diff --git a/.travis.yml b/.travis.yml
index 123e5ae8e32..ad445469e60 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,7 +22,7 @@ env:
     - BUILD_DOCS=false
     - PYTHON_VERSION=2.7
     - MAIN_CMD="python ./testsuite/MDAnalysisTests/mda_nosetests --processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50"
-    - MAIN_CMD_OPTIONS=""
+    - SETUP_CMD=""
     - COVERALLS=false
     - BUILD_CMD="pip install -v package/ && pip install testsuite/"
     - CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer"
@@ -33,14 +33,15 @@ env:
     - CONDA_CHANNEL_PRIORITY=True
     - NUMPY_VERSION=stable
   matrix:
-    - NAME='minimal' PYTHON_VERSION=2.7 MAIN_CMD_OPTIONS='--with-memleak'
+    - NAME='minimal' PYTHON_VERSION=2.7 SETUP_CMD='--with-memleak'
 
 matrix:
   fast_finish: true
   include:
     - os: linux
       env: NAME="Doc"
-           MAIN_CMD="cd package && python setup.py build_sphinx"
+           MAIN_CMD="cd package && python setup.py"
+           SETUP_CMD="build_sphinx"
            BUILD_DOCS=true
            BUILD_CMD="cd ${TRAVIS_BUILD_DIR}/package && python setup.py build_ext --inplace"
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
@@ -54,7 +55,7 @@ matrix:
 
     - os: linux
       env: NAME='full'
-           MAIN_CMD_OPTIONS='--with-coverage --cover-package MDAnalysis'
+           SETUP_CMD='--with-coverage --cover-package MDAnalysis'
            CONDA_DEPENDENCIES=${CONDA_ALL_DEPENDENCIES}
            COVERALLS='true'
 
@@ -83,14 +84,13 @@ install:
         HOLE_BINDIR="${HOME}/${MDA_OPTPACKAGES}/hole2/exe"; \
         export PATH=${PATH}:${HOLE_BINDIR}; \
     fi
-  - if [[ $BUILD_DOCS == "true" ]] ; then conda install sphinx=1.5.1; fi
   - eval $BUILD_CMD
 
 script:
   - cd ${TRAVIS_BUILD_DIR}
   - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then ulimit -S -n 2048; fi
-  - echo $MAIN_CMD $MAIN_CMD_OPTIONS
-  - eval $MAIN_CMD $MAIN_CMD_OPTIONS
+  - echo $MAIN_CMD $SETUP_CMD
+  - eval $MAIN_CMD $SETUP_CMD
 
 after_success:
   - if [[ $COVERALLS == 'true' ]]; then coveralls; fi
diff --git a/package/.pylintrc b/package/.pylintrc
index 3463e32a3dc..ab966147016 100644
--- a/package/.pylintrc
+++ b/package/.pylintrc
@@ -118,7 +118,6 @@ enable=abstract-class-instantiated,
        invalid-slots,
        invalid-slots-object,
        invalid-star-assignment-target,
-       invalid-unary-operand-type,
        logging-format-truncated,
        logging-not-lazy,
        logging-too-few-args,
@@ -156,7 +155,6 @@ enable=abstract-class-instantiated,
        old-octal-literal,
        old-raise-syntax,
        parameter-unpacking,
-       raising-bad-type,
        raising-non-exception,
        raising-string,
        raw_input-builtin,
@@ -270,6 +268,8 @@ enable=abstract-class-instantiated,
        # used-before-assignment,
        # wildcard-import,
        # wrong-import-order,
+       # invalid-unary-operand-type,
+       # raising-bad-type,
 
 
 [REPORTS]
diff --git a/package/CHANGELOG b/package/CHANGELOG
index 0090ff835c7..f1f48bab57d 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -24,8 +24,12 @@ Enhancements
   * Residues with the same residue ids are not merged by default now 
     (apply to PDB, GRO) (Issue #1306)
 
+Fixes
+  * Various documentation sphinx errors (PR #1312)
+
 Changes
   * Enable various pylint warnings to increase python 3 compatibility
+  * Change Mathjax cdn (Issue #1313)
 
 04/10/17 kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle
          euhruska, orbeckst, rbrtdlg, jbarnoud, wouterboomsma, shanmbic,
diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
index 7918c77ff0a..d4d24f78fbf 100644
--- a/package/MDAnalysis/analysis/align.py
+++ b/package/MDAnalysis/analysis/align.py
@@ -552,20 +552,21 @@ def __init__(self, mobile, reference, select='all', filename=None,
 
         Notes
         -----
-        If set to `verbose=False`, it is recommended to wrap the statement in a
-        ``try ...  finally`` to guarantee restoring of the log level in the
-        case of an exception.
+        - If set to ``verbose=False``, it is recommended to wrap the statement in a
+          ``try ...  finally`` to guarantee restoring of the log level in the
+          case of an exception.
+        - The ``in_memory`` option changes the `mobile` universe to an
+          in-memory representation (see :mod:`MDAnalysis.coordinates.memory`)
+          for the remainder of the Python session. If ``mobile.trajectory`` is
+          already a :class:`MemoryReader` then it is *always* treated as if
+          ``in_memory`` had been set to ``True``.
 
-        The `in_memory` option changes the `mobile` universe to an in-memory
-        representation (see :mod:`MDAnalysis.coordinates.memory`) for the
-        remainder of the Python session. If ``mobile.trajectory```is already a
-        :class:`MemoryReader` then it is *always* treated as if `in_memory` had
-        been set to ``True``.
 
         .. versionchanged:: 0.16.0
-           new general 'weights' kwarg replace mass_weights, deprecated 'mass_weights'
+           new general ``weights`` kwarg replace ``mass_weights``
+
         .. deprecated:: 0.16.0
-           Instead of ``mass_weighted=True`` use new ``weights='mass'`
+           Instead of ``mass_weighted=True`` use new ``weights='mass'``
 
         """
         select = rms.process_selection(select)
diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py
index 2325573614e..64f4eb93206 100644
--- a/package/MDAnalysis/analysis/contacts.py
+++ b/package/MDAnalysis/analysis/contacts.py
@@ -536,7 +536,6 @@ def q1q2(u, selection='all', radius=4.5,
 # until then it remains because we don't have the functionality
 # elsewhere.
 
-@deprecate(new_name="Contacts", message="This class will be removed in 0.17")
 class ContactAnalysis(object):
     """Perform a native contact analysis ("q1-q2").
 
@@ -564,48 +563,47 @@ class ContactAnalysis(object):
     accessible as the attribute
     :attr:`ContactAnalysis.timeseries`.
 
