Merge pull request #7 from chrisiacovella/docs

Docs

docs/getting_started.rst

@@ -119,6 +119,7 @@ Usage
 Basic usage
 ------------
 To load a HOOMD-blue XML file or GSD file, we need only pass the file path to the constructor.
+
 .. code:: ipython3
 
     import hoomdxml_reader as hxml

docs/requirements.yaml

@@ -9,7 +9,7 @@ dependencies:
   - networkx
   - numpydoc
   - sphinx_rtd_theme
-
+  - gsd
 
     # Pip-only installs
   #- pip:

hoomdxml_reader/hoomdxml_reader.py

@@ -180,7 +180,7 @@ def load(self, file=None, frame=0, identify_molecules=True, ignore_zero_bond_ord
             if molecule_dict is not None:
                 self.set_molecule_name_by_dictionary(molecule_dict)
 
-            
+    """
     def convert_mdtraj(self, mdtraj=None, frame=0, identify_molecules=True, ignore_zero_bond_order=False):
         if mdtraj is None:
             raise Exception("mdtraj traj not defined")
@@ -207,7 +207,7 @@ def convert_mdtraj(self, mdtraj=None, frame=0, identify_molecules=True, ignore_z
             self._calc_bond_order()
             if self._identify_molecules == True:
                 self._infer_molecules()
-
+    """
     # generic function to parse the topology entries,
     # takes the element as an argument and  number of entries per line
     def _parse_topology(self, element, length):

hoomdxml_reader/tests/test_hoomdxml_reader.py

@@ -59,6 +59,21 @@ def test_loader_gsd():
     assert len(system.unique_molecules) == 1
     assert 'AABB' in system.unique_molecules
 
+    system._clear()
+    assert len(system.box) == 0
+    assert system.n_particles == 0
+    assert len(system.xyz) == 0
+    assert len(system.masses) == 0
+    assert len(system.charges) == 0
+    assert len(system.bonds) == 0
+    assert len(system.angles) == 0
+    assert len(system.dihedrals) == 0
+    assert len(system.impropers) == 0
+    assert len(system.bond_order) == 0
+    assert len(system.molecules) == 0
+    assert len(system.unique_molecules) == 0
+    assert system._filename == None
+
 def test_loader_xml_basic():
     cwd = os.getcwd()
     system = hxml.System(cwd + "/hoomdxml_reader/tests/example.hoomdxml")