Numpyfy docstrings

Update the docstrings everywhere in the package but in the anlysis.

package/MDAnalysis/__init__.py

@@ -113,7 +113,9 @@
    9.72062
   ....
 
-.. SeeAlso:: :class:`MDAnalysis.core.universe.Universe` for details
+See Also
+--------
+See :class:`MDAnalysis.core.universe.Universe` for details
 
 
 Examples

package/MDAnalysis/auxiliary/XVG.py

@@ -226,9 +226,13 @@ def _go_to_step(self, i):
 
         Parameters
         ----------
-        i : int
+        i: int
             Step number (0-indexed) to move to
 
+        Returns
+        -------
+        :class:`XVGStep`
+
         Raises
         ------
         ValueError

package/MDAnalysis/coordinates/CRD.py

@@ -98,11 +98,14 @@ def _read_first_frame(self):
     def Writer(self, filename, **kwargs):
         """Returns a CRDWriter for *filename*.
 
-        :Arguments:
-          *filename*
-              filename of the output CRD file
-
-        :Returns: :class:`CRDWriter`
+        Parameters
+        ----------
+        filename: str
+            filename of the output CRD file
+
+        Returns
+        -------
+        :class:`CRDWriter`
 
         """
         return CRDWriter(filename, **kwargs)

package/MDAnalysis/coordinates/DCD.py

@@ -51,8 +51,10 @@
    :class:`MDAnalysis.coordinates.LAMMPS.DCDReader` for NAMD
    trajectories.
 
-.. SeeAlso:: The :mod:`MDAnalysis.coordinates.LAMMPS` module provides
-             a more flexible DCD reader/writer.
+See Also
+--------
+The :mod:`MDAnalysis.coordinates.LAMMPS` module provides a more flexible DCD
+reader/writer.
 
 The classes in this module are the reference implementations for the
 Trajectory API.
@@ -209,29 +211,31 @@ def __init__(self, filename, n_atoms, start=0, step=1,
                  remarks="Created by DCDWriter", convert_units=None):
         """Create a new DCDWriter
 
-        :Arguments:
-         *filename*
-           name of output file
-         *n_atoms*
-           number of atoms in dcd file
-         *start*
-           starting timestep
-         *step*
-           skip between subsequent timesteps (indicate that *step* MD
-           integrator steps (!) make up one trajectory frame); default is 1.
-         *delta*
-           timestep (MD integrator time step (!), in AKMA units); default is
-           20.45482949774598 (corresponding to 1 ps).
-         *remarks*
-           comments to annotate dcd file
-         *dt*
-           **Override** *step* and *delta* so that the DCD records that *dt* ps
-           lie between two frames. (It sets *step* = 1 and *delta* = ``AKMA(dt)``.)
-           The default is ``None``, in which case *step* and *delta* are used.
-         *convert_units*
-           units are converted to the MDAnalysis base format; ``None`` selects
-           the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
-           (see :ref:`flags-label`)
+        Parameters
+        ----------
+        filename: str
+            name of output file
+        n_atoms: int
+            number of atoms in dcd file
+        start: int
+            starting timestep
+        step: int
+            skip between subsequent timesteps (indicate that *step* MD
+            integrator steps (!) make up one trajectory frame); default is 1.
+        delta: float
+            timestep (MD integrator time step (!), in AKMA units); default is
+            20.45482949774598 (corresponding to 1 ps).
+        remarks: str
+            comments to annotate dcd file
+        dt: float
+            **Override** *step* and *delta* so that the DCD records that
+            *dt* ps lie between two frames. (It sets *step* = 1 and
+            *delta* = ``AKMA(dt)``.) The default is ``None``, in which case
+            *step* and *delta* are used.
+        convert_units: bool
+            units are converted to the MDAnalysis base format; ``None`` selects
+            the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
+            (see :ref:`flags-label`)
 
        .. Note::
 
@@ -336,7 +340,9 @@ def write_next_timestep(self, ts=None):
     def convert_dimensions_to_unitcell(self, ts, _ts_order=Timestep._ts_order):
         """Read dimensions from timestep *ts* and return appropriate native unitcell.
 
-        .. SeeAlso:: :attr:`Timestep.dimensions`
+        See Also
+        --------
+        :attr:`Timestep.dimensions`
         """
         # unitcell is A,B,C,alpha,beta,gamma - convert to order expected by low level DCD routines
         lengths, angles = ts.dimensions[:3], ts.dimensions[3:]
@@ -510,23 +516,24 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
                    format='afc'):
         """Return a subset of coordinate data for an AtomGroup
 
