Merge pull request #8 from dwhswenson/codacy

More code quality improvements

.codeclimate.yml

@@ -3,6 +3,8 @@ engines:
         enabled: true
         exclude_paths:
             - "*/tests/"
+        config:
+            threshold: "C"
 
     fixme:
         enabled: true
@@ -11,6 +13,9 @@ engines:
 
     duplication:
         enabled: true
+        languages:
+            python:
+                mass_threshold: 35
 
 ratings:
     paths:

.travis.yml

@@ -13,8 +13,11 @@ python:
     #- "3.7-dev"  # need to do custom requirements install for this
 
 env:
-    - MDTRAJ="release"
-    - MDTRAJ="dev"
+    global:
+        - CODECLIMATE=""  # add this later
+    matrix:
+        - MDTRAJ="release"
+        - MDTRAJ="dev"
 
 matrix:
     exclude:  # don't run MDTRAJ dev for everything
@@ -30,7 +33,8 @@ install:
     - pip list
 
 script:
-    - py.test -vv --cov=contact_map
+    - py.test -vv --cov=contact_map --cov-report xml:cov.xml
 
 after_success:
     - coveralls
+    - python-codacy-coverage -r cov.xml

README.md

@@ -1,6 +1,9 @@
 [![Linux Build Status](https://travis-ci.org/dwhswenson/contact_map.svg?branch=master)](https://travis-ci.org/dwhswenson/contact_map)
 [![Windows Build status](https://ci.appveyor.com/api/projects/status/em3fo96sjrg2vmcc/branch/master?svg=true)](https://ci.appveyor.com/project/dwhswenson/contact-map/branch/master)
 [![Coverage Status](https://coveralls.io/repos/github/dwhswenson/contact_map/badge.svg?branch=master)](https://coveralls.io/github/dwhswenson/contact_map?branch=master)
+[![codebeat badge](https://codebeat.co/badges/c7fb604a-35a8-4ccf-afea-18d6bd494726)](https://codebeat.co/projects/github-com-dwhswenson-contact_map-master)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com&utm_medium=referral&utm_content=dwhswenson/contact_map&utm_campaign=Badge_Grade)
+[![Code Climate](https://codeclimate.com/github/dwhswenson/contact_map/badges/gpa.svg)](https://codeclimate.com/github/dwhswenson/contact_map)
 
 # Contact Maps
 

bandit.yml

@@ -0,0 +1,2 @@
+exclude_dirs: 
+     - /tests

contact_map/contact_map.py

@@ -190,7 +190,7 @@ def residue_ignore_atom_idxs(self):
         return result
 
     def most_common_atoms_for_residue(self, residue):
-        (residue, residue_idx) = _residue_and_index(residue, self.topology)
+        residue = _residue_and_index(residue, self.topology)[0]
         residue_atoms = set(atom.index for atom in residue.atoms)
         results = []
         for contact in self.atom_contacts.most_common_idx():
@@ -203,16 +203,14 @@ def most_common_atoms_for_residue(self, residue):
         return results
 
     def most_common_atoms_for_contact(self, contact_pair):
-        contact_pair = frozenset(contact_pair)
-        res_A = list(contact_pair)[0]
-        res_B = list(contact_pair)[1]
-        (res_A, res_A_idx) = _residue_and_index(res_A, self.topology)
-        (res_B, res_B_idx) = _residue_and_index(res_B, self.topology)
-        atom_idxs_A = set(atom.index for atom in res_A.atoms)
-        atom_idxs_B = set(atom.index for atom in res_B.atoms)
+        contact_pair = list(contact_pair)
+        res_1 = _residue_and_index(contact_pair[0], self.topology)[0]
+        res_2 = _residue_and_index(contact_pair[1], self.topology)[0]
+        atom_idxs_1 = set(atom.index for atom in res_1.atoms)
+        atom_idxs_2 = set(atom.index for atom in res_2.atoms)
         all_atom_pairs = [
             frozenset(pair)
-            for pair in itertools.product(atom_idxs_A, atom_idxs_B)
+            for pair in itertools.product(atom_idxs_1, atom_idxs_2)
         ]
         result = [([self.topology.atom(idx) for idx in contact[0]], contact[1])
                   for contact in self.atom_contacts.most_common_idx()

contact_map/min_dist.py

@@ -1,3 +1,5 @@
+import collections
+import itertools
 import mdtraj as md
 
 class NearestAtoms(object):

contact_map/tests/test_contact_map.py

@@ -5,8 +5,9 @@
 from numpy.testing import assert_array_equal
 import mdtraj as md
 
-# pylint: disable=W0401, R0201
-# wildcard imports, method could be function
+# pylint: disable=wildcard-import, missing-docstring, protected-access
+# pylint: disable=attribute-defined-outside-init, invalid-name, no-self-use
+# pylint: disable=wrong-import-order, unused-wildcard-import
 
 from .utils import *