Merge remote-tracking branch 'escher/master'

Conflicts:
	escher/js/src/Draw.js

Author: zakandrewking

INSTALL

@@ -1,3 +1,3 @@
 For development, you can run the following command to install Escher with all its dependencies:
 
-pip install -e '.[docs]'
+pip install -e '.[all]'

README.md

@@ -1,8 +1,5 @@
 [![Travis](https://api.travis-ci.org/zakandrewking/escher.svg?branch=master)](https://travis-ci.org/zakandrewking/escher)
 
-
-Cite Escher v1.0 Beta 3:   [![DOI](https://zenodo.org/badge/6078/zakandrewking/escher.png)](http://dx.doi.org/10.5281/zenodo.11712)
-
 Escher
 ======
 
@@ -17,4 +14,4 @@ Follow [@zakandrewking](https://twitter.com/zakandrewking) for Escher updates.
 Built at SBRG
 =============
 
-[![SBRG](https://raw.githubusercontent.com/zakandrewking/escher/new-website/escher/resources/sbrg-logo.png)](http://systemsbiology.ucsd.edu/)
+[![SBRG](https://raw.githubusercontent.com/zakandrewking/escher/master/escher/resources/sbrg-logo.png)](http://systemsbiology.ucsd.edu/)

escher/css/builder-1.0.0rc1.css renamed to builder-1.0.0.css

@@ -43,7 +43,7 @@
     background-color: rgba(255, 255, 255, 0.95);
     border-radius: 0px;
 }
-    .help-button {
+.help-button {
     float: right;
     padding: 0 5px;
     font-size: 12px;
@@ -129,23 +129,31 @@
     height: 100%;
     z-index: 9;
     background: rgba(0, 0, 0, 0.4);
+    padding: 5% 0 5% 0;
+    text-align: center;
 }
 .settings-box-container {
-    position: absolute;
-    width: 100%;
+    display: inline-block;
+    position: relative;
+    width: 90%;
+    max-width: 520px;
     height: 100%;
-    top: 0px;
-    left: 0px;
-    margin: 0;
-    padding: 5% 0 5% 0;
-    text-align: center;
     z-index: 10;
 }
+.settings-button {
+    position: absolute;
+    top: 5px;
+    right: 20px;
+    z-index: 10;
+}
+.settings-button-close {
+    right: 60px;
+}
 .settings-box {
     display: inline-block;
     max-height: 100%;
-    width: 90%;
-    max-width: 520px;
+    width: 100%;
+    /* max-width: 520px; */
     overflow-y: scroll;
     overflow-x: hidden;
     background: rgba(255, 255, 255, 0.95);
@@ -308,7 +316,7 @@ td.options-label-wide {
     position: absolute;
     top: 17px;
 }
-/* For Settings and Search */
+/* For Search */
 .close-button {
     margin-left: 4px;
     float: right;

escher/css/builder-embed-1.0.0rc1.css renamed to builder-embed-1.0.0.css

@@ -51,7 +51,7 @@
     stroke: rgb(50, 50, 50);
 }
 g.selected .node-circle{
-    stroke-width: 3px;
+    stroke-width: 6px;
     stroke: rgb(20, 113, 199);
 }
 g.selected .label {

builder-embed-latest.css

@@ -51,7 +51,7 @@
     stroke: rgb(50, 50, 50);
 }
 g.selected .node-circle{
-    stroke-width: 3px;
+    stroke-width: 6px;
     stroke: rgb(20, 113, 199);
 }
 g.selected .label {

