) {
      * Execute or render cell outputs and select the next cell.
      */
     Notebook.prototype.execute_cell_and_select_below = function () {
-        // execute the marked cells, and don't select anything
-        var indices = this.get_marked_indices();
+        var indices = this.get_selected_cells_indices();
         if (indices.length > 1) {
             this.execute_cells(indices);
             return;
diff --git a/notebook/static/notebook/js/textcell.js b/notebook/static/notebook/js/textcell.js
index e5bde67be..dc7471c37 100644
--- a/notebook/static/notebook/js/textcell.js
+++ b/notebook/static/notebook/js/textcell.js
@@ -118,7 +118,7 @@ define([
     // Cell level actions
     
     TextCell.prototype.select = function () {
-        var cont = Cell.prototype.select.apply(this);
+        var cont = Cell.prototype.select.apply(this, arguments);
         if (cont) {
             if (this.mode === 'edit') {
                 this.code_mirror.refresh();
diff --git a/notebook/static/notebook/less/cell.less b/notebook/static/notebook/less/cell.less
index 85e0481ff..393626caa 100644
--- a/notebook/static/notebook/less/cell.less
+++ b/notebook/static/notebook/less/cell.less
@@ -1,59 +1,65 @@
 @_cell_padding_minus_border: @cell_padding - @cell_border_width;
 
-._marked_style(@n) {
-    border-left-width: @n;
-    padding-left: @cell_padding - @n;
+._selected_style(@c1, @c2, @sep:0, @border_width:@cell_border_width) {
+    border-left-width: @border_width;
+    padding-left: @cell_padding - @border_width;
+    background: linear-gradient(to right, @c1 -40px,@c1 @sep,@c2 @sep,@c2 100%);
 }
 
+
 div.cell {
-    border: @cell_border_width solid transparent;
     .vbox();
     .corner-all();
     .border-box-sizing();
+    
     border-width: @cell_border_width;
     border-style: solid;
+    border-color: transparent;
 
-    &.marked {
-        ._marked_style(3px);
-        border-left-color: @marked_border_color_light;
-
-        /* Don't border the cells when printing */
+    width: 100%;
+    padding: @_cell_padding_minus_border;
+    /* This acts as a spacer between cells, that is outside the border */
+    margin: 0px;
+    outline: none;
+   
+    ._selected_style(transparent, transparent, @cell_border_width);
+
+    .jupyter-multi-select &.jupyter-soft-selected {
+        border-left-color: @selected_border_color_light;
+        border-left-color: @soft_select_color;
+        ._selected_style(@selected_border_color_light, @soft_select_color, 5px, 0px);
+        
         @media print {
             border-color: transparent;
         }
     }
 
-    &.selected {
+     &.selected {
         border-color: @border_color;
-        border-left-color: @marked_border_color;
-        ._marked_style(2px);
-
-        &.marked {
-          ._marked_style(4px);
-        }
-
-        /* Don't border the cells when printing */
+        ._selected_style(@selected_border_color, transparent, 5px, 0px);
+        
+        
         @media print {
             border-color: transparent;
         }
     }
 
+    .jupyter-multi-select &.selected.jupyter-soft-selected {
+        ._selected_style(@selected_border_color, @soft_select_color, 7px, 0);
+    }
+
     .edit_mode &.selected {
         border-color: @edit_mode_border_color;
+        ._selected_style(@edit_mode_border_color, transparent, 5px, 0px);
 
-        /* Don't border the cells when printing */
         @media print {
             border-color: transparent;
         }
     }
 
-    width: 100%;
-    padding: @_cell_padding_minus_border;
-    /* This acts as a spacer between cells, that is outside the border */
-    margin: 0px;
-    outline: none;
 }
 
