Update documentation

Author: cthoyt

setup.py

@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 
+"""Setup.py for ComPath Utilities"""
+
 import codecs
 import os
 import re
@@ -40,7 +42,7 @@ def read(*parts):
 
 
 def find_meta(meta):
-    """Extract __*meta*__ from META_FILE"""
+    """Extract __*meta*__ from META_FILE."""
     meta_match = re.search(
         r'^__{meta}__ = ["\']([^"\']*)["\']'.format(meta=meta),
         META_FILE, re.M

tests/test_manager.py

@@ -23,45 +23,53 @@ def _base(self):
 
 
 class ManagerMissingPathway(ManagerMissingFunctions):
-    """Test ComPath manager for abstract class."""
+    """A bad implementation of a manager that is missing the pathway model."""
 
     def get_pathway_by_id(self, pathway_id):
-        pass
+        """Get a pathway by its database identifier."""
 
     def get_pathway_names_to_ids(self):
-        pass
+        """Get a dictionary from pathway names to their identifiers."""
 
     def populate(self, *args, **kwargs):
-        pass
+        """Populate the database."""
 
     def query_gene_set(self, gene_set):
-        pass
+        """Find pathways with genes in the given set."""
 
 
 class ManagerMissingProtein(ManagerMissingPathway):
+    """A bad implementation of a manager that is missing the protein model."""
     pathway_model = object()
 
 
 class ManagerOkay(ManagerMissingProtein):
+    """An example of a good implementation of a manager."""
     protein_model = object()
 
 
 class TestManagerFailures(unittest.TestCase):
-    """Tests bad implementations of the manager"""
+    """Tests bad implementations of the manager."""
 
     def test_abstract_methods(self):
+        """Test a TypeError is thrown when required functions aren't implemented."""
         with self.assertRaises(TypeError):
             ManagerMissingFunctions()
 
     def test_pathway_model_error(self):
+        """Test an error is thrown when the pathway model is not defined."""
         with self.assertRaises(CompathManagerPathwayModelError):
             ManagerMissingPathway()
 
     def test_protein_model_error(self):
+        """Tests an error is thrown when the protein model is not defined."""
         with self.assertRaises(CompathManagerProteinModelError):
             ManagerMissingProtein()
 
 
 class TestManager(TemporaryConnectionMethodMixin):
+    """Tests for good managers."""
+
     def test_instantiation(self):
+        """Test that a good implementation of the manager can be instantiated."""
         ManagerOkay(connection=self.connection)

tox.ini

@@ -58,7 +58,7 @@ deps =
     pep8-naming
     flake8-colors
 commands =
-    flake8 src/bio2bel/ tests/ setup.py
+    flake8 src/compath_utils/ tests/ setup.py
 
 
 [flake8]
@@ -86,7 +86,7 @@ deps =
     pyflakes
     pylint
 commands =
-    pylint src/bio2bel
+    pylint src/compath_utils
 
 [testenv:doc8]
 basepython = python3