builder-latest.css

@@ -43,7 +43,7 @@
     background-color: rgba(255, 255, 255, 0.95);
     border-radius: 0px;
 }
-    .help-button {
+.help-button {
     float: right;
     padding: 0 5px;
     font-size: 12px;
@@ -129,23 +129,31 @@
     height: 100%;
     z-index: 9;
     background: rgba(0, 0, 0, 0.4);
+    padding: 5% 0 5% 0;
+    text-align: center;
 }
 .settings-box-container {
-    position: absolute;
-    width: 100%;
+    display: inline-block;
+    position: relative;
+    width: 90%;
+    max-width: 520px;
     height: 100%;
-    top: 0px;
-    left: 0px;
-    margin: 0;
-    padding: 5% 0 5% 0;
-    text-align: center;
     z-index: 10;
 }
+.settings-button {
+    position: absolute;
+    top: 5px;
+    right: 20px;
+    z-index: 10;
+}
+.settings-button-close {
+    right: 60px;
+}
 .settings-box {
     display: inline-block;
     max-height: 100%;
-    width: 90%;
-    max-width: 520px;
+    width: 100%;
+    /* max-width: 520px; */
     overflow-y: scroll;
     overflow-x: hidden;
     background: rgba(255, 255, 255, 0.95);
@@ -308,7 +316,7 @@ td.options-label-wide {
     position: absolute;
     top: 17px;
 }
-/* For Settings and Search */
+/* For Search */
 .close-button {
     margin-left: 4px;
     float: right;

builder.html

@@ -8,7 +8,7 @@
   <script src="escher/lib/bootstrap-3.1.1.min.js"></script>
 
   <link rel="stylesheet" href="escher/lib/bootstrap-3.1.1.min.css"/>
-  <link rel="stylesheet" href="escher/css/builder-1.0.0rc1.css"/>
+  <link rel="stylesheet" href="escher/css/builder-1.0.0.css"/>
 
     <!-- Require only loaded in standalone file. -->
     <script src="escher/lib/require.min.js"></script>
@@ -29,7 +29,7 @@
 var reaction_data_static = null;
 var metabolite_data_static = null;
 var gene_data_static = null;
-var embedded_css_static = '@charset "utf-8";#mouse-node {    fill: none;}#canvas {    stroke: #ccc;    stroke-width: 7px;    fill: white;}.resize-rect {    fill: black;    opacity: 0;    stroke: none;}.label {    font-family: sans-serif;     font-style: italic;     font-weight: bold;     font-size: 8px;     fill: black;     stroke: none;    text-rendering: optimizelegibility;    cursor: default;}.reaction-label {    font-size: 30px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.node-label {    font-size: 20px;}.gene-label {    font-size: 18px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.text-label .label {    font-size: 50px;}.text-label-input {    font-size: 50px;}.node-circle {    stroke-width: 2px;}.midmarker-circle,.multimarker-circle {    fill: white;    fill-opacity: 0.2;    stroke: rgb(50, 50, 50);}g.selected .node-circle{    stroke-width: 3px;    stroke: rgb(20, 113, 199);}g.selected .label {    fill: rgb(20, 113, 199);}.metabolite-circle {    stroke: rgb(162, 69, 16);    fill: rgb(224, 134, 91);}g.selected .metabolite-circle {    stroke: rgb(5, 2, 0);}.segment {    stroke: #334E75;    stroke-width: 10px;    fill: none;}.arrowhead {    fill: #334E75;}.stoichiometry-label-rect {    fill: white;    opacity: 0.5;}.stoichiometry-label {    fill: #334E75;    font-size: 17px;}.membrane {    fill: none;    stroke: rgb(255, 187, 0);}.brush .extent {     fill-opacity: 0.1;    fill: black;    stroke: #fff;    shape-rendering: crispEdges;}#brush-container .background {    fill: none;}.bezier-circle {    fill: rgb(255,255,255);     }.bezier-circle.b1 {    stroke: red;}.bezier-circle.b2 {    stroke: blue;}.connect-line{     stroke: rgb(200,200,200);}.direction-arrow {    stroke: black;    stroke-width: 1px;    fill: white;    opacity: 0.3;}.start-reaction-cursor {    cursor: pointer;}.start-reaction-target {    stroke: rgb(100,100,100);    fill: none;    opacity: 0.5;}.rotation-center-line {    stroke: red;    stroke-width: 5px;}.highlight {    fill: #106F94;}.cursor-grab {    cursor: grab;    cursor: -webkit-grab;}.cursor-grabbing {    cursor: grabbing;    cursor: -webkit-grabbing;}.edit-text-cursor {    cursor: text;}';
+var embedded_css_static = '@charset "utf-8";#mouse-node {    fill: none;}#canvas {    stroke: #ccc;    stroke-width: 7px;    fill: white;}.resize-rect {    fill: black;    opacity: 0;    stroke: none;}.label {    font-family: sans-serif;     font-style: italic;     font-weight: bold;     font-size: 8px;     fill: black;     stroke: none;    text-rendering: optimizelegibility;    cursor: default;}.reaction-label {    font-size: 30px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.node-label {    font-size: 20px;}.gene-label {    font-size: 18px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.text-label .label {    font-size: 50px;}.text-label-input {    font-size: 50px;}.node-circle {    stroke-width: 2px;}.midmarker-circle,.multimarker-circle {    fill: white;    fill-opacity: 0.2;    stroke: rgb(50, 50, 50);}g.selected .node-circle{    stroke-width: 6px;    stroke: rgb(20, 113, 199);}g.selected .label {    fill: rgb(20, 113, 199);}.metabolite-circle {    stroke: rgb(162, 69, 16);    fill: rgb(224, 134, 91);}g.selected .metabolite-circle {    stroke: rgb(5, 2, 0);}.segment {    stroke: #334E75;    stroke-width: 10px;    fill: none;}.arrowhead {    fill: #334E75;}.stoichiometry-label-rect {    fill: white;    opacity: 0.5;}.stoichiometry-label {    fill: #334E75;    font-size: 17px;}.membrane {    fill: none;    stroke: rgb(255, 187, 0);}.brush .extent {     fill-opacity: 0.1;    fill: black;    stroke: #fff;    shape-rendering: crispEdges;}#brush-container .background {    fill: none;}.bezier-circle {    fill: rgb(255,255,255);     }.bezier-circle.b1 {    stroke: red;}.bezier-circle.b2 {    stroke: blue;}.connect-line{     stroke: rgb(200,200,200);}.direction-arrow {    stroke: black;    stroke-width: 1px;    fill: white;    opacity: 0.3;}.start-reaction-cursor {    cursor: pointer;}.start-reaction-target {    stroke: rgb(100,100,100);    fill: none;    opacity: 0.5;}.rotation-center-line {    stroke: red;    stroke-width: 5px;}.highlight {    fill: #106F94;}.cursor-grab {    cursor: grab;    cursor: -webkit-grab;}.cursor-grabbing {    cursor: grabbing;    cursor: -webkit-grabbing;}.edit-text-cursor {    cursor: text;}';
 