+    Parameters
+    ----------
+    topology : filename as str
+        topology file
+    trajectory : filename as str
+        trajectory
+    ref1 : filename or ``None``, optional
+        structure of the reference conformation 1 (pdb); if ``None`` the
+        *first* frame of the trajectory is chosen
+    ref2 : filename or ``None``, optional
+        structure of the reference conformation 2 (pdb); if ``None`` the
+        *last* frame of the trajectory is chosen
+    radius : float, optional, default 8 A
+        contacts are deemed any Ca within radius
+    targetdir : path, optional, default ``.``
+        output files are saved in this directory
+    infix : string, optional
+        additional tag string that is inserted into the output filename of
+        the data file
+     selection : string, optional, default ``"name CA"``
+        MDAnalysis selection string that selects the particles of
+        interest; the default is to only select the C-alpha atoms
+        in `ref1` and `ref2`
+
+        .. Note:: If `selection` produces more than one atom per
+                  residue then you will get multiple contacts per
+                  residue unless you also set `centroids` = ``True``
+     centroids : bool
+        If set to ``True``, use the centroids for the selected atoms on a
+        per-residue basis to compute contacts. This allows, for instance
+        defining the sidechains as `selection` and then computing distances
+        between sidechain centroids.
+
 
     .. deprecated:: 0.15.0
     """
 
+    @deprecate(new_name="Contacts", message="This class will be removed in 0.17")
     def __init__(self, topology, trajectory, ref1=None, ref2=None, radius=8.0,
                  targetdir=os.path.curdir, infix="", force=False,
                  selection="name CA", centroids=False):
-        """
-        Parameters
-        ----------
-        topology : filename as str
-            topology file
-        trajectory : filename as str
-            trajectory
-        ref1 : filename or ``None``, optional
-            structure of the reference conformation 1 (pdb); if ``None`` the
-            *first* frame of the trajectory is chosen
-        ref2 : filename or ``None``, optional
-            structure of the reference conformation 2 (pdb); if ``None`` the
-            *last* frame of the trajectory is chosen
-        radius : float, optional, default 8 A
-            contacts are deemed any Ca within radius
-        targetdir : path, optional, default ``.``
-            output files are saved in this directory
-        infix : string, optional
-            additional tag string that is inserted into the output filename of
-            the data file
-         selection : string, optional, default ``"name CA"``
-            MDAnalysis selection string that selects the particles of
-            interest; the default is to only select the C-alpha atoms
-            in `ref1` and `ref2`
-
-            .. Note:: If `selection` produces more than one atom per
-                      residue then you will get multiple contacts per
-                      residue unless you also set `centroids` = ``True``
-         centroids : bool
-            If set to ``True``, use the centroids for the selected atoms on a
-            per-residue basis to compute contacts. This allows, for instance
-            defining the sidechains as `selection` and then computing distances
-            between sidechain centroids.
-
-        """
 
         self.topology = topology
         self.trajectory = trajectory
@@ -834,7 +832,6 @@ def plot(self, **kwargs):
         ylabel(r"$q_2$")
 
 
-@deprecate(new_name="Contacts", message="This class will be removed in 0.17")
 class ContactAnalysis1(object):
     """Perform a very flexible native contact analysis with respect to a single
     reference.
@@ -900,6 +897,7 @@ class ContactAnalysis1(object):
     .. deprecated:: 0.15.0
     """
 
+    @deprecate(new_name="Contacts", message="This class will be removed in 0.17")
     def __init__(self, *args, **kwargs):
         """Calculate native contacts within a group or between two groups.
 
diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
index d305d51bb69..b05a5078bbe 100644
--- a/package/MDAnalysis/analysis/diffusionmap.py
+++ b/package/MDAnalysis/analysis/diffusionmap.py
@@ -115,6 +115,7 @@
 map method. The :class:`DistanceMatrix` exists in
 :mod:`~MDAnalysis.analysis.diffusionmap` and can be passed
 as an initialization argument for :class:`DiffusionMap`.
+
     >>> import MDAnalysis as mda
     >>> import MDAnalysis.analysis.diffusionmap as diffusionmap
     >>> from MDAnalysis.tests.datafiles import PSF, DCD
diff --git a/package/MDAnalysis/analysis/gnm.py b/package/MDAnalysis/analysis/gnm.py
index c13b8fdcef9..b4a39065028 100644
--- a/package/MDAnalysis/analysis/gnm.py
+++ b/package/MDAnalysis/analysis/gnm.py
@@ -24,7 +24,7 @@
 #Ben Hall (benjamin.a.hall@ucl.ac.uk) is to blame
 #Copyright 2011; Consider under GPL v2 or later
 
-"""
+r"""
 Elastic network analysis of MD trajectories --- :mod:`MDAnalysis.analysis.gnm`
 ==============================================================================
 
@@ -37,21 +37,22 @@
 
 An example is provided in the MDAnalysis Cookbook_, listed as GNMExample_.
 
-.. GNMExample_: https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/GNMExample.py
-.. Cookbook_: https://github.com/MDAnalysis/MDAnalysisCookbook
+.. _GNMExample: https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/GNMExample.py
+.. _Cookbook: https://github.com/MDAnalysis/MDAnalysisCookbook
 
 The basic approach is to pass a trajectory to :class:`GNMAnalysis` and then run
 the analysis::
 
-   u = MDAnalysis.Universe(PSF, DCD)
-   C = MDAnalysis.analysis.gnm.GNMAnalysis(u, ReportVector="output.txt")
+    u = MDAnalysis.Universe(PSF, DCD)
+    C = MDAnalysis.analysis.gnm.GNMAnalysis(u, ReportVector="output.txt")
+
+    C.run()
+    output = zip(*C.results)
 
-   C.run()
-   output = zip(*C.results)
+    with open("eigenvalues.dat", "w") as outputfile:
+        for item in output[1]:
+            outputfile.write(item + "\n")
 
-   with open("eigenvalues.dat", "w") as outputfile:
-      for item in output[1]:
-           outputfile.write(item + "\n")
 
 The results are found in :attr:`GNMAnalysis.results`, which can be
 used for further processing (see [Hall2007]_).
@@ -181,7 +182,10 @@ class GNMAnalysis(object):
           `Bonus_groups` is contained in `selection` as this could lead to
           double counting. No checks are applied. Default is ``None``.
 
-    .. SeeAlso:: :class:`closeContactGNMAnalysis`
+    See Also
+    --------
+    :class:`closeContactGNMAnalysis`
+
 
     .. versionchanged:: 0.16.0
        Made :meth:`generate_output` a private method :meth:`_generate_output`.
@@ -337,13 +341,18 @@ class closeContactGNMAnalysis(GNMAnalysis):
           the atoms that form a contact.
     MassWeight : bool (deprecated, optional)
           if set to ``True`` equivalent to `weights` set to "size".
-          .. Note:: This option does not perform a true mass weighting but
-                    weighting by the number of atoms in each residue; the name
-                    of the parameter exists for historical reasons and will
-                    be removed in 0.17.0. Until then, setting `MassWeight` to
-                    anything but ``None`` will override `weights`.
 