+
 .prompt {
     /* This needs to be wide enough for 3 digit prompt numbers: In[100]: */
     min-width: 14ex;
diff --git a/notebook/static/notebook/less/variables.less b/notebook/static/notebook/less/variables.less
index 441395491..c1dad6927 100644
--- a/notebook/static/notebook/less/variables.less
+++ b/notebook/static/notebook/less/variables.less
@@ -11,12 +11,17 @@
 @code_line_height:              1.21429em;  // changed from 1.231 to get 17px even
 @code_padding:                  0.4em;  // 5.6 px
 @rendered_html_border_color:    black;
-@input_prompt_color:            navy;
-@output_prompt_color:           darkred;
+@input_prompt_color:            #303F9F;
+@output_prompt_color:           #D84315;
 @output_pre_color:              black;
 @notification_widget_bg:        rgba(240, 240, 240, 0.5);
-@marked_border_color:           #009AF5;
-@marked_border_color_light:     #7AC7F5;
-@edit_mode_border_color:        green;
+
+
+@selected_border_color:           #42A5F5;
+@selected_border_color_light:     #90CAF9;
+@soft_select_color:             #E3F2FD;
+
+
+@edit_mode_border_color:        #66BB6A;
 @cell_padding:                  6px;
-@cell_border_width:             1px;
\ No newline at end of file
+@cell_border_width:             1px;
diff --git a/notebook/tests/notebook/dualmode_merge.js b/notebook/tests/notebook/dualmode_merge.js
index 2a6520595..b39f753fa 100644
--- a/notebook/tests/notebook/dualmode_merge.js
+++ b/notebook/tests/notebook/dualmode_merge.js
@@ -41,7 +41,7 @@ casper.notebook_test(function () {
         this.test.assertEquals(this.get_cell_text(1), 'cd', 'split; Verify that cell 1 has the second half.');
         this.validate_notebook_state('split', 'edit', 1);
         this.select_cell(0); // Move up to cell 0
-        this.evaluate(function() { IPython.notebook.extend_marked(1);});
+        this.evaluate(function() { IPython.notebook.extend_selection_by(1);});
         this.trigger_keydown('shift-m'); // Merge
         this.validate_notebook_state('merge', 'command', 0);
         this.test.assertEquals(this.get_cell_text(0), a, 'merge; Verify that cell 0 has the merged contents.');
diff --git a/notebook/tests/notebook/execute_marked_cells.js b/notebook/tests/notebook/execute_selected_cells.js
similarity index 61%
rename from notebook/tests/notebook/execute_marked_cells.js
rename to notebook/tests/notebook/execute_selected_cells.js
index 2ce0f08e0..67119f397 100644
--- a/notebook/tests/notebook/execute_marked_cells.js
+++ b/notebook/tests/notebook/execute_selected_cells.js
@@ -3,16 +3,18 @@
 //
 casper.notebook_test(function () {
     var that = this;
-    var assert_outputs = function (expected) {
+    var assert_outputs = function (expected, msg_prefix) {
         var msg, i;
+        msg_prefix = "(assert_outputs) "+(msg_prefix || 'no prefix')+": ";
         for (i = 0; i < that.get_cells_length(); i++) {
             if (expected[i] === undefined) {
-                msg = 'cell ' + i + ' not executed';
+                msg = msg_prefix + 'cell ' + i + ' not executed';
                 that.test.assertFalse(that.cell_has_outputs(i), msg);
 
             } else {
-                msg = 'cell ' + i + ' executed';
-                that.test.assertEquals(that.get_output_cell(i).text, expected[i], msg);
+                msg = msg_prefix + 'cell ' + i + ' executed';
+                var out = that.get_output_cell(i, undefined, msg_prefix).text
+                that.test.assertEquals(out, expected[i], msg + 'out is: '+out);
             }
         }
     };
@@ -23,69 +25,54 @@ casper.notebook_test(function () {
         this.append_cell('print("c")');
         this.append_cell('print("d")');
         this.test.assertEquals(this.get_cells_length(), 4, "correct number of cells");
-
-        this.evaluate(function () {
-            IPython.notebook.unmark_all_cells();
-            IPython.notebook.set_marked_indices([1, 2]);
-        });
     });
 
     this.then(function () {
-        this.evaluate(function () {
-            IPython.notebook.clear_all_output();
-        });
-
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
-        this.trigger_keydown('ctrl-enter');
-    });
-
-    this.wait_for_output(1);
-    this.wait_for_output(2);
-
-    this.then(function () {
-        assert_outputs([undefined, 'b\n', 'c\n', undefined]);
-        this.validate_notebook_state('run marked cells', 'command', 2);
+        this.select_cell(2, false);
     });
 
-    // execute cells in place when there are marked cells
     this.then(function () {
         this.evaluate(function () {
             IPython.notebook.clear_all_output();
         });
+    })
 
