Merge pull request #10 from dwhswenson/0.1.1

v0.1.1

.codeclimate.yml

@@ -0,0 +1,25 @@
+engines:
+    radon:
+        enabled: true
+        exclude_paths:
+            - "*/tests/"
+        config:
+            threshold: "C"
+
+    fixme:
+        enabled: true
+        issue_override:
+            severity: info
+        exclude_paths:
+            - "**pdb"
+
+    duplication:
+        enabled: true
+        config:
+            languages:
+                python:
+                    mass_threshold: 35
+
+ratings:
+    paths:
+        - "**py"

.travis.yml

@@ -1,5 +1,10 @@
 language: python
 
+branches:
+    only:
+        - master
+        - stable
+
 python:
     - "2.7"
     - "3.4"
@@ -8,8 +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
@@ -25,8 +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

ci/conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: contact_map
-  version: "0.1.0"
+  version: "0.1.1"
 
 source:
   path: ../../

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_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():
@@ -199,24 +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]
-        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)
-        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()
@@ -256,14 +250,14 @@ def contact_map(self, trajectory, frame_number, residue_query_atom_idxs,
                 contact_neighbors = contact_neighbors & self._haystack
                 # frozenset is unique key independent of order
                 # local_pairs = set(frozenset((atom_idx, neighb))
-                                  # for neighb in contact_neighbors)
+                #                   for neighb in contact_neighbors)
                 local_pairs = set(map(
                     frozenset,
                     itertools.product([atom_idx], contact_neighbors)
                 ))
                 contact_pairs |= local_pairs
                 # contact_pairs |= set(frozenset((atom_idx, neighb))
-                                     # for neighb in contact_neighbors)
+                #                      for neighb in contact_neighbors)
                 local_residue_partners = set(self._atom_idx_to_residue_idx[a]
                                              for a in contact_neighbors)
                 local_res_pairs = set(map(
@@ -274,8 +268,8 @@ def contact_map(self, trajectory, frame_number, residue_query_atom_idxs,
 
         atom_contacts = collections.Counter(contact_pairs)
         # residue_pairs = set(
-            # frozenset(self._atom_idx_to_residue_idx[aa] for aa in pair)
-            # for pair in contact_pairs
+        #     frozenset(self._atom_idx_to_residue_idx[aa] for aa in pair)
+        #     for pair in contact_pairs
         # )
         residue_contacts = collections.Counter(residue_pairs)
         return (atom_contacts, residue_contacts)
@@ -359,9 +353,7 @@ 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 +421,7 @@ 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/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

@@ -1,15 +1,20 @@
 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=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 *
 
 # 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 +44,10 @@
 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 +257,7 @@ 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 +285,7 @@ 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 +374,32 @@ 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

@@ -3,15 +3,15 @@
 """
 #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
 import subprocess
 
 ##########################
-VERSION = "0.1.0"
-ISRELEASED = False
+VERSION = "0.1.1"
+ISRELEASED = True
 __version__ = VERSION
 PACKAGE_VERSION = VERSION
 REQUIREMENTS=['future', 'numpy', 'mdtraj', 'scipy', 'pandas']