fix example notebooks

g2nb · Jan 19, 2019 · b36548b · b36548b
1 parent f1dbf55
commit b36548b
Show file tree

Hide file tree

Showing 9 changed files with 93 additions and 40 deletions.
diff --git a/README.md b/README.md
@@ -17,6 +17,8 @@ Requirements:
 
 ```bash
 pip install igv
+jupyter nbextensioninstall --py igv
+jupyter nbextension enable --py igv
 ```
 
 ## Usage
@@ -155,7 +157,7 @@ b.search('myc')
 
 ### SVG output
 
-Saving the current IGV view as an SVG image requires to calls.  
+Saving the current IGV view as an SVG image requires two calls.  
 
 ```python
 b.get_svg()

diff --git a/examples/BamFiles.ipynb b/examples/BamFiles.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,9 +25,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div id=\"igv_4433498\" class=\"igv-js\"></div>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "b.show()"
    ]
@@ -48,24 +61,6 @@
     "    })\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "b.get_svg()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "b.display_svg()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -78,21 +73,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.1"
   }
  },
  "nbformat": 4,

diff --git a/examples/Embeded-DataURI.ipynb b/examples/Embeded-DataURI.ipynb
@@ -61,6 +61,24 @@
     "b.search(\"CIC--DUX4:10,796-10,844\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.get_svg()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.display_svg()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/examples/LocalFiles.ipynb b/examples/LocalFiles.ipynb
@@ -77,25 +77,43 @@
    "source": [
     "b.zoom_out()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.get_svg()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.display_svg()"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.7.1"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.15"
   }
  },
  "nbformat": 4,

diff --git a/examples/RemoteFiles.ipynb b/examples/RemoteFiles.ipynb
@@ -74,6 +74,31 @@
    "source": [
     "b.zoom_out()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.get_svg()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "b.display_svg()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/igv/browser.py b/igv/browser.py
@@ -123,9 +123,6 @@ def load_track(self, track):
         # Check for minimal igv.js requirements (the only required field for all tracks is url, which must be a string)
         if isinstance(track, dict) == False:
             raise Exception("track parameter must be a dictionary")
-        if "url" not in track:
-            raise Exception("track dictionary must contain a 'url' field")
-
 
         return self._send({
             "id": self.igv_id,

diff --git a/igv/static/extension.js b/igv/static/extension.js
@@ -1,5 +1,5 @@
 define(
-    ["/nbextensions/igv/igvjs/igv.min.js"],
+    ["/nbextensions/igv/igvjs/igv.js"],
     //["https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.min.js"],
     function (igv) {
 

diff --git a/igv/static/igvjs/igv.min.js b/igv/static/igvjs/igv.min.js
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(name='igv',
                  packages=['igv'],
-                 version='0.9.2',
+                 version='0.9.4',
                  description='Jupyter extension for embedding the genome visualation igv.js in a notebook',
                  long_description=long_description,
                  long_description_content_type="text/markdown",