+    this.then(function(){
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
-        this.trigger_keydown('shift-enter');
+        this.validate_notebook_state('before execute 1', 'command', 1);
+        this.select_cell(1);
+        this.select_cell(2, false);
+        this.trigger_keydown('ctrl-enter');
     });
 
     this.wait_for_output(1);
     this.wait_for_output(2);
 
     this.then(function () {
-        assert_outputs([undefined, 'b\n', 'c\n', undefined]);
-        this.validate_notebook_state('run marked cells', 'command', 2);
+        assert_outputs([undefined, 'b\n', 'c\n', undefined], 'run selected 1');
+        this.validate_notebook_state('run selected cells 1', 'command', 2);
     });
 
-    // execute and insert below when there are marked cells
+
+    // execute and insert below when there are selected cells
     this.then(function () {
         this.evaluate(function () {
             IPython.notebook.clear_all_output();
         });
 
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
+        this.validate_notebook_state('before execute 2', 'command', 1);
         this.evaluate(function () {
             $("#run_cell_insert_below").click();
         });
     });
 
     this.wait_for_output(1);
-    this.wait_for_output(2);
 
     this.then(function () {
-        assert_outputs([undefined, 'b\n', 'c\n', undefined]);
-        this.validate_notebook_state('run marked cells', 'command', 2);
+        assert_outputs([undefined, 'b\n', undefined, undefined , undefined],'run selected cells 2');
+        this.validate_notebook_state('run selected cells 2', 'edit', 2);
     });
 
     // check that it doesn't affect run all above
@@ -95,7 +82,7 @@ casper.notebook_test(function () {
         });
 
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
+        this.validate_notebook_state('before execute 3', 'command', 1);
         this.evaluate(function () {
             $("#run_all_cells_above").click();
         });
@@ -104,7 +91,7 @@ casper.notebook_test(function () {
     this.wait_for_output(0);
 
     this.then(function () {
-        assert_outputs(['a\n', undefined, undefined, undefined]);
+        assert_outputs(['a\n', undefined, undefined, undefined],'run cells above');
         this.validate_notebook_state('run cells above', 'command', 0);
     });
 
@@ -115,7 +102,7 @@ casper.notebook_test(function () {
         });
 
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
+        this.validate_notebook_state('before execute 4', 'command', 1);
         this.evaluate(function () {
             $("#run_all_cells_below").click();
         });
@@ -126,8 +113,8 @@ casper.notebook_test(function () {
     this.wait_for_output(3);
 
     this.then(function () {
-        assert_outputs([undefined, 'b\n', 'c\n', 'd\n']);
-        this.validate_notebook_state('run cells below', 'command', 3);
+        assert_outputs([undefined, 'b\n', undefined, 'c\n', 'd\n'],'run cells below');
+        this.validate_notebook_state('run cells below', 'command', 4);
     });
 
     // check that it doesn't affect run all
@@ -137,7 +124,7 @@ casper.notebook_test(function () {
         });
 
         this.select_cell(1);
-        this.validate_notebook_state('before execute', 'command', 1);
+        this.validate_notebook_state('before execute 5', 'command', 1);
         this.evaluate(function () {
             $("#run_all_cells").click();
         });
@@ -149,7 +136,7 @@ casper.notebook_test(function () {
     this.wait_for_output(3);
 
