Move main.py into package and add vanity CLI

Closes callahantiff#56

README.rst

@@ -199,12 +199,12 @@ There are a few ways to run ``omop2obo``. An example workflow is provided below.
 
 |
 
-*COMMAND LINE* ➞ `main.py <https://github.com/callahantiff/OMOP2OBO/blob/master/main.py>`_
+*COMMAND LINE* ➞ after installing with pip, the `omop2obo` command is available directly in your shell.
 
 .. code:: bash
 
-  python main.py --help
-  Usage: main.py [OPTIONS]
+  omop2obo --help
+  Usage: omop2obo [OPTIONS]
 
   The OMOP2OBO package provides functionality to assist with mapping OMOP standard clinical terminology
   concepts to OBO terms. Successfully running this program requires several input parameters, which are
@@ -246,7 +246,7 @@ If you follow the instructions for how to format clinical data (`here <https://g
 
 .. code:: bash
 
- python main.py --clinical_domain condition --onts hp --onts mondo --clinical_data resources/clinical_data/omop2obo_conditions_june2020.csv
+ $ omop2obo --clinical_domain condition --onts hp --onts mondo --clinical_data resources/clinical_data/omop2obo_conditions_june2020.csv
 
 |
 

omop2obo/__main__.py

@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+
+"""Entrypoint module, in case you use `python -m omop2obo`.
+
+Why does this file exist, and why ``__main__``? For more info, read:
+
+- https://www.python.org/dev/peps/pep-0338/
+- https://docs.python.org/3/using/cmdline.html#cmdoption-m
+"""
+
+from .main import main
+
+if __name__ == '__main__':
+    main()

main.py → omop2obo/main.py

@@ -1,6 +1,17 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+"""Command line interface for :mod:`omop2obo`.
+
+Why does this file exist, and why not put this in ``__main__``? You might be tempted to import things from ``__main__``
+later, but that will cause problems--the code will get executed twice:
+
+- When you run ``python3 -m omop2obo`` python will execute``__main__.py`` as a script.
+  That means there won't be any ``omop2obo.__main__`` in ``sys.modules``.
+- When you import __main__ it will get executed again (as a module) because
+  there's no ``omop2obo.__main__`` in ``sys.modules``.
+
+.. seealso:: https://click.palletsprojects.com/en/7.x/setuptools/#setuptools-integration
+"""
 
 # import needed libraries
 import click

setup.py

@@ -80,4 +80,9 @@ def find_version(*file_paths):
         'scikit-learn==0.23.2',
         'tqdm==4.54.1'],
     extras_require=extras,
+    entry_points={
+        "console_scripts": [
+            'omop2obo = omop2obo.main:main',
+        ],
+    },
 )