   </script>
   <script>
@@ -46,7 +46,7 @@
      // require.js is available: use it to load d3 and escher
 
      require.config({paths: { d3: "escher/lib/d3.min",
-			      escher: "escher/lib/escher-1.0.0rc1.min" }});
+			      escher: "escher/lib/escher-1.0.0.min" }});
      require(["d3", "escher"], function(d3, escher) {
        window.d3 = d3;
        options = { enable_editing: true,
@@ -93,7 +93,7 @@
      } else {
        // require.js not available: dynamically load d3 & escher
        escher_load_lib("escher/lib/d3.min.js", function() {
-	 escher_load_lib("escher/lib/escher-1.0.0rc1.min.js", function() {
+	 escher_load_lib("escher/lib/escher-1.0.0.min.js", function() {
 	   options = { enable_editing: true,
 menu: "all",
 enable_keys: true,

builder_not_minified.html

@@ -8,7 +8,7 @@
   <script src="escher/lib/bootstrap-3.1.1.min.js"></script>
 
   <link rel="stylesheet" href="escher/lib/bootstrap-3.1.1.min.css"/>
-  <link rel="stylesheet" href="escher/css/builder-1.0.0rc1.css"/>
+  <link rel="stylesheet" href="escher/css/builder-1.0.0.css"/>
 