     this.then(function () {
-        assert_outputs(['a\n', 'b\n', 'c\n', 'd\n']);
-        this.validate_notebook_state('run all cells', 'command', 3);
+        assert_outputs(['a\n', 'b\n', undefined, 'c\n', 'd\n'],'run all cells');
+        this.validate_notebook_state('run all cells', 'command', 4);
     });
 });
diff --git a/notebook/tests/notebook/marks.js b/notebook/tests/notebook/marks.js
deleted file mode 100644
index a59823491..000000000
--- a/notebook/tests/notebook/marks.js
+++ /dev/null
@@ -1,73 +0,0 @@
-
-// Test
-casper.notebook_test(function () {
-    var that = this;
-    
-    var a = 'print("a")';
-    var index = this.append_cell(a);
-
-    var b = 'print("b")';
-    index = this.append_cell(b);
-
-    var c = 'print("c")';
-    index = this.append_cell(c);
-
-    this.then(function () {
-        var selectedIndex = this.evaluate(function () {
-            Jupyter.notebook.select(0);
-            return Jupyter.notebook.get_selected_index();
-        });
-
-        this.test.assertEquals(this.evaluate(function() { 
-            return Jupyter.notebook.get_marked_cells().length; 
-        }), 1, 'only one cell is marked programmatically');
-
-        this.test.assertEquals(this.evaluate(function() {
-            return Jupyter.notebook.get_marked_indices()[0];
-        }), selectedIndex, 'marked cell is selected cell');
-
-        this.test.assertEquals(this.evaluate(function() { 
-            return $('.cell.marked').length; 
-        }), 0, 'no cells are marked visibily');
-        
-        this.evaluate(function() {
-            Jupyter.notebook.mark_all_cells();
-        });
-        
-        var cellCount = this.evaluate(function() { 
-            return Jupyter.notebook.ncells(); 
-        });
-        
-        this.test.assertEquals(this.evaluate(function() { 
-            return Jupyter.notebook.get_marked_cells().length; 
-        }), cellCount, 'mark_all');
-        
-        this.test.assertEquals(this.evaluate(function() { 
-            return $('.cell.marked').length; 
-        }), cellCount, 'marked cells are marked visibily');
-        
-        this.evaluate(function() {
-            Jupyter.notebook.unmark_all_cells();
-        });
-        
-        this.test.assertEquals(this.evaluate(function() { 
-            return Jupyter.notebook.get_marked_cells().length; 
-        }), 1, 'unmark_all');
-
-        this.test.assertEquals(this.evaluate(function() {
-            return Jupyter.notebook.get_marked_indices()[0];
-        }), selectedIndex, 'marked cell is selected cell');
-
-        this.evaluate(function() {
-            Jupyter.notebook.set_marked_indices([1]);
-        });
-
-        this.test.assertEquals(this.evaluate(function() {
-            return Jupyter.notebook.get_marked_cells().length;
-        }), 2, 'two cells are marked');
-
-        this.test.assertEquals(this.evaluate(function() {
-            return Jupyter.notebook.get_marked_indices();
-        }), [selectedIndex, 1], 'get/set_marked_indices');
-    });
-});
diff --git a/notebook/tests/notebook/multiselect.js b/notebook/tests/notebook/multiselect.js
new file mode 100644
index 000000000..0e0df023a
--- /dev/null
+++ b/notebook/tests/notebook/multiselect.js
@@ -0,0 +1,49 @@
+
+// Test
+casper.notebook_test(function () {
+    var that = this;
+    
+    var a = 'print("a")';
+    var index = this.append_cell(a);
+
+    var b = 'print("b")';
+    index = this.append_cell(b);
+
+    var c = 'print("c")';
+    index = this.append_cell(c);
+
+    this.then(function () {
+        var selectedIndex = this.evaluate(function () {
+            Jupyter.notebook.select(0);
+            return Jupyter.notebook.get_selected_index();
+        });
+
+        this.test.assertEquals(this.evaluate(function() { 
+            return Jupyter.notebook.get_selected_cells().length; 
+        }), 1, 'only one cell is selected programmatically');
+
+        this.test.assertEquals(this.evaluate(function() { 
+            return $('.cell.jupyter-soft-selected').length; 
+        }), 1, 'one cell is selected');
+        
+                
+        
+        this.test.assertEquals(this.evaluate(function() { 
+            Jupyter.notebook.extend_selection_by(1);
+            return Jupyter.notebook.get_selected_cells().length; 
+        }), 2, 'extend selection by one');
+
+        
+        this.test.assertEquals(this.evaluate(function() { 
+            Jupyter.notebook.extend_selection_by(-1);
+            return Jupyter.notebook.get_selected_cells().length; 
+        }), 1, 'contract selection by one');
+        
+        this.test.assertEquals(this.evaluate(function() { 
+            Jupyter.notebook.select(1);
+            Jupyter.notebook.extend_selection_by(-1);
+            return Jupyter.notebook.get_selected_cells().length; 
+        }), 2, 'extend selection by one up');
+
+    });
+});
diff --git a/notebook/tests/notebook/undelete.js b/notebook/tests/notebook/undelete.js
index 6269b6f17..371c1838c 100644
--- a/notebook/tests/notebook/undelete.js
+++ b/notebook/tests/notebook/undelete.js
@@ -4,11 +4,11 @@
 casper.notebook_test(function () {
     var that = this;
 
