Packaging updates

g2nb · Jan 3, 2019 · 83cfe98 · 83cfe98
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diff --git a/DEPLOY.md b/DEPLOY.md
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,8 +1,6 @@
 The MIT License (MIT)
 
-
-Copyright (c) 2016 Broad Institute
-
+Copyright (c) 2016-2019 The Broad Institute and The Regents of the University of California
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,28 +1,34 @@
 # igv.js Jupyter Extension
 
-This is an extension for [Jupyter Notebook](http://jupyter.org/) which
+IGV is an extension for [Jupyter Notebook](http://jupyter.org/) which
 wraps [igv.js](https://github.com/igvteam/igv.js).  With this
 extension you can render igv.js in a cell and call its API from
-the notebook.
+the notebook. The extension exposes a python API that mimics the igv.js 
+Browser creation and control APIs.   Dictionaries are used for browser and track 
+configuration objects.   Track data can be loaded from local or remote 
+URLs,  or supplied directly as lists of objects.
 
-## Installation_
+## Installation
 
-Tested against Python 3.7.1 and Jupyter version 4.4.0. It will not work on Python 2.X.
+Requirements:
+* python >= 3.6.4
+* jupyter >= 4.2.0
 
-This extension has not been released to pipy and can only be installed
-in development mode.  To install run the following from the project
-root folder.
 
 ```bash
-python setup.py build
-pip install -e .
-jupyter nbextension install --py igv
-jupyter nbextension enable --py igv
-
+pip install igv
 ```
 
 ## Usage
 
+### Examples
+
+Example notebooks are available in the github repository.   To download without cloning the repository use 
+this [link](https://github.com/igvteam/igv.js-jupyter/archive/master.zip).   Notebooks are available in the
+"examples" directory.
+
+
+
 ### Initialization
 
 To insert an IGV instance into a cell:  
@@ -34,20 +40,7 @@ Example:
 ```python
 import igv
 
-b = igv.Browser(
-    {"reference": {
-        "id": "hg19",
-        "fastaURL": "files/data/hg19.snippet.fasta",
-        "indexed": False,
-        "cytobandURL": "files/data/cytoband.hg19.snippet.txt",
-        "tracks": [
-            {
-                "name": "RefGene",
-                "url": "files/data/refgene.hg19.snippet.bed"
-            }
-        ]
-    }}
-)
+b = igv.Browser({"genome": "hg19"})
 ```
 
 The igv.Browser initializer takes a configuration object which is converted to JSON and passed to the igv.js
@@ -88,7 +81,7 @@ b.load_track(
 #### Local File
 
 Tracks can be loaded from local files using the Jupyter web server by prepending "files" to the path.  The path
-is relative to the notebook file.  This method is 
+is relative to the notebook file.  
 
 ```python
 b.load_track(
@@ -178,3 +171,14 @@ return b.locus
 
 ```
 
+#### Development
+
+To build and install from source:
+
+```bash
+python setup.py build
+pip install -e .
+jupyter nbextension install --py igv
+jupyter nbextension enable --py igv
+
+```
diff --git a/setup.py b/setup.py
@@ -1,26 +1,26 @@
-from distutils.core import setup
+import setuptools
 
-setup(name='igv',
-      packages=['igv'],
-      version='0.9',
-      description='Jupyter extension for embedding igv.js in a notebook',
-      license='MIT',
-      author='Jim Robinson',
-      #author_email='igv[email protected]',
-      url='https://github.com/igvteam/igv.js-jupyter',
-      #download_url='https://github.com/igvteam/igv.js-jupyter/archive/0.2.1.tar.gz',
-      keywords=['igv', 'visualization', 'ipython', 'jupyter'],
-      classifiers=[
-          'Development Status :: 4 - Beta',
-          'Intended Audience :: Science/Research',
-          'Intended Audience :: Developers',
-          'License :: OSI Approved :: MIT License',
-          'Programming Language :: Python',
-          'Framework :: IPython',
-      ],
-      install_requires=[
-          'jupyter',
-          'notebook>=4.2.0',
-      ],
-      package_data={'igv': ['static/extension.js', 'static/igvjs/*']},
-      )
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(name='igv',
+                 packages=['igv'],
+                 version='0.9.1',
+                 description='Jupyter extension for embedding the genome visualation igv.js in a notebook',
+                 long_description=long_description,
+                 long_description_content_type="text/markdown",
+                 license='MIT',
+                 author='Jim Robinson',
+                 url='https://github.com/igvteam/igv.js-jupyter',
+                 # download_url='https://github.com/igvteam/igv.js-jupyter/archive/0.2.1.tar.gz',
+                 keywords=['igv', 'bioinformatics', 'genomics', 'visualization', 'ipython', 'jupyter'],
+                 classifiers=[
+                     'Development Status :: 4 - Beta',
+                     'Intended Audience :: Science/Research',
+                     'Intended Audience :: Developers',
+                     'License :: OSI Approved :: MIT License',
+                     'Programming Language :: Python',
+                     'Framework :: IPython',
+                 ],
+                 package_data={'igv': ['static/extension.js', 'static/igvjs/*']},
+                 )