Refactor project such that it can be build and deployed via pip

.gitignore

-*.pyc
-docs/build/
+build/
+dist/
+*.egg-info/
+*.egg
+*.py[cod]
+__pycache__/
+*.so
+*~
+docs/_build/

LICENSE

 The MIT License (MIT)
 
-Copyright (c) 2017 SOaAS
+Copyright (c) 2017 Lukas Jelonek
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

 # DB XREF resolver and retriever tool
 
-A tool that resolves db_xrefs into URLs and that retrieves the data as json documents.
+A tool that resolves database cross references (dbxrefs). It can return a list of
+locations where the cross reference points to in different formats, like HTML,
+XML, flat file or json. It can also retrieve the data for some of the supported
+databases and convert it into json.
 
-# Getting started (Setup)
+The intended audience for this tool are bioinformatician that need to collect
+data for dbxrefs and postprocess it. By returning everything in json format the
+need for normalization and special parsing of the data is reduced.
+
+# Getting started for development (Setup)
 
 Prerequisites:
 
@@ -11,10 +18,24 @@ Prerequisites:
 
 Supported bioinformatic databases:
 
-* None yet
+* Ontologies
+  * Gene Ontology
 
 Checkout the repository:
 
 ~~~~
 git clone git@git.computational.bio.uni-giessen.de:SOaAS/dbxref.git
 ~~~~
+
+Setup a virtualenv for development and install it in editable mode:
+
+~~~~
+virtualenv --python=python3 venv; source venv/bin/activate;
+pip install -e .
+~~~~
+
+Use the application:
+
+~~~~
+dbxref resolve GO:0097281
+~~~~

bin/dbxref

-#!/usr/bin/env python3
-import os
-import sys
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
-
-from dbxref.main import main
-main()

dbxref/config.py

-def get_install_location():
-    """Finds the location directory of the tool"""
-    import os
-    script_path = os.path.realpath(__file__)
-    script_dir = os.path.dirname(script_path)
-    install_dir = os.path.dirname(script_dir)
-    return install_dir
+def get_providers_path():
+    import pkg_resources
+    return pkg_resources.resource_filename('dbxref', 'providers.yaml')
 
 def load_providers():
     import yaml
     data = []
-    with open(get_install_location() + '/providers.yaml') as data_file:
+    with open(get_providers_path()) as data_file:
         data = yaml.load(data_file)
     return index_providers(data)
 

setup.py

+from setuptools import setup, find_packages
+from codecs import open
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the README file
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
+setup(
+    name='dbxref',
+    version='0.1.0',
+    description='A library for resolving database cross references',
+    long_description=long_description, 
+    url='https://git.computational.bio.uni-giessen.de/SOaAS/dbxref',
+    author='Lukas Jelonek',
+    author_email='Lukas.Jelonek@computational.bio.uni-giessen.de',
+    keywords='dbxref',
+    packages=find_packages(exclude=['contrib', 'docs', 'tests']),
+    package_data={'dbxref':['*.yaml']},
+    install_requires=[
+      'requests',
+      'cachecontrol',
+      'pyyaml',
+      'lockfile'
+    ],
+    entry_points={ 
+        'console_scripts': [
+          'dbxref=dbxref.main:main',
+        ],
+    },
+)