-    var assert_marked_cells = function (action, indices) {
-        var marked = that.evaluate(function () {
-            return IPython.notebook.get_marked_indices();
+    var assert_selected_cells = function (action, indices) {
+        var  selected = that.evaluate(function () {
+            return IPython.notebook.get_selected_cells_indices();
         });
-        that.test.assertEquals(marked, indices, action + "; verify marked cells");
+        that.test.assertEquals( selected, indices, action + "; verify  selected cells");
     };
 
     var assert_cells = function (action, cells, index) {
@@ -22,7 +22,7 @@ casper.notebook_test(function () {
         }
 
         that.validate_notebook_state(action, 'command', index);
-        assert_marked_cells(action, [index]);
+        assert_selected_cells(action, [index]);
     };
 
     var a = 'print("a")';
@@ -59,7 +59,7 @@ casper.notebook_test(function () {
     this.select_cell(1);
     this.trigger_keydown('esc');
     this.trigger_keydown('shift-j');
-    assert_marked_cells("select cells 1-2", [1, 2]);
+    assert_selected_cells("select cells 1-2", [1, 2]);
     this.trigger_keydown('shift-m');
     this.trigger_keydown('esc');
     assert_cells("merge cells 1-2", [a, bc, d], 1);
@@ -75,7 +75,7 @@ casper.notebook_test(function () {
     this.select_cell(3);
     this.trigger_keydown('esc');
     this.trigger_keydown('shift-k');
-    assert_marked_cells("select cells 3-2", [2, 3]);
+    assert_selected_cells("select cells 3-2", [2, 3]);
     this.trigger_keydown('shift-m');
     this.trigger_keydown('esc');
     assert_cells("merge cells 3-2", [a, bc, cd], 2);
diff --git a/notebook/tests/util.js b/notebook/tests/util.js
index 8a15b1d56..8a82c9a37 100644
--- a/notebook/tests/util.js
+++ b/notebook/tests/util.js
@@ -169,11 +169,11 @@ casper.wait_for_output = function (cell_num, out_num) {
         },
         function then() { },
         function timeout() {
-            this.echo("wait_for_output timed out on cell "+cell_num+", waiting for "+out_num+"outputs .");
+            this.echo("wait_for_output timed out on cell "+cell_num+", waiting for "+out_num+" outputs .");
             var pn = this.evaluate(function get_prompt(c) {
-                return IPython.notebook.get_cell(c).input_prompt_number;
+                return (IPython.notebook.get_cell(c)|| {'input_prompt_number':'no cell'}).input_prompt_number;
             });
-            this.echo("cell prompt was :'"+pn+"'.")
+            this.echo("cell prompt was :'"+pn+"'.");
         });
     });
 };
@@ -229,7 +229,8 @@ casper.cell_has_outputs = function (cell_num) {
     return result > 0;
 };
 
-casper.get_output_cell = function (cell_num, out_num) {
+casper.get_output_cell = function (cell_num, out_num, message) {
+    messsge  = message+': ' ||'no category :'
     // return an output of a given cell
     out_num = out_num || 0;
     var result = casper.evaluate(function (c, o) {
@@ -244,7 +245,7 @@ casper.get_output_cell = function (cell_num, out_num) {
         },
         {c : cell_num});
         this.test.assertTrue(false,
-            "Cell " + cell_num + " has no output #" + out_num + " (" + num_outputs + " total)"
+            message+"Cell " + cell_num + " has no output #" + out_num + " (" + num_outputs + " total)"
         );
     } else {
         return result;
@@ -394,14 +395,19 @@ casper.cell_element_function = function(index, selector, function_name, function
 casper.validate_notebook_state = function(message, mode, cell_index) {
     // Validate the entire dual mode state of the notebook.  Make sure no more than
     // one cell is selected, focused, in edit mode, etc...
-
     // General tests.
     this.test.assertEquals(this.get_keyboard_mode(), this.get_notebook_mode(),
         message + '; keyboard and notebook modes match');
     // Is the selected cell the only cell that is selected?
     if (cell_index!==undefined) {
         this.test.assert(this.is_only_cell_selected(cell_index),
-            message + '; cell ' + cell_index + ' is the only cell selected');
+            message + '; expecting cell ' + cell_index + ' to be the only cell selected. Got selected cell(s):'+
+            (function(){
+                return casper.evaluate(function(){
+                    return IPython.notebook.get_selected_cells_indices();
+                })
+            })()
+            );
     }
 
