Cleanup

.travis.yml

@@ -4,6 +4,8 @@ language: python
 dist: trusty
 
 matrix:
+  allow_failures:
+    - env: OPTIONAL=true
   include:
     # Extra includes for OSX since python language is not available by default on OSX
     - os: osx
@@ -12,13 +14,20 @@ matrix:
     - os: osx
       language: generic
       env: PYTHON_VER=3.6
+    - os: osx
+      language: generic
+      env: PYTHON_VER=3.7
 
     - os: linux
       python: 3.5
       env: PYTHON_VER=3.5
     - os: linux
       python: 3.6
       env: PYTHON_VER=3.6
+    - os: linux
+      python: 3.7
+      env: PYTHON_VER=3.7
+      env: OPTIONAL=true
 
 before_install:
     # Additional info about the build

appveyor.yml

@@ -1,14 +1,18 @@
 environment:
 
   matrix:
-    - PYTHON: "C:\\Miniconda35-x64"
+    - PYTHON: "C:\\Miniconda36-x64"
       PYTHON_VERSION: "3.5"
       PYTHON_ARCH: "64"
 
     - PYTHON: "C:\\Miniconda36-x64"
       PYTHON_VERSION: "3.6"
       PYTHON_ARCH: "64"
-
+
+    - PYTHON: "C:\\Miniconda36-x64"
+      PYTHON_VERSION: "3.7"
+      PYTHON_ARCH: "64"
+
 
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"

pairing/__init__.py

@@ -8,7 +8,8 @@
 from __future__ import absolute_import
 
 # Add imports here
-from .pairing import *
+from pairing.pairing import *
+from pairing.utils import *
 
 # Handle versioneer
 from ._version import get_versions

pairing/pairing.py

@@ -1,11 +1,19 @@
 from copy import deepcopy
-import itertools
 
 import numpy as np
 import mdtraj as md
 from pairing.utils.misc import make_comtrj
 
 
+__all__ = [
+    'calc_direct',
+    'calc_indirect',
+    'calc_reduc',
+    'check_pairs',
+    'analyze_clusters'
+]
+
+
 def calc_indirect(direct_array):
     """
     Calculate indirect matrices for all frames of trajectory
@@ -16,6 +24,7 @@ def calc_indirect(direct_array):
         indirect_results.append(np.asarray(indirect))
     return(indirect_results)
 
+
 def calc_reduc(indirect_array):
     """
     Reduce indirect matrices for all frames of trajectory
@@ -29,15 +38,15 @@ def calc_reduc(indirect_array):
 
 def check_pairs(trj, cutoff, first_direct):
     """
-    Checks pairs at various frames against direct correlation matrix 
+    Checks pairs at various frames against direct correlation matrix
     from frame zero
     """
     trj = make_comtrj(trj)
     direct_list = []
     for frame in trj:
-       c = deepcopy(first_direct)
-       matrix = _check_direct(c, frame, cutoff)
-       direct_list.append(matrix)
+        c = deepcopy(first_direct)
+        matrix = _check_direct(c, frame, cutoff)
+        direct_list.append(matrix)
 
     return direct_list
 
@@ -51,7 +60,7 @@ def calc_direct(trj, cutoff=1.0):
     for frame in com_trj:
         direct = _generate_direct_correlation(frame, cutoff)
         direct_list.append(direct)
-    
+
     return direct_list
 
 
@@ -94,8 +103,7 @@ def _check_direct(direct_corr, frame, cutoff):
     for row in range(len(direct_corr[0])):
         for col in range(len(direct_corr[0])):
             if direct_corr[row][col] == 1:
-                dist = md.compute_distances(frame,
-                        atom_pairs=[(row, col)])
+                dist = md.compute_distances(frame, atom_pairs=[(row, col)])
                 if dist < cutoff:
                     continue
                 else:
@@ -124,9 +132,9 @@ def _generate_indirect_connectivity(direct_corr):
             continue
         else:
             intersect = np.maximum.reduce(
-                    [c[:,ele] for ele in ones])
+                    [c[:, ele] for ele in ones])
             for ele in ones:
-                c[:,ele] = intersect
+                c[:, ele] = intersect
     indirect = c
 
     return indirect

pairing/tests/test_pairing.py

@@ -1,4 +1,3 @@
-import pytest
 import numpy as np
 import mdtraj as md