license; dot files; formatting

.coveragerc

@@ -0,0 +1,6 @@
+[report]
+exclude_lines =
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

.gitignore

@@ -0,0 +1,42 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+htmlcov
+
+# Translations
+*.mo
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx
+docs/_build
+
+# PyCharm
+.idea
+.idea/*

.travis.yml

@@ -0,0 +1,38 @@
+language: python
+
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "2.7"
+  - "3.3"
+  - "3.4"
+install:
+  - sudo apt-get update
+  # You may want to periodically update this, although the conda update
+  # conda line below will keep everything up-to-date.  We do this
+  # conditionally because it saves us some downloading if the version is
+  # the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget http://repo.continuum.io/miniconda/Miniconda-3.4.2-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget http://repo.continuum.io/miniconda/Miniconda3-3.4.2-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # Replace dep1 dep2 ... with your dependencies
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
+  - source activate test-environment
+  - conda install future coverage pytest
+  - pip install coveralls
+  - python setup.py install
+
+script:
+  - coverage run --rcfile=.coveragerc --source=mbuild setup.py test
+
+after_success:
+  - coveralls

foyer/atomtyper.py

@@ -6,12 +6,6 @@
 import matplotlib.pyplot as plt
 import networkx as nx
 
-
-
-
-
-
-
 # Map rule ids to the functions that check for them (see `find_atomtypes()`).
 RULE_NUMBER_TO_RULE = dict()
 # Organizes the rules (see `builrule_map()`).
@@ -466,23 +460,15 @@ def sanitize():
             if len(nx.descendants(graph, node)) == 0:
                 sinks.append(node)
         if len(sinks) > 1:
-            # Cases with multiple sinks that we can safely ignore.
-            # TODO: Provide more robust way to add approved exceptions.
-            if '141' in sinks and '142' in sinks and '145' in graph.nodes():
-                # This case occurs because 145 requires AT LEAST 2 carbon
-                # neighbors (3 total) and thus can match multiple patterns.
-                continue
-            draw_rule_graph('multiple_sinks', graph, element_type, pattern,
-                            sinks=sinks)
+            draw_rule_graph('multiple_sinks', graph, element_type, pattern, sinks)
 
         # Check for multiple sources. This is not necessarily incorrect.
         sources = []
         for node in graph.nodes():
             if len(nx.ancestors(graph, node)) == 0:
                 sources.append(node)
         if len(sources) > 1:
-            draw_rule_graph('multiple_sources', graph, element_type, pattern,
-                            sources=sources)
+            draw_rule_graph('multiple_sources', graph, element_type, pattern, sources)
 
 
 def find_all_supported_elements():
@@ -706,5 +692,4 @@ def draw_rule_graph(issue, graph, element, pattern, sinks=None, sources=None):
     plt.savefig(fig_name)
     plt.clf()
 
-    warn("{} connected to {} {}. See '{}'".format(
-        element, pattern, phrase, fig_name))
+    warn("{element} connected to {pattern} {phrase}. See '{fig_name}'".format(**locals()))

foyer/forcefield.py

@@ -2,7 +2,7 @@
 
 import simtk.unit as units
 
-from mbuild.orderedset import OrderedSet
+from foyer.orderedset import OrderedSet
 from foyer.atomtyper import find_atomtypes
 
 

foyer/orderedset.py

@@ -0,0 +1,54 @@
+import collections
+from copy import deepcopy
+
+
+class OrderedSet(collections.Set):
+    """ """
+    def __init__(self, iterable=()):
+        self.d = collections.OrderedDict.fromkeys(iterable)
+
+    def add(self, key):
+        self.d[key] = None
+
+    def discard(self, key):
+        del self.d[key]
+
+    def difference_update(self, *args, **kwargs):
+        intersection = set(self.d.keys()).intersection(args[0])
+        self.intersection_update(intersection)
+
+    def intersection_update(self, *args, **kwargs):
+        for part in args[0]:
+            del self.d[part]
+
+    def __len__(self):
+        return len(self.d)
+
+    def __contains__(self, element):
+        return element in self.d
+
+    def __iter__(self):
+        return self.d.__iter__()
+
+    def __le__(self, other):
+        if not isinstance(other, collections.Set):
+            return NotImplemented
+        if len(self) > len(other):
+            return False
+
+        for e1, e2 in zip(self, other):
+            if e1 != e2:
+                return False
+        return True
+
+    def __repr__(self):
+        class_name = self.__class__.__name__
+        if not self:
+            return '{0!s}()'.format(class_name)
+        return '{0!s}({1!r})'.format(class_name, list(self))
+
+    def __deepcopy__(self, memo):
+        result = OrderedSet()
+        for elt in self:
+            result.add(deepcopy(elt, memo))
+        return result

foyer/utils/io.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import os
 
 import mdtraj as md

requirements.txt

@@ -0,0 +1,3 @@
+matplotlib
+networkx
+simtk.units