-    .. SeeAlso:: :class:`GNMAnalysis`
+    Notes
+    -----
+    The `MassWeight` option does not perform a true mass weighting but
+    weighting by the number of atoms in each residue; the name of the parameter
+    exists for historical reasons and will be removed in 0.17.0. Until then,
+    setting `MassWeight` to anything but ``None`` will override `weights`.
+
+    See Also
+    --------
+    :class:`GNMAnalysis`
+
 
     .. versionchanged:: 0.16.0
        Made :meth:`generate_output` a private method :meth:`_generate_output`.
diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
index 6c8156f75ac..88d8880486d 100644
--- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
+++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
@@ -21,7 +21,7 @@
 #
 
 # Hydrogen Bonding Analysis
-"""
+r"""
 Hydrogen Bond analysis --- :mod:`MDAnalysis.analysis.hbonds.hbond_analysis`
 ===========================================================================
 
@@ -283,6 +283,7 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
             ],
             ...
         ]
+
       The time of each step is not stored with each hydrogen bond frame but in
       :attr:`~HydrogenBondAnalysis.timesteps`.
 
@@ -467,7 +468,7 @@ 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']
@@ -1019,14 +1020,15 @@ def generate_table(self):
           2. "acceptor_idx"
           3. "donor_index"
           4. "acceptor_index"
-          4. "donor_resnm"
-          5. "donor_resid"
-          6. "donor_atom"
-          7. "acceptor_resnm"
-          8. "acceptor_resid"
-          9. "acceptor_atom"
-          10. "distance"
-          11. "angle"
+          5. "donor_resnm"
+          6. "donor_resid"
+          7. "donor_atom"
+          8. "acceptor_resnm"
+          9. "acceptor_resid"
+          10. "acceptor_atom"
+          11. "distance"
+          12. "angle"
+
 
         .. _recsql: http://pypi.python.org/pypi/RecSQL
         """
diff --git a/package/MDAnalysis/analysis/leaflet.py b/package/MDAnalysis/analysis/leaflet.py
index 78594e82252..71595045cb1 100644
--- a/package/MDAnalysis/analysis/leaflet.py
+++ b/package/MDAnalysis/analysis/leaflet.py
@@ -45,7 +45,7 @@
 (slow) heuristic method to find the best cut off for the LeafletFinder
 algorithm.
 
-.. MDAnalysisCookbook_: https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples
+.. _MDAnalysisCookbook: https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples
 
 
 Algorithm
diff --git a/package/MDAnalysis/analysis/pca.py b/package/MDAnalysis/analysis/pca.py
index b0453b0ae72..553f89125c6 100644
--- a/package/MDAnalysis/analysis/pca.py
+++ b/package/MDAnalysis/analysis/pca.py
@@ -67,6 +67,7 @@
 PCA class.
 
 First load all modules and test data
+
     >>> import MDAnalysis as mda
     >>> import MDAnalysis.analysis.pca as pca
     >>> from MDAnalysis.tests.datafiles import PSF, DCD
@@ -74,6 +75,7 @@
 Given a universe containing trajectory data we can perform Principal Component
 Analyis by using the class :class:`PCA` and retrieving the principal
 components.
+
     >>> u = mda.Universe(PSF, DCD)
     >>> PSF_pca = pca.PCA(u, select='backbone')
     >>> PSF_pca.run()
@@ -117,8 +119,10 @@ class PCA(AnalysisBase):
     After initializing and calling method with a universe or an atom group,
     principal components ordering the atom coordinate data by decreasing
     variance will be available for analysis. As an example:
+
         >>> pca = PCA(universe, select='backbone').run()
         >>> pca_space =  pca.transform(universe.select_atoms('backbone'), 3)
+
     generates the principal components of the backbone of the atomgroup and
     then transforms those atomgroup coordinates by the direction of those
     variances. Please refer to the :ref:`PCA-tutorial` for more detailed
@@ -151,7 +155,6 @@ class PCA(AnalysisBase):
         used for the calculation in :meth:`PCA.run` and project it onto the
         principal components.
 
-
     Notes
     -----
     Computation can be speed up by supplying a precalculated mean structure
diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py
index d013f0682d1..e5c8a68b533 100644
--- a/package/MDAnalysis/analysis/psa.py
+++ b/package/MDAnalysis/analysis/psa.py
@@ -1978,14 +1978,14 @@ def get_num_atoms(self):
         """Return the number of atoms used to construct the :class:`Path` instances in
         :class:`PSA`.
 
-        .. note::
-           Must run :meth:`PSAnalysis.generate_paths` prior to calling this
-           method.
-
         Returns
         -------
-        int
-           the number of atoms in :class:`PSA`'s :class:`Path`s'
+        the number of atoms
+
+        Note
+        ----
+        Must run :meth:`PSAnalysis.generate_paths` prior to calling this
+        method.
         """
         if self.natoms is None:
             err_str = "No path data; do 'PSAnalysis.generate_paths()' first."
diff --git a/package/MDAnalysis/analysis/waterdynamics.py b/package/MDAnalysis/analysis/waterdynamics.py
index fdfae89c70f..81ceb579d4f 100644
--- a/package/MDAnalysis/analysis/waterdynamics.py
+++ b/package/MDAnalysis/analysis/waterdynamics.py
@@ -74,9 +74,6 @@
                    10.1063/1.3657408
 
 
-
-.. _examples:
-
 Example use of the analysis classes
 -----------------------------------
 
@@ -865,9 +862,9 @@ class AngularDistribution(object):
     universe : Universe
         Universe object
     selection : str
-        Selection string to evaluate its angular distribution [‘byres name OH2’]
+        Selection string to evaluate its angular distribution ['byres name OH2']
     bins : int (optional)
-        Number of bins to create the histogram by means of :func:`numpy.histogram [40]
+        Number of bins to create the histogram by means of :func:`numpy.histogram`
     axis : {'x', 'y', 'z'} (optional)
         Axis to create angle with the vector (HH, OH or dipole) and calculate
         cosine theta ['z'].
diff --git a/package/MDAnalysis/auxiliary/__init__.py b/package/MDAnalysis/auxiliary/__init__.py
index 3b32e9cd3f8..c6e891c75b7 100644
--- a/package/MDAnalysis/auxiliary/__init__.py
+++ b/package/MDAnalysis/auxiliary/__init__.py
@@ -497,6 +497,7 @@
 :class:`~MDAnalysis.auxiliary.base.AuxFileReader` 
 extends :class:`~MDAnalysis.auxiliary.base.AuxReader` by providing the
 following (these may be overwritten by subclasses as appropriate):
+
   ``__init__(auxfile, **kwargs)``
     Open *auxfile* and any additional processing of *kwargs*.
 
diff --git a/package/MDAnalysis/auxiliary/base.py b/package/MDAnalysis/auxiliary/base.py
index 5364feb540d..945c6a34421 100644
--- a/package/MDAnalysis/auxiliary/base.py
+++ b/package/MDAnalysis/auxiliary/base.py
@@ -66,7 +66,7 @@ def __init__(cls, name, bases, classdict):
 
 
 class AuxStep(object):
-    """ Base class for auxiliary timesteps.
+    """Base class for auxiliary timesteps.
 
