Hi.
I am new to using Sphinx to build Python docs and was wondering if there was a
good best practice for debugging sphinx builds.
More specifically, when running Sphinx I get pretty good output (i.d. the final
HTML) but I also see the following warning messages:
[u'SparseBinning(snap, grid_spacing=array([ 1., 1., 1.]),
use_selection=True)', u':module: mdhandle.properties.cell_decomposition', u'',
u'', u'', u'3D space in the simulation domain is divided into a sparse grid
with', u'atoms assigned into the appropriate bin using on a nearest-grid-point
(NGP)', u'algorithm.', u'', u'Each cell in the grid is called a bin.', u'',
u'Each bin contains a set of atoms ids, or ``None`` if no atoms are present.',
u'', u'All bins are uniquely defined by their indices ``(i,j,k)``. ', u'',
u'This implementation works with sparse bins as a bin is only created', u'as
required.', u'', u':Parameters:', u'', u' **snap** :
:class:`mdhandle.snap.Snap`', u'', u' Snap object to be sorted into
cells.', u'', u' **grid_spacing** : :class:`numpy.ndhandle`', u'', u'
Grid spacing along each coordinate direction.', u' Grid spacing must be
an even divisor of the primary simulation', u' cell dimensions.', u'
``[default=np.ones(3,dtype=np.float)]``', u'', u' **use_selection** :
boolean [default=False]', u'', u' If ``True``, selections are applied
to snap object when getting atom', u' coordinates.', u'', u'.. rubric::
Notes', u'', u'', u'**Class Attributes**:', u'', u'* ``full_compare_indices`` :
:class:`numpy.ndarray`', u' Deltas required to move through all neighbouring
cells.', u'* ``N3_compare_indices`` : :class:`numpy.ndarray`', u' Deltas
required to move through neighbouring cells with the help', u" of Newton's
Third law such that only half interactions are required", u' at each grid
cell.', u'', u'.. rubric:: Attributes', u'', u'============
============================ ==========', u' snap
:class:`mdhandle.snap.Snap` ', u"
Snap object. Active dataset must be of type ``'atoms'``.", u'grid_spacing
:class:`numpy.ndarray` (3x1) ', u'
Grid spacing along coordinate directions: ``[dx, dy, dz]``.', u'
Must be even divisor of the simulation domain in
each direction.', u' xyz :class:`numpy.ndarray` (Nx3) ', u'
Atomic positions.', u' bins
dict ', u' Organized
by tuples corresponding to cell location', u'
(i.e. ``(1, 1, 1 )``). Each dictionary entries contains atom ids', u'
for atoms located in that grid
cell.', u' This is the sparse
element of implementation as dictionary entries', u'
only created as needed.', u'max_bins_idx
:class:`numpy.ndarray` (3x1) ', u'
Largest grid cell index along each coordinate direction.', u'min_bins_idx
:class:`numpy.ndarray` (3x1) ', u'
Smallest grid cell index along each coordinate direction.', u' nbins
:class:`numpy.ndarray` (3x1) ', u'
Number of bins along each coordinate direction.', u'============
============================ ==========', u'', u'.. rubric:: Methods', u'',
u'.. autosummary::', u' :toctree:', u'', u' get_surrounding', u' run',
u'', u'.. document private functions', u'.. automethod:: _ngp', u'', u'..
py:method:: SparseBinning.get_surrounding(r, deltas=array([[-1, -1, -1],\n
[-1, -1, 0],\n [-1, -1, 1],\n [-1, 0, -1],\n [-1, 0,
0],\n [-1, 0, 1],\n [-1, 1, -1],\n [-1, 1, 0],\n
[-1, 1, 1],\n [ 0, -1, -1],\n [ 0, -1, 0],\n [ 0, -1,
1],\n [ 0, 0, -1],\n [ 0, 0, 0],\n [ 0, 0, 1],\n [
0, 1, -1],\n [ 0, 1, 0],\n [ 0, 1, 1],\n [ 1, -1, -1],\n
[ 1, -1, 0],\n [ 1, -1, 1],\n [ 1, 0, -1],\n [ 1,
0, 0],\n [ 1, 0, 1],\n [ 1, 1, -1],\n [ 1, 1, 0],\n
[ 1, 1, 1]]))', u' :module: mdhandle.properties.cell_decomposition', u'',
u' ', u' ', u' Iterate over all atoms in the surrounding bins as defined
by', u' deltas parameter.', u' ', u' ', u' :Parameters:', u' ', u'
**r** : :class:`numpy.ndarray` (3x1)', u' ', u' Atom position in
``(x,y,z)`` format.', u' ', u' **deltas** : :class:`numpy.ndarray`
[default=full_compare_indices]', u' ', u' Array of tuples with
format ``(dx,dy,dz)`` giving integer deltas', u' to neighbouring
cells. For example, ``(-1, -1, -1)`` looks in the ', u' bin ``dx =
-1``, ``dy = -1``, ``dz = -1`` bin from the bin', u' containing the
position defined by ``r``.', u' ', u' :Returns:', u' ', u'
**bin_total** : list', u' ', u' List of ``atom_id`` for atoms in
bins surrouding position ``r``.', u' ', u'', u'.. py:method::
SparseBinning.run()', u' :module: mdhandle.properties.cell_decomposition',
u'', u' ', u' ', u' Run cell decomposition for :attr:`SparseBinning.snap`
object. ', u' ', u' Cell decomposition is stored in
:attr:`SparseBinning.bins`.']:71: (ERROR/3) Unknown directive type
"autosummary".
.. autosummary::
:toctree:
get_surrounding
run
Sorry for the lengthy output - but I wasn't able to get very far by Google
searching for "(ERROR/3) Unknown directive type "autosummary"." Is there any
way to get a more precise indication from Sphinx as to the location of the
error?
Thanks.
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