     <!-- Require only loaded in standalone file. -->
     <script src="escher/lib/require.min.js"></script>
@@ -29,7 +29,7 @@
 var reaction_data_static = null;
 var metabolite_data_static = null;
 var gene_data_static = null;
-var embedded_css_static = '@charset "utf-8";#mouse-node {    fill: none;}#canvas {    stroke: #ccc;    stroke-width: 7px;    fill: white;}.resize-rect {    fill: black;    opacity: 0;    stroke: none;}.label {    font-family: sans-serif;     font-style: italic;     font-weight: bold;     font-size: 8px;     fill: black;     stroke: none;    text-rendering: optimizelegibility;    cursor: default;}.reaction-label {    font-size: 30px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.node-label {    font-size: 20px;}.gene-label {    font-size: 18px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.text-label .label {    font-size: 50px;}.text-label-input {    font-size: 50px;}.node-circle {    stroke-width: 2px;}.midmarker-circle,.multimarker-circle {    fill: white;    fill-opacity: 0.2;    stroke: rgb(50, 50, 50);}g.selected .node-circle{    stroke-width: 3px;    stroke: rgb(20, 113, 199);}g.selected .label {    fill: rgb(20, 113, 199);}.metabolite-circle {    stroke: rgb(162, 69, 16);    fill: rgb(224, 134, 91);}g.selected .metabolite-circle {    stroke: rgb(5, 2, 0);}.segment {    stroke: #334E75;    stroke-width: 10px;    fill: none;}.arrowhead {    fill: #334E75;}.stoichiometry-label-rect {    fill: white;    opacity: 0.5;}.stoichiometry-label {    fill: #334E75;    font-size: 17px;}.membrane {    fill: none;    stroke: rgb(255, 187, 0);}.brush .extent {     fill-opacity: 0.1;    fill: black;    stroke: #fff;    shape-rendering: crispEdges;}#brush-container .background {    fill: none;}.bezier-circle {    fill: rgb(255,255,255);     }.bezier-circle.b1 {    stroke: red;}.bezier-circle.b2 {    stroke: blue;}.connect-line{     stroke: rgb(200,200,200);}.direction-arrow {    stroke: black;    stroke-width: 1px;    fill: white;    opacity: 0.3;}.start-reaction-cursor {    cursor: pointer;}.start-reaction-target {    stroke: rgb(100,100,100);    fill: none;    opacity: 0.5;}.rotation-center-line {    stroke: red;    stroke-width: 5px;}.highlight {    fill: #106F94;}.cursor-grab {    cursor: grab;    cursor: -webkit-grab;}.cursor-grabbing {    cursor: grabbing;    cursor: -webkit-grabbing;}.edit-text-cursor {    cursor: text;}';
+var embedded_css_static = '@charset "utf-8";#mouse-node {    fill: none;}#canvas {    stroke: #ccc;    stroke-width: 7px;    fill: white;}.resize-rect {    fill: black;    opacity: 0;    stroke: none;}.label {    font-family: sans-serif;     font-style: italic;     font-weight: bold;     font-size: 8px;     fill: black;     stroke: none;    text-rendering: optimizelegibility;    cursor: default;}.reaction-label {    font-size: 30px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.node-label {    font-size: 20px;}.gene-label {    font-size: 18px;    fill: rgb(32, 32, 120);    text-rendering: optimizelegibility;}.text-label .label {    font-size: 50px;}.text-label-input {    font-size: 50px;}.node-circle {    stroke-width: 2px;}.midmarker-circle,.multimarker-circle {    fill: white;    fill-opacity: 0.2;    stroke: rgb(50, 50, 50);}g.selected .node-circle{    stroke-width: 6px;    stroke: rgb(20, 113, 199);}g.selected .label {    fill: rgb(20, 113, 199);}.metabolite-circle {    stroke: rgb(162, 69, 16);    fill: rgb(224, 134, 91);}g.selected .metabolite-circle {    stroke: rgb(5, 2, 0);}.segment {    stroke: #334E75;    stroke-width: 10px;    fill: none;}.arrowhead {    fill: #334E75;}.stoichiometry-label-rect {    fill: white;    opacity: 0.5;}.stoichiometry-label {    fill: #334E75;    font-size: 17px;}.membrane {    fill: none;    stroke: rgb(255, 187, 0);}.brush .extent {     fill-opacity: 0.1;    fill: black;    stroke: #fff;    shape-rendering: crispEdges;}#brush-container .background {    fill: none;}.bezier-circle {    fill: rgb(255,255,255);     }.bezier-circle.b1 {    stroke: red;}.bezier-circle.b2 {    stroke: blue;}.connect-line{     stroke: rgb(200,200,200);}.direction-arrow {    stroke: black;    stroke-width: 1px;    fill: white;    opacity: 0.3;}.start-reaction-cursor {    cursor: pointer;}.start-reaction-target {    stroke: rgb(100,100,100);    fill: none;    opacity: 0.5;}.rotation-center-line {    stroke: red;    stroke-width: 5px;}.highlight {    fill: #106F94;}.cursor-grab {    cursor: grab;    cursor: -webkit-grab;}.cursor-grabbing {    cursor: grabbing;    cursor: -webkit-grabbing;}.edit-text-cursor {    cursor: text;}';
 