     Stores the auxiliary data for the current auxiliary step. On creation, 
     ``step`` is set to -1.
@@ -82,11 +82,11 @@ class AuxStep(object):
         determine from auxiliary data; otherwise defaults to 0 ps. Ignored if
         ``constant_dt`` is False.
     time_selector: optional
-        Key to select 'time' value from the full set of data read for each step,
-        if time selection is enabled; type will vary depending on the auxiliary
-        data format (see individual AuxReader documentation). 
-        If ``None`` (default value), time is instead calculated as::
-            time = step * dt + initial_time
+        Key to select 'time' value from the full set of data read for each
+        step, if time selection is enabled; type will vary depending on the
+        auxiliary data format (see individual AuxReader documentation). If
+        ``None`` (default value), time is instead calculated as: ``time = step
+        * dt + initial_time``
     data_selector: optional
         Key(s) to select auxiliary data values of interest from the full set of
         data read for each step, if data selection is enabled by the reader; 
@@ -97,13 +97,13 @@ class AuxStep(object):
         (Default: True) Set to False if ``dt`` is not constant 
         throughout the auxiliary data set, in which case a valid 
         ``time_selector`` must be provided. 
-        
 
     Attributes
     ----------
     step : int
         Number of the current auxiliary step (0-based).
-    """ 
+
+    """
     def __init__(self, dt=1, initial_time=0, time_selector=None, 
                  data_selector=None, constant_dt=True):
         self.step = -1
diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py
index 1aae2da2acc..302b15a0e41 100644
--- a/package/MDAnalysis/coordinates/GRO.py
+++ b/package/MDAnalysis/coordinates/GRO.py
@@ -40,8 +40,7 @@
 xyz
   An atom line without velocities.  Requires that the 'resid', 'resname',
   'name', 'index' and 'pos' keys be supplied.
-  Eg: fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2,
-      pos=(0.0, 1.0, 2.0))
+  Eg: fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2, pos=(0.0, 1.0, 2.0))
 
 xyz_v
   As above, but with velocities.  Needs an additional keyword 'vel'.
@@ -267,10 +266,13 @@ def write(self, obj):
         -----------
         obj : AtomGroup / Universe / Timestep
 
+        Note
+        ----
         The GRO format only allows 5 digits for resid and atom
         number. If these number become larger than 99,999 then this
         routine will chop off the leading digits.
 
+
         .. versionchanged:: 0.7.6
            resName and atomName are truncated to a maximum of 5 characters
         .. versionchanged:: 0.16.0
diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py
index 297dbef40d2..afb62f42538 100644
--- a/package/MDAnalysis/coordinates/LAMMPS.py
+++ b/package/MDAnalysis/coordinates/LAMMPS.py
@@ -51,12 +51,12 @@
 :class:`~MDAnalysis.topology.LAMMPSParser.DATAParser`) together with a
 LAMMPS DCD with "*real*" provide the keyword *format="LAMMPS*"::
 
->>> u = MDAnalysis.Universe("lammps.data", "lammps_real.dcd", format="LAMMPS")
+    >>> u = MDAnalysis.Universe("lammps.data", "lammps_real.dcd", format="LAMMPS")
 
 If the trajectory uses *units nano* then use ::
 
->>> u = MDAnalysis.Universe("lammps.data", "lammps_nano.dcd", format="LAMMPS",
-...                          lengthunit="nm", timeunit="ns")
+    >>> u = MDAnalysis.Universe("lammps.data", "lammps_nano.dcd", format="LAMMPS",
+    ...                          lengthunit="nm", timeunit="ns")
 
 To scan through a trajectory to find a desirable frame and write to a LAMMPS
 data file,
diff --git a/package/MDAnalysis/coordinates/MMTF.py b/package/MDAnalysis/coordinates/MMTF.py
index f506665f8b5..87ad92fcc7e 100644
--- a/package/MDAnalysis/coordinates/MMTF.py
+++ b/package/MDAnalysis/coordinates/MMTF.py
@@ -23,8 +23,8 @@
 """MMTF trajectory reader --- :mod:`MDAnalysis.coordinates.MMTF`
 ================================================================
 
-Reads coordinates data from the `Macromolecular Transmission Format
-(MMTF) format`_.  This should generally be a quicker alternative to PDB.
+Reads coordinates data from the Macromolecular Transmission Format format
+(MMTF_). This should generally be a quicker alternative to PDB.
 
 .. versionadded:: 0.16.0
 
@@ -35,7 +35,8 @@
    :members:
 .. autofunction:: fetch_mmtf
 
-.. _Macromolecular Transmission Format (MMTF) format: https://mmtf.rcsb.org/
+.. _MMTF: https://mmtf.rcsb.org/
+
 """
 from __future__ import absolute_import
 
@@ -53,10 +54,8 @@ def _parse_mmtf(fn):
 
 
 class MMTFReader(base.SingleFrameReaderBase):
-    """Topology parser for the MMTF_ format.
+    """Topology parser for the Macromolecular Transmission Format format (MMTF_).
 
-    .. _Macromolecular Transmission Format (MMTF) format:
-       https://mmtf.rcsb.org/
     """
     format = 'MMTF'
 
diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 86cbeba7fae..6f2318cc0dd 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -55,7 +55,7 @@
   W.close()
 
 It is important to *always close the trajectory* when done because only at this
-step is the final END_ record written, which is required by the `PDB
+step is the final END_ record written, which is required by the `PDB 3.2
 standard`_.
 
 
@@ -72,7 +72,7 @@
 -----------------------------------------
 A pure-Python implementation for PDB files commonly encountered in MD
 simulations comes under the names :class:`PDBReader` and
-:class:`PDBWriter`. It only implements a subset of the `PDB standard`_
+:class:`PDBWriter`. It only implements a subset of the `PDB 3.2 standard`_
 (for instance, it does not deal with insertion codes) and also allows some
 typical enhancements such as 4-letter resids (introduced by CHARMM/NAMD).
 
@@ -140,6 +140,9 @@
     The "permissive" flag is not used anymore (and effectively defaults to True);
     it will be completely removed in 0.16.0.
 
+
+.. _`PDB 3.2 standard`:
+    http://www.wwpdb.org/documentation/format32/v3.2.html
 """
 from __future__ import absolute_import
 
@@ -1030,8 +1033,6 @@ class MultiPDBWriter(PDBWriter):
     *multiframe* = ``True``), consisting of multiple models (using the MODEL_
     and ENDMDL_ records).
 
-    .. _`PDB 3.2 standard`:
-       http://www.wwpdb.org/documentation/format32/v3.2.html
 
     .. _MODEL: http://www.wwpdb.org/documentation/format32/sect9.html#MODEL
     .. _ENDMDL: http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL
diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py
index 2749fa651b7..2e0a40ba18d 100644
--- a/package/MDAnalysis/coordinates/PDBQT.py
+++ b/package/MDAnalysis/coordinates/PDBQT.py
@@ -230,11 +230,12 @@ def write(self, selection, frame=None):
         frame : int, optional
             optionally move to *frame* before writing
 
-        .. Note::
+        Note
+        ----
+        The first letter of the
+        :attr:`~MDAnalysis.core.groups.Atom.segid` is used as the PDB
+        chainID.
 
-           The first letter of the
-           :attr:`~MDAnalysis.core.groups.Atom.segid` is used as the PDB
-           chainID.
 