     // Mode specific tests.
@@ -433,11 +439,11 @@ casper.validate_notebook_state = function(message, mode, cell_index) {
     }
 };
 
-casper.select_cell = function(index) {
+casper.select_cell = function(index, moveanchor) {
     // Select a cell in the notebook.
-    this.evaluate(function (i) {
-        IPython.notebook.select(i);
-    }, {i: index});
+    this.evaluate(function (i, moveanchor) {
+        IPython.notebook.select(i, moveanchor);
+    }, {i: index, moveanchor: moveanchor});
 };
 
 casper.click_cell_editor = function(index) {

From 5639ac71342baa850ff601c72a93094650d3984a Mon Sep 17 00:00:00 2001
From: Michael Marchetti <mmarchetti@continuum.io>
Date: Thu, 3 Dec 2015 08:38:50 -0500
Subject: [PATCH 38/40] Fix secondary error that occurs during handling of HTTP
 500 status

In log.py, we're attempting to log the request headers when a
500-series error occurs, but tornado.httputil.HTTPHeaders isn't a dict -
it inherits from collections.MutableMapping. So it fails during
JSON serialization. The fix is to convert it to a dict first.

Unfortunately, the HTTPHeaders class doesn't expose any methods
to access the underlying dictionary (`request.headers._dict`) directly,
so we recreate it using the public API.
---
 notebook/log.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/notebook/log.py b/notebook/log.py
index eecd39a00..9e727f0b7 100644
--- a/notebook/log.py
+++ b/notebook/log.py
@@ -43,6 +43,7 @@ def log_request(handler):
         msg = msg + ' referer={referer}'
     if status >= 500 and status != 502:
         # log all headers if it caused an error
-        log_method(json.dumps(request.headers, indent=2))
+        headers = { k: request.headers[k] for k in request.headers }
+        log_method(json.dumps(headers, indent=2))
     log_method(msg.format(**ns))
 

From 536a6d64dc2a80347d5917ce955ff8cd9eab59be Mon Sep 17 00:00:00 2001
From: Michael Marchetti <mmarchetti@continuum.io>
Date: Thu, 3 Dec 2015 12:49:12 -0500
Subject: [PATCH 39/40] Use `dict()` to convert the mapping to a dictionary

---
 notebook/log.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/notebook/log.py b/notebook/log.py
index 9e727f0b7..dab330cb4 100644
--- a/notebook/log.py
+++ b/notebook/log.py
@@ -43,7 +43,6 @@ def log_request(handler):
         msg = msg + ' referer={referer}'
     if status >= 500 and status != 502:
         # log all headers if it caused an error
-        headers = { k: request.headers[k] for k in request.headers }
-        log_method(json.dumps(headers, indent=2))
+        log_method(json.dumps(dict(request.headers), indent=2))
     log_method(msg.format(**ns))
 

From 2ace23d8419f2ea3f41cdef35f851f0243c6ae8e Mon Sep 17 00:00:00 2001
From: Peter Parente <parente@cs.unc.edu>
Date: Fri, 4 Dec 2015 09:46:11 -0500
Subject: [PATCH 40/40] Fix ConfigWithDefaults "this" context

Within the promise callback, refer to the ConfigWithDefaults instance, not the Promise
---
 notebook/static/services/config.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/notebook/static/services/config.js b/notebook/static/services/config.js
index f4b6cb802..fbf0f6bc0 100644
--- a/notebook/static/services/config.js
+++ b/notebook/static/services/config.js
@@ -93,7 +93,7 @@ function($, utils) {
     ConfigWithDefaults.prototype.get = function(key) {
         var that = this;
         return this.section.loaded.then(function() {
-            return this._class_data()[key] || this.defaults[key]
+            return that._class_data()[key] || that.defaults[key]
         });
     };