Merge 47daf03 into 6f8b1ae

.bandit

@@ -0,0 +1,2 @@
+[bandit]
+exclude: */tests

.codeclimate.yml

@@ -0,0 +1,17 @@
+engines:
+    radon:
+        enabled: true
+        exclude_paths:
+            - "*/tests/"
+
+    fixme:
+        enabled: true
+        exclude_paths:
+            - "**pdb"
+
+    duplication:
+        enabled: true
+
+ratings:
+    paths:
+        - "**py"

.travis.yml

@@ -1,5 +1,10 @@
 language: python
 
+branches:
+    only:
+        - master
+        - stable
+
 python:
     - "2.7"
     - "3.4"
@@ -29,4 +34,3 @@ script:
 
 after_success:
     - coveralls
-

ci/pip-install/install.sh

@@ -1,3 +1,5 @@
+#!/usr/bin/env bash
+
 pip install --upgrade pip
 pip install cython  # may be required for numpy override?
 pip install --upgrade --force-reinstall numpy  # override Travis numpy

ci/pip-install/testing_requirements.txt

@@ -1,3 +1,4 @@
 pytest
 pytest-cov
 python-coveralls
+codacy-coverage

contact_map/contact_map.py

@@ -40,6 +40,15 @@ def residue_neighborhood(residue, n=1):
     # good, and it only gets run once per residue
     return [idx for idx in neighborhood if idx in chain]
 
+def _residue_and_index(residue, topology):
+    res = residue
+    try:
+        res_idx = res.index
+    except AttributeError:
+        res_idx = residue
+        res = topology.residue(res_idx)
+    return (res, res_idx)
+
 
 class ContactCount(object):
     def __init__(self, counter, object_f, n_x, n_y):
@@ -181,12 +190,7 @@ def residue_ignore_atom_idxs(self):
         return result
 
     def most_common_atoms_for_residue(self, residue):
-        try:
-            residue_idx = residue.index
-        except AttributeError:
-            residue_idx = residue
-            residue = self.topology.residue(residue_idx)
-
+        (residue, residue_idx) = _residue_and_index(residue, self.topology)
         residue_atoms = set(atom.index for atom in residue.atoms)
         results = []
         for contact in self.atom_contacts.most_common_idx():
@@ -202,16 +206,8 @@ 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]
-        try:
-            res_A_idx = res_A.index
-        except AttributeError:
-            res_A_idx = res_A
-            res_A = self.topology.residue(res_A_idx)
-        try:
-            res_B_idx = res_B.index
-        except AttributeError:
-            res_B_idx = res_B
-            res_B = self.topology.residue(res_B_idx)
+        (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)
         all_atom_pairs = [
@@ -359,9 +355,7 @@ def _build_contact_map(self):
         # TODO: this whole thing should be cleaned up and should replace
         # MDTraj's really slow old computer_contacts by using MDTraj's new
         # neighborlists (unless the MDTraj people do that first).
-        topology = self.topology
         trajectory = self.trajectory
-        cutoff = self.cutoff
         self._atom_contacts_count = collections.Counter([])
         self._residue_contacts_count = collections.Counter([])
 
@@ -429,7 +423,7 @@ def __init__(self, positive, negative):
     def __sub__(self, other):
         raise NotImplementedError
 
-    def contact_map(self, *args, **kwargs):
+    def contact_map(self, *args, **kwargs):  #pylint: disable=W0221
         raise NotImplementedError
 
     @property

contact_map/tests/test_contact_map.py

@@ -1,15 +1,19 @@
 import os
 import collections
-import itertools
 import pytest
 import numpy as np
 from numpy.testing import assert_array_equal
 import mdtraj as md
+
+# pylint: disable=W0401, R0201
+# wildcard imports, method could be function
+
 from .utils import *
 
 # stuff to be testing in this file
 from contact_map.contact_map import *
 
+
 traj = md.load(test_file("trajectory.pdb"))
 
 traj_atom_contact_count = {
@@ -39,6 +43,10 @@
 def counter_of_inner_list(ll):
     return collections.Counter([frozenset(i) for i in ll])
 
+def check_most_common_order(most_common):
+    for i in range(len(most_common) - 1):
+        assert most_common[i][1] >= most_common[i+1][1]
+
 def test_residue_neighborhood():
     top = traj.topology
     residues = list(top.residues)
@@ -248,9 +256,7 @@ def test_most_common_atoms_for_residue(self, select_by):
             raise RuntimeError("This should not happen")
         # call both by residue and residue number
         most_common_2 = self.map.most_common_atoms_for_residue(res_2)
-        # check order is correct
-        for i in range(len(most_common_2) - 1):
-            assert most_common_2[i][1] >= most_common_2[i+1][1]
+        check_most_common_order(most_common_2)
 
         most_common_numbers_2 = {frozenset([k[0].index, k[1].index]): v
                                  for (k, v) in most_common_2}
@@ -278,11 +284,7 @@ def test_most_common_atoms_for_contact(self, select_by):
             raise RuntimeError("This should not happen")
 
         most_common_2_3 = self.map.most_common_atoms_for_contact(pair)
-
-        # check order is correct
-        for i in range(len(most_common_2_3) - 1):
-            assert most_common_2_3[i][1] >= most_common_2_3[i+1][1]
-
+        check_most_common_order(most_common_2_3)
         most_common_2_3_frozenset = [(frozenset(ll[0]), ll[1])
                                      for ll in most_common_2_3]
 
@@ -371,42 +373,32 @@ def test_most_common(self, obj_type):
         most_common = contacts.most_common()
         cleaned = [(frozenset(ll[0]), ll[1]) for ll in most_common]
 
-        # check order
-        for i in range(len(most_common) - 1):
-            assert most_common[i][1] >= most_common[i+1][1]
-
-        # check contents
+        check_most_common_order(most_common)
         assert set(cleaned) == set(expected)
 
     @pytest.mark.parametrize("obj_type", ['atom', 'res'])
     def test_most_common_with_object(self, obj_type):
         top = self.topology
         if obj_type == 'atom':
-            source_expected = traj_atom_contact_count
             contacts = self.map.atom_contacts
             obj = top.atom(4)
             expected = [(frozenset([obj, top.atom(6)]), 1.0),
                         (frozenset([obj, top.atom(1)]), 0.8),
                         (frozenset([obj, top.atom(7)]), 0.4),
                         (frozenset([obj, top.atom(8)]), 0.2)]
         elif obj_type == 'res':
-            source_expected = traj_residue_contact_count
             contacts = self.map.residue_contacts
             obj = self.topology.residue(2)
             expected = [(frozenset([obj, top.residue(0)]), 1.0),
                         (frozenset([obj, top.residue(3)]), 1.0),
                         (frozenset([obj, top.residue(4)]), 0.2)]
         else:
             raise RuntimeError("This shouldn't happen")
-    
+
         most_common = contacts.most_common(obj)
         cleaned = [(frozenset(ll[0]), ll[1]) for ll in most_common]
 
-        # check order
-        for i in range(len(most_common) - 1):
-            assert most_common[i][1] >= most_common[i+1][1]
-
-        # check contents
+        check_most_common_order(most_common)
         assert set(cleaned) == set(expected)
 
     @pytest.mark.parametrize("obj_type", ['atom', 'res'])

setup.py

@@ -3,7 +3,7 @@
 """
 #from distutils.sysconfig import get_config_var
 # from distutils.core import setup, Extension
-from setuptools import setup, Extension
+from setuptools import setup
 # import numpy
 # import glob
 import os