         .. versionchanged:: 0.11.0
            Frames now 0-based instead of 1-based
diff --git a/package/MDAnalysis/coordinates/PQR.py b/package/MDAnalysis/coordinates/PQR.py
index cc62d48d3ad..181ef6272fa 100644
--- a/package/MDAnalysis/coordinates/PQR.py
+++ b/package/MDAnalysis/coordinates/PQR.py
@@ -77,9 +77,9 @@
 *whitespace* separation between *all* entries). The chainID is optional
 and can be omitted::
 
-ATOM      1  N    MET     1     -11.921   26.307   10.410 -0.3000 1.8500
-ATOM     36  NH1  ARG     2      -6.545   25.499    3.854 -0.8000 1.8500
-ATOM     37 HH11  ARG     2      -6.042   25.480    4.723  0.4600 0.2245
+  ATOM      1  N    MET     1     -11.921   26.307   10.410 -0.3000 1.8500
+  ATOM     36  NH1  ARG     2      -6.545   25.499    3.854 -0.8000 1.8500
+  ATOM     37 HH11  ARG     2      -6.042   25.480    4.723  0.4600 0.2245
 
 
 .. Warning:: Fields *must be white-space separated* or data are read
@@ -202,11 +202,12 @@ def write(self, selection, frame=None):
 
         Parameters
         ----------
-        selection
+        selection : AtomGroup or Universe
             MDAnalysis AtomGroup or Universe
         frame : int, optional
             optionally move to frame number *frame*
 
+
         .. versionchanged:: 0.11.0
            Frames now 0-based instead of 1-based
         """
diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py
index 144e0a95f1d..02e08348f4f 100644
--- a/package/MDAnalysis/coordinates/XYZ.py
+++ b/package/MDAnalysis/coordinates/XYZ.py
@@ -408,7 +408,7 @@ def Writer(self, filename, n_atoms=None, **kwargs):
 
         See Also
         --------
-        :class: `XYZWriter`
+        :class:`XYZWriter`
         """
         if n_atoms is None:
             n_atoms = self.n_atoms
diff --git a/package/MDAnalysis/coordinates/chain.py b/package/MDAnalysis/coordinates/chain.py
index e419bfd588e..0497f333ba6 100644
--- a/package/MDAnalysis/coordinates/chain.py
+++ b/package/MDAnalysis/coordinates/chain.py
@@ -94,11 +94,9 @@ def __init__(self, filenames, **kwargs):
            names in either plain file names format or ``(filename, format)``
            tuple combination. This allows explicit setting of the format for
            each individual trajectory file.
-
         skip : int, optional
            skip step (also passed on to the individual trajectory readers);
            must be same for all trajectories
-
         dt : float, optional
           Passed to individual trajectory readers to enforce a common time
           difference between frames, in MDAnalysis time units. If not set, each
@@ -106,15 +104,15 @@ def __init__(self, filenames, **kwargs):
           files, or set to the reader's default) when reporting frame times;
           note that this might lead an inconsistent time difference between
           frames.
-
         **kwargs : dict, optional
           all other keyword arguments are passed on to each trajectory reader
           unchanged
 
+
         .. versionchanged:: 0.8
-           The *delta* keyword was added.
+           The ``delta`` keyword was added.
         .. versionchanged:: 0.13
-           The *delta* keyword was deprecated in favor of using *dt*.
+           The ``delta`` keyword was deprecated in favor of using ``dt``.
 
         """
         super(ChainReader, self).__init__()
diff --git a/package/MDAnalysis/coordinates/core.py b/package/MDAnalysis/coordinates/core.py
index d50924daa06..fbd918b03fe 100644
--- a/package/MDAnalysis/coordinates/core.py
+++ b/package/MDAnalysis/coordinates/core.py
@@ -103,15 +103,10 @@ def writer(filename, n_atoms=None, **kwargs):
         a multiframe writer and then fall back to single frame [``None``]
     kwargs : optional
         Keyword arguments for the writer; all trajectory Writers accept
-        at least
-            *start*
-                starting time [0]
-            *step*
-                step size in frames [1]
-            *dt*
-                length of time between two frames, in ps [1.0]
-       Some readers accept additional arguments, which need to be looked
-       up in the documentation of the reader.
+        ``start``: starting time [0], ``step``: step size in frames [1],
+        ``dt``: length of time between two frames, in ps [1.0] Some readers
+        accept additional arguments, which need to be looked up in the
+        documentation of the reader.
 
     Returns
     -------
@@ -123,8 +118,10 @@ def writer(filename, n_atoms=None, **kwargs):
     MDAnalysis.coordinates.XTC.XTCWriter : Gromacs XTC trajectories
     MDAnalysis.coordinates.TRR.TRRWriter : Gromacs TRR trajectories
 
+
     .. versionchanged:: 0.7.6
        Added *multiframe* keyword. See also :func:`get_writer_for`.
+
     """
     Writer = get_writer_for(filename, format=kwargs.pop('format', None),
                             multiframe=kwargs.pop('multiframe', None))
diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py
index 44f124bb20b..6ec7b43dffd 100644
--- a/package/MDAnalysis/core/groups.py
+++ b/package/MDAnalysis/core/groups.py
@@ -648,16 +648,17 @@ def bbox(self, **kwargs):
             If ``True``, move all atoms within the primary unit cell before
             calculation. [``False``]
 
-        .. note::
-            The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
-            ``True`` allows the *pbc* flag to be used by default.
-
         Returns
         -------
          corners : array
             2x3 array giving corners of bounding box as
             [[xmin, ymin, zmin], [xmax, ymax, zmax]].
 
+        Note
+        ----
+        The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
+        ``True`` allows the *pbc* flag to be used by default.
+
 
         .. versionadded:: 0.7.2
         .. versionchanged:: 0.8 Added *pbc* keyword
@@ -683,10 +684,6 @@ def bsphere(self, **kwargs):
             If ``True``, move all atoms within the primary unit cell before
             calculation. [``False``]
 
-        .. note::
-            The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
-            ``True`` allows the *pbc* flag to be used by default.
-
         Returns
         -------
         R : float
@@ -694,6 +691,11 @@ def bsphere(self, **kwargs):
         center : array
             Coordinates of sphere center as ``[xcen,ycen,zcen]``.
 