   </script>
   <script>
@@ -46,7 +46,7 @@
      // require.js is available: use it to load d3 and escher
 
      require.config({paths: { d3: "escher/lib/d3.min",
-			      escher: "escher/lib/escher-1.0.0rc1" }});
+			      escher: "escher/lib/escher-1.0.0" }});
      require(["d3", "escher"], function(d3, escher) {
        window.d3 = d3;
        options = { enable_editing: true,
@@ -93,7 +93,7 @@
      } else {
        // require.js not available: dynamically load d3 & escher
        escher_load_lib("escher/lib/d3.min.js", function() {
-	 escher_load_lib("escher/lib/escher-1.0.0rc1.js", function() {
+	 escher_load_lib("escher/lib/escher-1.0.0.js", function() {
 	   options = { enable_editing: true,
 menu: "all",
 enable_keys: true,

docs/conf.py

@@ -51,9 +51,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.0rc1'
+version = '1.0.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0rc1'
+release = '1.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/getting_started.rst

@@ -45,6 +45,8 @@ beta version of COBRApy which can be found here_.
 Once you have COBRApy v0.3.0b1 (or later) installed, then you can generate a
 JSON model by following this `example code`_.
 
+.. _loading-reaction-gene-and-metabolite-data:
+
 Loading reaction, gene, and metabolite data
 ===========================================
 
@@ -99,6 +101,8 @@ reaction data comparisons::
 Gene data and gene reaction rules
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. _editing-and-building:
+
 Editing and building
 ====================
 

docs/index.rst

@@ -13,15 +13,44 @@ the `Escher website`_.
 
 .. image:: _static/screen1.png
 
+Features
+--------
+
+#. View pathway maps in any modern web browser
+#. :ref:`Build maps <editing-and-building>` using the content of genome-scale metabolic models
+#. :ref:`Visualize data <loading-reaction-gene-and-metabolite-data>` on
+   reactions, genes, and metabolites
+#. Full text search
+#. Detailed options for changing colors, sizes, and more, all from the web
+   browser
+#. View maps :doc:`inside the IPython Notebook <ipython_notebook>`
+#. :doc:`Embed maps <development>` within any website, with minimal dependencies
+   (escher.js, d3.js, and optionally Twitter Bootstrap)
+
 Supported browsers
 ------------------
 
 We recommend using Google Chrome for optimal performance, but Escher will also
 run in the latest versions of Firefox, Internet Explorer, and Safari (including
 mobile Safari).
 
-Contents:
----------
+Installation
+------------
+
+Escher can be used without any installation by visiting the `Escher
+website`_. However, you can install escher if you would like to (1) run Escher
+offline, (2) include your own maps and models in the launch page, (3) view Escher maps
+in an IPython Notebook, or (4) modify the source code. 
+
+To install the latest stable version of Escher, run::
+
+    pip install escher
+
+For more information, see the documentation on :doc:`ipython_notebook` and
+:doc:`development`.
+
+Contents
+--------
 
 .. toctree::
    :maxdepth: 2
@@ -32,13 +61,13 @@ Contents:
    contribute_maps
    javascript_api
    python_api
+   
+* :ref:`genindex`
 
+License
+-------
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+Escher is licensed under the `MIT license`_.
 
-.. _Escher website: http://escher.github.io/
+.. _`Escher website`: http://escher.github.io/
+.. _`MIT license`: https://github.com/zakandrewking/escher/blob/master/LICENSE