Merge branch 'refactor-cli-to-match-other-python-repos' of github.com…

…:hammerlab/topiary into refactor-cli-to-match-other-python-repos

RELEASING.md

@@ -0,0 +1,8 @@
+# Releasing Topiary
+
+This document explains what do once your [Pull Request](https://www.atlassian.com/git/tutorials/making-a-pull-request/) has been reviewed and all final changes applied. Now you're ready merge your branch into master and release it to the world:
+
+1. Bump the [version](http://semver.org/) on __init__.py, as part of the PR you want to release.
+2. Merge your branch into master.
+3. After the Topiary unit tests complete successfully on Travis then the latest version
+of the code (with the version specified above) will be pushed to [PyPI](https://pypi.python.org/pypi) automatically. If you're curious about how automatic deployment is achieved, see our [Travis configuration](https://github.com/hammerlab/topiary/blob/master/.travis.yml#L58).

requirements.txt

@@ -1,8 +1,8 @@
 numpy>=1.7
 pandas>=0.13.1
-mhctools>=1.0.0
+mhctools>=1.3.0
 varcode>=0.3.17
 pylint>=1.4.4
 nose>=1.3.6
 gtfparse>=0.0.4
-mhcnames
+mhcnames

setup.py

@@ -66,7 +66,7 @@
         install_requires=[
             'numpy >=1.7, <2.0',
             'pandas >=0.13.1',
-            'mhctools >= 1.0.0',
+            'mhctools >= 1.3.0',
             'varcode >=0.3.17',
             'nose >=1.3.6',
             'gtfparse >=0.0.4',

topiary/__init__.py

@@ -19,6 +19,7 @@
     protein_subsequences_around_mutations,
 )
 
+
 __version__ = '2.0.0'
 
 __all__ = [