+        Note
+        ----
+        The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
+        ``True`` allows the *pbc* flag to be used by default.
+
 
         .. versionadded:: 0.7.3
         .. versionchanged:: 0.8 Added *pbc* keyword
@@ -2089,7 +2091,7 @@ def write(self, filename=None, file_format="PDB",
         Parameters
         ----------
         filename : str, optional
-           ``None``: create TRJNAME_FRAME.FORMAT from filenamefmt [``None``]
+            ``None``: create TRJNAME_FRAME.FORMAT from filenamefmt [``None``]
         file_format : str, optional
             PDB, CRD, GRO, VMD (tcl), PyMol (pml), Gromacs (ndx) CHARMM (str)
             Jmol (spt); case-insensitive and can also be supplied as the
@@ -2098,13 +2100,12 @@ def write(self, filename=None, file_format="PDB",
             format string for default filename; use substitution tokens
             'trjname' and 'frame' ["%(trjname)s_%(frame)d"]
         bonds : str, optional
-           how to handle bond information, especially relevant for PDBs;
-           default is ``"conect"``.
-           * ``"conect"``: write only the CONECT records defined in the original
-             file
-           * ``"all"``: write out all bonds, both the original defined and those
-             guessed by MDAnalysis
-           * ``None``: do not write out bonds
+            how to handle bond information, especially relevant for PDBs.
+            ``"conect"``: write only the CONECT records defined in the original
+            file. ``"all"``: write out all bonds, both the original defined and
+            those guessed by MDAnalysis. ``None``: do not write out bonds.
+            Default os ``"conect"``.
+
 
         .. versionchanged:: 0.9.0
            Merged with write_selection.  This method can now write both
diff --git a/package/MDAnalysis/core/topology.py b/package/MDAnalysis/core/topology.py
index edc5d397406..2c11d2f3632 100644
--- a/package/MDAnalysis/core/topology.py
+++ b/package/MDAnalysis/core/topology.py
@@ -151,8 +151,12 @@ class TransTable(object):
 
     Parameters
     ----------
-    n_atoms, n_residues, n_segments : int
-        number of atoms, residues, segments in topology
+    n_atoms : int
+        number of atoms in topology
+    n_residues : int
+        number of residues in topology
+    n_segments : int
+        number of segments in topology
     atom_resindex : 1-D array
         resindex for each atom in the topology; the number of unique values in
         this array must be <= `n_residues`, and the array must be length
@@ -165,8 +169,12 @@ class TransTable(object):
 
     Attributes
     ----------
-    n_atoms, n_residues, n_segments : int
-        number of atoms, residues, segments in topology
+    n_atoms : int
+        number of atoms in topology
+    n_residues : int
+        number of residues in topology
+    n_segments : int
+        number of segments in topology
     size
         tuple describing the shape of the TransTable
 
@@ -428,24 +436,29 @@ 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 : int
+            number of atoms in topology. Must be larger then 1 at each level
+        n_residues : int
+            number of residues in topology. Must be larger then 1 at each level
+        n_segments : int
+            number of segments in topology. Must be larger then 1 at each level
+        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)
diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
index ba421c85d06..90535b582eb 100644
--- a/package/MDAnalysis/core/topologyattrs.py
+++ b/package/MDAnalysis/core/topologyattrs.py
@@ -1362,7 +1362,7 @@ class Bonds(_Connection):
 
     Must be initialised by a list of zero based tuples.
     These indices refer to the atom indices.
-        Eg:  [(0, 1), (1, 2), (2, 3)]
+    E.g., ` [(0, 1), (1, 2), (2, 3)]`
 
     Also adds the `bonded_atoms`, `fragment` and `fragments`
     attributes.
@@ -1416,8 +1416,7 @@ class Angles(_Connection):
     """Angles between three atoms
 
     Initialise with a list of 3 long tuples
-    Eg:
-      [(0, 1, 2), (1, 2, 3), (2, 3, 4)]
+    E.g.,  `[(0, 1, 2), (1, 2, 3), (2, 3, 4)]`
 
     These indices refer to the atom indices.
     """
diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
index cc77bb14453..5d8a794d472 100644
--- a/package/MDAnalysis/core/topologyobjects.py
+++ b/package/MDAnalysis/core/topologyobjects.py
@@ -332,15 +332,6 @@ class TopologyDict(object):
 
       topologydict = TopologyDict(members)
 
-    Arguments
-    ---------
-    *members*
-      A list of :class:`TopologyObject` instances
-
-    Returns
-    -------
-    *topologydict*
-      A specialised dictionary of the topology instances passed to it
 
     TopologyDicts are also built lazily from a :class:`TopologyGroup.topDict`
     attribute.
@@ -378,6 +369,12 @@ class TopologyDict(object):
     Two :class:`TopologyDict` instances can be combined using
     addition and it will not create any duplicate bonds in the process.
 
+    Arguments
+    ---------
+    members :
+      A list of :class:`TopologyObject` instances
+
+
     .. versionadded:: 0.8
     .. versionchanged:: 0.9.0
        Changed initialisation to use a list of :class:`TopologyObject`
@@ -624,6 +621,7 @@ def atomgroup_intersection(self, ag, **kwargs):
             Only retrieve bonds which are completely contained within the
             AtomGroup. [``False``]
 
+
         .. versionadded:: 0.9.0
         """
         # Issue #780 - if self is empty, return self to avoid invalid mask
diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 067efc331e3..05fb4d47f9f 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/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
diff --git a/package/MDAnalysis/lib/NeighborSearch.py b/package/MDAnalysis/lib/NeighborSearch.py
index 0bd1ae9ddda..81d9e190753 100644
--- a/package/MDAnalysis/lib/NeighborSearch.py
+++ b/package/MDAnalysis/lib/NeighborSearch.py
@@ -68,7 +68,7 @@ def search(self, atoms, radius, level='A'):
 
         Parameters
         ----------
-        atoms : AtomGroup or Atom
+        atoms : AtomGroup, MDAnalysis.core.groups.Atom
           list of atoms
         radius : float
           Radius for search in Angstrom.
diff --git a/package/MDAnalysis/lib/c_distances.pyx b/package/MDAnalysis/lib/c_distances.pyx
index b3c4c35d4f5..d3f39029713 100644
--- a/package/MDAnalysis/lib/c_distances.pyx
+++ b/package/MDAnalysis/lib/c_distances.pyx
@@ -23,7 +23,7 @@
 
 """
 Distance calculation library --- :mod:`MDAnalysis.lib.c_distances`
-=================================================================
+==================================================================
 
 Serial versions of all distance calculations
 """
diff --git a/package/MDAnalysis/lib/c_distances_openmp.pyx b/package/MDAnalysis/lib/c_distances_openmp.pyx
index 6b3b9e74705..6424d2215b1 100644
--- a/package/MDAnalysis/lib/c_distances_openmp.pyx
+++ b/package/MDAnalysis/lib/c_distances_openmp.pyx
@@ -23,7 +23,7 @@
 
 """
 Parallel distance calculation library --- :mod:`MDAnalysis.lib.c_distances_openmp`
-=================================================================================
+==================================================================================
 
 
 Contains OpenMP versions of the contents of "calc_distances.h"
diff --git a/package/MDAnalysis/lib/formats/libmdaxdr.pyx b/package/MDAnalysis/lib/formats/libmdaxdr.pyx
index ba204904e39..bcba535a34a 100644
--- a/package/MDAnalysis/lib/formats/libmdaxdr.pyx
+++ b/package/MDAnalysis/lib/formats/libmdaxdr.pyx
@@ -502,7 +502,7 @@ cdef class TRRFile(_XDRFile):
 
         Parameters
         ----------
-        xyz : ndarray, shape=(n_atoms, 3)
+        xyz : ndarray, shape=(`n_atoms`, 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=(`n_atoms`, 3)
             cartesion coordinates
         box : ndarray, shape=(3, 3)
             Box vectors for this frame
diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py
index a8ded68d246..85284ca98bc 100644
--- a/package/MDAnalysis/lib/util.py
+++ b/package/MDAnalysis/lib/util.py
@@ -559,28 +559,26 @@ def __init__(self, stream, filename, reset=True, close=False):
         the keyword *reset* is set to ``False``. If rewinding fails, a
         :class:`MDAnalysis.StreamWarning` is issued.
 
