Merge branch 'release/1.2.0'

.travis.yml

@@ -12,7 +12,7 @@ deploy:
   skip_existing: true
   user: __token__
   password:
-    secure: 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
+    secure: pypi-AgEIcHlwaS5vcmcCJDg4ZjkzNGNkLTllZGYtNDg1My1iMThjLTMzMmIzNzRkYWI3NwACPHsicGVybWlzc2lvbnMiOiB7InByb2plY3RzIjogWyJpYW5ub3RhdGVzdiJdfSwgInZlcnNpb24iOiAxfQAABiDhmk7nEtxhl_TRlyhU030vSTHAQeBmK7h3VWPC-jQuAw
   on:
     tags: true
     repo: rhshah/iAnnotateSV

CHANGES.rst

@@ -1,25 +1,25 @@
-v0.0.2
+## v0.0.2
 RS:Added funtionality to visualize SV, though not clean, but a start.
-v0.0.3
+## v0.0.3
 RS:Added funtionality to add annotation of repeat regions, cosmic census and database of genomic variants (DGv)
-v0.0.4
+## v0.0.4
 RS:Added logging
-v0.0.6
+## v0.0.6
 RS:Addition of coloredlogs and some trivial bug fixes
-v1.0.3
+## v1.0.3
 RS:Added Functionality to use multiple tracks to annotate.
-v1.0.4
+## v1.0.4
 Minor Bug fixes
 v1.0.5
 Major Bug Fix:
 Did not assign intron number properly in some cases and that might give wrong annotation
-v1.0.6
+## v1.0.6
 RS:Added funtionality to get counts of events from Cosmic Fusion Export.
-v1.0.7
+## v1.0.7
 Updated to have no padding and proper transcript selection
-v1.0.8
+## v1.0.8
 Removing TIMM23B for proper annotation of RET-NCOA4
-v1.0.9
+## v1.0.9
 RS:Added functionality to kinase domain involvement in the annotation
-v1.2.0
+## v1.2.0
 RS:Bug fix for running auto selection mode and upgrading requirements

README.rst

@@ -6,6 +6,9 @@ iAnnotateSV: Annotation of structural variants detected from NGS
 :Source code: http://github.com/rhshah/iAnnotateSV
 :License: `Apache License 2.0 <http://www.apache.org/licenses/LICENSE-2.0>`_
 
+.. image:: https://img.shields.io/pypi/v/iAnnotateSV.svg
+        :target: https://pypi.python.org/pypi/iAnnotateSV
+
 .. image:: https://landscape.io/github/rhshah/iAnnotateSV/master/landscape.svg?style=flat
    :target: https://landscape.io/github/rhshah/iAnnotateSV/master
    :alt: Code Health

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 28894c8d3c2921d47047283801d617fa
+config: 9f362582164ff56ce148b5cb1ccd33fe
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -81,10 +81,26 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
 div.sphinxsidebar #searchbox input[type="text"] {
-    width: 170px;
+    float: left;
+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
 }
 
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
+    border-left: none;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+
 img {
     border: 0;
     max-width: 100%;
@@ -199,6 +215,11 @@ table.modindextable td {
 
 /* -- general body styles --------------------------------------------------- */
 
+div.body {
+    min-width: 450px;
+    max-width: 800px;
+}
+
 div.body p, div.body dd, div.body li, div.body blockquote {
     -moz-hyphens: auto;
     -ms-hyphens: auto;
@@ -332,6 +353,11 @@ table.docutils {
     border-collapse: collapse;
 }
 
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
 table caption span.caption-number {
     font-style: italic;
 }
@@ -405,6 +431,13 @@ table.field-list td, table.field-list th {
     hyphens: manual;
 }
 
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {

docs/_build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -70,7 +70,9 @@ jQuery.fn.highlightText = function(text, className) {
     if (node.nodeType === 3) {
       var val = node.nodeValue;
       var pos = val.toLowerCase().indexOf(text);
-      if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+      if (pos >= 0 &&
+          !jQuery(node.parentNode).hasClass(className) &&
+          !jQuery(node.parentNode).hasClass("nohighlight")) {
         var span;
         var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
         if (isInSVG) {
@@ -148,7 +150,9 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
   },
 
   /**
@@ -308,4 +312,4 @@ _ = Documentation.gettext;
 
 $(document).ready(function() {
   Documentation.init();
-});
+});

docs/_build/html/_static/nature.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- nature theme.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -125,14 +125,11 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
-div.sphinxsidebar input[type=text]{
+div.sphinxsidebar .searchformwrapper {
     margin-left: 20px;
+    margin-right: 20px;
 }
 
-div.sphinxsidebar input[type=submit]{
-    margin-left: 20px;
-}
-
 /* -- body styles ----------------------------------------------------------- */
 
 a {