Merge pull request #41 from lewisamarshall/development

Data structure upgrades.

.codeclimate.yml

@@ -19,6 +19,9 @@ ratings:
 # You can globally exclude files from being analyzed by any engine using the
 # exclude_paths key.
 
-#exclude_paths:
+exclude_paths:
+  - emigrate/tests.py
+  - examples/*
+  - benchmark.py
 #- spec/**/*
 #- vendor/**/*

.travis.yml

@@ -15,18 +15,15 @@ before_install:
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda/bin:$PATH
   - conda update --yes conda
-  - pip install coveralls simplejson
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
 
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy nose h5py coverage click matplotlib
-  - pip install ionize
-  - python setup.py install
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy nose h5py coverage click matplotlib pip
+  - pip install coveralls simplejson ionize
 
 script:
   - coverage run --source=emigrate setup.py test
-  - bash test.sh
 
 after_success:
   - coveralls

emigrate/Frame.py

@@ -16,8 +16,9 @@ class Frame(object):
 
     # Core Properties
     nodes = None
-    ions = []
+    ions = None
     concentrations = None
+    time = None
 
     # Solution Properties
     pH = None
@@ -137,12 +138,12 @@ def _resolve_current(self):
             self.current = self.area * self.current_density
 
     # I/O
-    def serialize(self, compact=False):
+    def serialize(self, compact=True):
         serial = {'__frame__': True}
         serial.update(self.__dict__)
 
         if compact:
-            sort_keys, indent, separators = False, None, (',', ':')
+            sort_keys, indent, separators = True, None, (',', ':')
         else:
             sort_keys, indent, separators = True, 4, (', ', ': ')
 
@@ -151,7 +152,7 @@ def serialize(self, compact=False):
 
     def _encode(self, obj):
         if isinstance(obj, ionize.Ion):
-            ion = obj.serialize()
+            ion = obj.serialize(nested=True)
             ion.update({'__ion__': True})
             return ion
         elif isinstance(obj, np.ndarray):
@@ -162,13 +163,12 @@ def _encode(self, obj):
         return json.JSONEncoder().default(obj)
 
 
-
 if __name__ == '__main__':
     my_solutions = [ionize.Solution(['hydrochloric acid', 'tris'], [.05, .1]),
                     ionize.Solution(['caproic acid', 'tris'], [.05, .1])
                     ]
     system = Frame({'lengths': [0.01]*2,
                     'solutions': my_solutions})
     print system.concentrations
-    print Frame(system.serialize())
-    print Frame(system.serialize()).__dict__
+    print system
+    print system.serialize(compact=False)