-        .. Note::
-
-           By default, this stream will *not* be closed by :keyword:`with` and
-           :meth:`close` (see there) unless the *close* keyword is set to
-           ``True``.
-
-        Arguments
-        ---------
+        Parameters
+        ----------
         stream : stream
-               an open stream (e.g. :class:`file` or :func:`cStringIO.StringIO`)
+            an open stream (e.g. :class:`file` or :func:`cStringIO.StringIO`)
         filename : str
-               the filename that should be associated with the stream
-
-        Keywords
-        --------
-        reset : boolean, default ``True``
-               start the stream from the beginning (either :meth:`reset` or :meth:`seek`)
-               when the class instance is constructed
-        close : booelan, default ``True``
-               close the stream when a :keyword:`with` block exits or when
-               :meth:`close` is called; note that the default is **not to close
-               the stream**
+            the filename that should be associated with the stream
+        reset : bool
+            start the stream from the beginning (either :meth:`reset` or :meth:`seek`)
+            when the class instance is constructed
+        close : bool
+            close the stream when a :keyword:`with` block exits or when
+            :meth:`close` is called; note that the default is **not to close
+            the stream**
+
+        Notes
+        -----
+        By default, this stream will *not* be closed by :keyword:`with` and
+        :meth:`close` (see there) unless the `close` keyword is set to
+        ``True``.
+
 
         .. versionadded:: 0.9.0
         """
diff --git a/package/MDAnalysis/topology/TPRParser.py b/package/MDAnalysis/topology/TPRParser.py
index f2eae75326e..90cb748425a 100644
--- a/package/MDAnalysis/topology/TPRParser.py
+++ b/package/MDAnalysis/topology/TPRParser.py
@@ -152,7 +152,7 @@
 
 
 class TPRParser(TopologyReaderBase):
-    """Read topology information from a Gromacs_ TPR_ file.
+    """Read topology information from a Gromacs_ `TPR file`_.
 
     .. _Gromacs: http://www.gromacs.org
     .. _TPR file: http://manual.gromacs.org/current/online/tpr.html
diff --git a/package/MDAnalysis/topology/guessers.py b/package/MDAnalysis/topology/guessers.py
index 639e9b93e9a..68fc1f84fe2 100644
--- a/package/MDAnalysis/topology/guessers.py
+++ b/package/MDAnalysis/topology/guessers.py
@@ -113,7 +113,7 @@ def guess_atom_element(atomname):
         return atomname[0]
 
 
-def guess_bonds(atoms, coords, **kwargs):
+def guess_bonds(atoms, coords, box=None, **kwargs):
     r"""Guess if bonds exist between two atoms based on their distance.
 
     Bond between two atoms is created, if the two atoms are within
@@ -135,21 +135,18 @@ def guess_bonds(atoms, coords, **kwargs):
     fudge_factor : float, optional
         The factor by which atoms must overlap eachother to be considered a
         bond.  Larger values will increase the number of bonds found. [0.72]
-
     vdwradii : dict, optional
         To supply custom vdwradii for atoms in the algorithm. Must be a dict
         of format {type:radii}. The default table of van der Waals radii is
         hard-coded as :data:`MDAnalysis.topology.tables.vdwradii`.  Any user
         defined vdwradii passed as an argument will supercede the table
         values. [``None``]
-
     lower_bound : float, optional
         The minimum bond length. All bonds found shorter than this length will
         be ignored. This is useful for parsing PDB with altloc records where
         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``]
@@ -203,7 +200,8 @@ def guess_bonds(atoms, coords, **kwargs):
 
     lower_bound = kwargs.get('lower_bound', 0.1)
 
-    box = kwargs.get('box', None)
+    if box is not None:
+        box = np.asarray(box)
 
     # to speed up checking, calculate what the largest possible bond
     # atom that would warrant attention.
diff --git a/package/MDAnalysis/visualization/__init__.py b/package/MDAnalysis/visualization/__init__.py
index aec0554fca2..24c0fd27743 100644
--- a/package/MDAnalysis/visualization/__init__.py
+++ b/package/MDAnalysis/visualization/__init__.py
@@ -26,7 +26,7 @@
 ================================================================
 """
 from __future__ import absolute_import
-__all__ = ['streamlines', 'streamlines_3D']
+from . import streamlines
+from . import streamlines_3D
 
-import streamlines
-import streamlines_3D
+__all__ = ['streamlines', 'streamlines_3D']
diff --git a/package/MDAnalysis/visualization/streamlines.py b/package/MDAnalysis/visualization/streamlines.py
index fa21b823bc3..4b4d2d3cf75 100644
--- a/package/MDAnalysis/visualization/streamlines.py
+++ b/package/MDAnalysis/visualization/streamlines.py
@@ -170,7 +170,7 @@ def produce_list_centroids_this_frame(list_indices_in_polygon):
 
 def generate_streamlines(coordinate_file_path, trajectory_file_path, grid_spacing, MDA_selection, start_frame,
                          end_frame, xmin, xmax, ymin, ymax, maximum_delta_magnitude, num_cores='maximum'):
-    '''Produce the x and y components of a 2D streamplot data set.
+    """Produce the x and y components of a 2D streamplot data set.
 
     :Parameters:
         **coordinate_file_path** : str
@@ -234,10 +234,10 @@ def generate_streamlines(coordinate_file_path, trajectory_file_path, grid_spacin
     .. image:: testing_streamline.png
 
     .. [Chavent2014] Chavent, M.\*, Reddy, T.\*, Dahl, C.E., Goose, J., Jobard, B., and Sansom, M.S.P. (2014)
-    Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
-    *Faraday Discussions* **169**: **Accepted**
+       Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
+       *Faraday Discussions* **169**: **Accepted**
 
-    '''
+    """
     # work out the number of cores to use:
     if num_cores == 'maximum':
         num_cores = multiprocessing.cpu_count()  # use all available cores
diff --git a/package/doc/sphinx/source/conf.py b/package/doc/sphinx/source/conf.py
index 8e5a0284532..73a1e484f9f 100644
--- a/package/doc/sphinx/source/conf.py
+++ b/package/doc/sphinx/source/conf.py
@@ -58,8 +58,9 @@ def __getattr__(cls, name):
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx',
               'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
-              'sphinx.ext.napoleon',]
-mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+              'sphinx.ext.napoleon', 'sphinx.ext.todo']
+
+mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
index ac2123acffe..a7b8e3ee86d 100644
--- a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
+++ b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
@@ -10,8 +10,8 @@
 .. versionadded:: 0.16.0
 
 The module contains implementations of similarity measures between protein
-ensembles described in [Lindorff-Larsen2009]_. The implementation and examples
-are described in [Tiberti2015]_.
+ensembles described in [Lindorff-Larsen2009_doc]_. The implementation and examples
+are described in [Tiberti2015_doc]_.
 
