various changes to get rid of errors

.travis.yml

@@ -42,6 +42,7 @@ matrix:
       env: NAME="Doc"
            MAIN_CMD="cd package && python setup.py build_sphinx"
            BUILD_DOCS=true
+           SPHINX_VERSION=1.5.1
            BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
 

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -467,7 +467,7 @@ def __init__(self, universe, selection1='protein', selection2='all', selection1_
 
         Parameters
         ----------
-        universe : universe
+        universe : Universe
             Universe object
         selection1 : str (optional)
             Selection string for first selection ['protein']

package/MDAnalysis/core/topology.py

@@ -165,7 +165,7 @@ class TransTable(object):
 
     Attributes
     ----------
-    n_atoms, n_residues, n_segments : int
+    :ivar:`n_atoms`, n_residues, n_segments : int
         number of atoms, residues, segments in topology
     size
         tuple describing the shape of the TransTable
@@ -428,24 +428,26 @@ class Topology(object):
     to residues, residues to segments, and vice-versa, are handled internally
     by this object.
 
-    Parameters
-    ----------
-    n_atoms, n_residues, n_segments : int
-        number of atoms, residues, segments in topology; there must be at least
-        1 element of each level in the system
-    attrs : TopologyAttr objects
-        components of the topology to be included
-    atom_resindex : array
-        1-D array giving the resindex of each atom in the system
-    residue_segindex : array
-        1-D array giving the segindex of each residue in the system
-
     """
 
     def __init__(self, n_atoms=1, n_res=1, n_seg=1,
                  attrs=None,
                  atom_resindex=None,
                  residue_segindex=None):
+        """
+        Parameters
+        ----------
+        n_atoms, n_residues, n_segments : int
+            number of atoms, residues, segments in topology; there must be at least
+            1 element of each level in the system
+        attrs : TopologyAttr objects
+            components of the topology to be included
+        atom_resindex : array
+            1-D array giving the resindex of each atom in the system
+        residue_segindex : array
+            1-D array giving the segindex of each residue in the system
+
+        """
         self.tt = TransTable(n_atoms, n_res, n_seg,
                              atom_resindex=atom_resindex,
                              residue_segindex=residue_segindex)

package/MDAnalysis/core/universe.py

@@ -141,7 +141,7 @@ class Universe(object):
 
     Parameters
     ----------
-    topology : filename, Topology object or stream
+    topology : str, Topology object or stream
         A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to
         define the list of atoms. If the file includes bond information,
         partial charges, atom masses, ... then these data will be available to

package/MDAnalysis/lib/NeighborSearch.py

@@ -68,7 +68,7 @@ def search(self, atoms, radius, level='A'):
 
         Parameters
         ----------
-        atoms : AtomGroup or Atom
+        atoms : AtomGroup or :class:`Atom`
           list of atoms
         radius : float
           Radius for search in Angstrom.

package/MDAnalysis/lib/formats/libmdaxdr.pyx

@@ -502,7 +502,7 @@ cdef class TRRFile(_XDRFile):
 
         Parameters
         ----------
-        xyz : ndarray, shape=(n_atoms, 3)
+        xyz : ndarray, shape=(natoms, 3)
             cartesion coordinates
         box : ndarray, shape=(3, 3)
             Box vectors for this frame
@@ -685,7 +685,7 @@ cdef class XTCFile(_XDRFile):
 
         Parameters
         ----------
-        xyz : ndarray, shape=(n_atoms, 3)
+        xyz : ndarray, shape=(number, 3)
             cartesion coordinates
         box : ndarray, shape=(3, 3)
             Box vectors for this frame

package/MDAnalysis/topology/guessers.py

@@ -149,7 +149,7 @@ def guess_bonds(atoms, coords, **kwargs):
         atoms with altloc A and B maybe very close together and there should be
         no chemical bond between them. [0.1]
 
-    box : dimensions, optional
+    box : array_like, optional
         Bonds are found using a distance search, if unit cell information is
         given, periodic boundary conditions will be considered in the distance
         search. [``None``]
@@ -204,6 +204,8 @@ def guess_bonds(atoms, coords, **kwargs):
     lower_bound = kwargs.get('lower_bound', 0.1)
 
     box = kwargs.get('box', None)
+    if box:
+        box = np.asarray(box)
 
     # to speed up checking, calculate what the largest possible bond
     # atom that would warrant attention.

package/setup.cfg

@@ -5,7 +5,7 @@
 ## depend on whether the current version is a release or not.
 ## Uncomment the following two lines to get the _release_ behavior.
 #use_cython=False
-#keep_cythonized=True
+keep_cythonized=True
 [wheel]
 universal = 1