 The module includes facilities for handling ensembles and trajectories through
 the :class:`Universe` class, performing clustering or dimensionality reduction
@@ -34,7 +34,7 @@ as well as two methods to evaluate the convergence of trajectories:
 + **Dimensionality-reduction based convergence evaluation** : :func:`~MDAnalysis.analysis.encore.similarity.dres_convergence`
 
 
-When using this module in published work please cite [Tiberti2015]_.
+When using this module in published work please cite [Tiberti2015_doc]_.
 
 
 Modules
@@ -55,7 +55,6 @@ Modules
 References
 ----------
 
-.. [Lindorff-Larsen2009] Similarity Measures for Protein Ensembles. Lindorff-Larsen, K. Ferkinghoff-Borg, J. PLoS ONE 2008, 4, e4203.
-
-.. [Tiberti2015] ENCORE: Software for Quantitative Ensemble.. Comparison. Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff- Larsen. PLoS Comput Biol. 2015, 11, e1004415
+.. [Lindorff-Larsen2009_doc] Similarity Measures for Protein Ensembles. Lindorff-Larsen, K. Ferkinghoff-Borg, J. PLoS ONE 2008, 4, e4203.
 
+.. [Tiberti2015_doc] ENCORE: Software for Quantitative Ensemble.. Comparison. Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff- Larsen. PLoS Comput Biol. 2015, 11, e1004415
diff --git a/package/doc/sphinx/source/documentation_pages/analysis_modules.rst b/package/doc/sphinx/source/documentation_pages/analysis_modules.rst
index d1982e281c0..7da649d8683 100644
--- a/package/doc/sphinx/source/documentation_pages/analysis_modules.rst
+++ b/package/doc/sphinx/source/documentation_pages/analysis_modules.rst
@@ -75,7 +75,6 @@ Nucleic acids
    :maxdepth: 1
 
    analysis/nuclinfo
-   analysis/legacy/x3dna
 
 Polymers
 ========
diff --git a/package/doc/sphinx/source/documentation_pages/lib/c_distances.rst b/package/doc/sphinx/source/documentation_pages/lib/c_distances.rst
index ad0d800efd5..962e1d9055a 100644
--- a/package/doc/sphinx/source/documentation_pages/lib/c_distances.rst
+++ b/package/doc/sphinx/source/documentation_pages/lib/c_distances.rst
@@ -1,2 +1,2 @@
-.. automodule:: MDAnalysis.lib._distances
+.. automodule:: MDAnalysis.lib.c_distances
    :members:
diff --git a/package/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst b/package/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst
index ab1af2de950..d03ca6e6f7f 100644
--- a/package/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst
+++ b/package/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst
@@ -1,2 +1,2 @@
-.. automodule:: MDAnalysis.lib._distances_openmp
+.. automodule:: MDAnalysis.lib.c_distances_openmp
    :members:
diff --git a/package/doc/sphinx/source/documentation_pages/references.rst b/package/doc/sphinx/source/documentation_pages/references.rst
index eec47bfa642..3df14b09839 100644
--- a/package/doc/sphinx/source/documentation_pages/references.rst
+++ b/package/doc/sphinx/source/documentation_pages/references.rst
@@ -48,18 +48,18 @@ code (:mod:`MDAnalysis.analysis.align`) that uses the
 :mod:`~MDAnalysis.core.qcprot` module please also cite [Theobald2005]_ and
 [Liu2010]_.
 
-.. [Theobald2005] Douglas L. Theobald. Rapid calculation of RMSD using a
+.. [Theobald2005b] Douglas L. Theobald. Rapid calculation of RMSD using a
    quaternion-based characteristic polynomial. *Acta Crystallographica A*
    **61** (2005), 478-480.
 
-.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
+.. [Liu2010b] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
    determination of the optimal rotational matrix for macromolecular
    superpositions. *J. Comput. Chem.* **31** (2010), 1561–1563.
 
 If you use the helix analysis algorithm HELANAL_ in
 :mod:`MDAnalysis.analysis.helanal` please cite [Bansal2000]_.
 
-.. [Bansal2000] Bansal M, Kumar S, Velavan R. HELANAL — A program to
+.. [Bansal2000b] Bansal M, Kumar S, Velavan R. HELANAL — A program to
    characterise helix geometry in proteins. *J. Biomol. Struct. Dyn.* **17**
    (2000), 811–819
 
@@ -68,14 +68,14 @@ If you use the helix analysis algorithm HELANAL_ in
 If you use the GNM trajectory analysis code in
 :mod:`MDAnalysis.analysis.gnm` please cite [Hall2007]_.
 
-.. [Hall2007] Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
+.. [Hall2007b] Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
    Philip C. Biggin. Characterization of Protein Conformational States by
    Normal-Mode Frequencies. *JACS* **129** (2007), 11394–11401.
 
 If you use the water analysis code in
 :mod:`MDAnalysis.analysis.waterdynamics` please cite [Araya-Secchi2014]_.
 
-.. [Araya-Secchi2014] R. Araya-Secchi., Tomas Perez-Acle, Seung-gu Kang, Tien
+.. [Araya-Secchi2014b] R. Araya-Secchi., Tomas Perez-Acle, Seung-gu Kang, Tien
    Huynh, Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate,
    Agustin D. Martinez, Isaac E. Garcia, Juan C. Saez, Ruhong
    Zhou. Characterization of a novel water pocket inside the human Cx26
@@ -84,7 +84,7 @@ If you use the water analysis code in
 If you use the Path Similarity Analysis (PSA) code in
 :mod:`MDAnalysis.analysis.psa` please cite [Seyler2015]_.
 
-.. [Seyler2015] Seyler SL, Kumar A, Thorpe MF, Beckstein O. Path Similarity
+.. [Seyler2015b] Seyler SL, Kumar A, Thorpe MF, Beckstein O. Path Similarity
   Analysis: A Method for Quantifying Macromolecular Pathways. *PLoS
   Comput Biol* **11** (2015), e1004568. doi: `10.1371/journal.pcbi.1004568`_
 
@@ -93,7 +93,7 @@ If you use the Path Similarity Analysis (PSA) code in
 If you use the implementation of the ENCORE ensemble analysis in
 :mod:`MDAnalysis.analysis.encore` please cite [Tiberti2015]_.
 
-.. [Tiberti2015] M. Tiberti, E. Papaleo, T. Bengtsen, W. Boomsma,
+.. [Tiberti2015b] M. Tiberti, E. Papaleo, T. Bengtsen, W. Boomsma,
    and K. Lindorff-Larsen. ENCORE: Software for quantitative ensemble
    comparison. *PLoS Comput Biol*, **11** (2015), e1004415.  doi:
    `10.1371/journal.pcbi.1004415`_
diff --git a/package/setup.cfg b/package/setup.cfg
index 039cda196f0..9d74e31fb86 100644
--- a/package/setup.cfg
+++ b/package/setup.cfg
@@ -13,4 +13,4 @@ universal = 1
 all-files = 1
 source-dir = doc/sphinx/source
 build-dir = doc/html
-#warning-is-error = 1
+warning-is-error = 1