-        :Arguments:
-            *asel*
-               :class:`~MDAnalysis.core.groups.AtomGroup` object
-               Defaults to None, in which case the full set of coordinate data
-               is returned.
-            *start*, *stop*, *step*
-               A range of the trajectory to access, with start being inclusive
-               and stop being exclusive.
-            *format*
-               the order/shape of the return data array, corresponding
-               to (a)tom, (f)rame, (c)oordinates all six combinations
-               of 'a', 'f', 'c' are allowed ie "fac" - return array
-               where the shape is (frame, number of atoms,
-               coordinates)
-        :Deprecated:
-            *skip*
-                Skip has been deprecated in favor of the standard keyword step.
+        Parameters
+        ----------
+        asel: :class:`~MDAnalysis.core.groups.AtomGroup`
+            The :class:`~MDAnalysis.core.groups.AtomGroup` to read the
+            coordinates from. Defaults to None, in which case the full set of
+            coordinate data is returned.
+        start, stop, step: int
+            A range of the trajectory to access, with start being inclusive
+            and stop being exclusive.
+        format: str
+            the order/shape of the return data array, corresponding
+            to (a)tom, (f)rame, (c)oordinates all six combinations
+            of 'a', 'f', 'c' are allowed ie "fac" - return array
+            where the shape is (frame, number of atoms,
+            coordinates)
+
+        .. deprecated:: 0.016.0
+            *skip* has been deprecated in favor of the standard keyword step.
         """
         if skip is not None:
             step = skip
@@ -553,15 +560,15 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
     def correl(self, timeseries, start=None, stop=None, step=None, skip=None):
         """Populate a TimeseriesCollection object with timeseries computed from the trajectory
 
-        :Arguments:
-            *timeseries*
-               :class:`MDAnalysis.core.Timeseries.TimeseriesCollection`
-            *start, stop, step*
-               A subset of the trajectory to use, with start being inclusive
-               and stop being exclusive.
-        :Deprecated:
-            *skip*
-                Skip has been deprecated in favor of the standard keyword step.
+        Parameters
+        ----------
+        timeseries: :class:`MDAnalysis.core.Timeseries.TimeseriesCollection`
+        start, stop, step: int
+            A subset of the trajectory to use, with start being inclusive and
+            stop being exclusive.
+
+        .. deprecated:: 0.16.0
+            *skip* has been deprecated in favor of the standard keyword step.
         """
         if skip is not None:
             step = skip
@@ -590,34 +597,38 @@ def Writer(self, filename, **kwargs):
 
         All values can be changed through keyword arguments.
 
-        :Arguments:
-          *filename*
-              filename of the output DCD trajectory
-        :Keywords:
-          *n_atoms*
-              number of atoms
-          *start*
-              number of the first recorded MD step
-          *step*
-              indicate that *step* MD steps (!) make up one trajectory frame
-          *delta*
-              MD integrator time step (!), in AKMA units
-          *dt*
-             **Override** *step* and *delta* so that the DCD records that *dt* ps
-             lie between two frames. (It sets *step* = 1 and *delta* = ``AKMA(dt)``.)
-             The default is ``None``, in which case *step* and *delta* are used.
-          *remarks*
-              string that is stored in the DCD header [XXX -- max length?]
-
-        :Returns: :class:`DCDWriter`
+        Parameters
+        ----------
+        filename: str
+            filename of the output DCD trajectory
+        n_atoms: int
+            number of atoms
+        start: int
+            number of the first recorded MD step
+        step: int
+            indicate that *step* MD steps (!) make up one trajectory frame
+        delta: float
+            MD integrator time step (!), in AKMA units
+        dt: float
+            **Override** *step* and *delta* so that the DCD records that
+            *dt* ps lie between two frames. (It sets *step* = 1 and
+            *delta* = ``AKMA(dt)``.) The default is ``None``, in which case
+            *step* and *delta* are used.  *remarks* string that is stored in
+            the DCD header
+
+        Returns
+        -------
+        :class:`DCDWriter`
 
         .. Note::
 
            The keyword arguments set the low-level attributes of the DCD
            according to the CHARMM format. The time between two frames would be
            *delta* * *step* !
 
-        .. SeeAlso:: :class:`DCDWriter` has detailed argument description
+        See Also
+        --------
+        :class:`DCDWriter` has detailed argument description
         """
         n_atoms = kwargs.pop('n_atoms', self.n_atoms)
         kwargs.setdefault('start', self.start_timestep)

package/MDAnalysis/coordinates/GRO.py

@@ -189,11 +189,14 @@ def _read_first_frame(self):
     def Writer(self, filename, **kwargs):
         """Returns a CRDWriter for *filename*.
 
-        :Arguments:
-          *filename*
+        Parameters
+        ----------
+        filename: str
             filename of the output GRO file
 
-        :Returns: :class:`GROWriter`
+        Returns
+        -------
+        :class:`GROWriter`
 
         """
         return GROWriter(filename, **kwargs)
@@ -240,9 +243,13 @@ class GROWriter(base.WriterBase):
     def __init__(self, filename, convert_units=None, **kwargs):
         """Set up a GROWriter with a precision of 3 decimal places.
 
-        :Arguments:
-           *filename*
-              output filename
+        Parameters
+        ----------
+        filename: str
+            output filename
+        convert_units: bool
+            units are converted to the MDAnalysis base format; ``None`` selects
+            the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
         """
         self.filename = util.filename(filename, ext='gro')
 
@@ -253,13 +260,13 @@ def __init__(self, filename, convert_units=None, **kwargs):
     def write(self, selection, frame=None):
         """Write selection at current trajectory frame to file.
 
-        :Arguments:
-          selection
-              MDAnalysis AtomGroup (selection or Universe.atoms)
-              or also Universe
-        :Keywords:
-          frame
-              optionally move to frame number *frame*
+        Parameters
+        ----------
+        selection:
+            The :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`Universe`
+            to write
+        frame: int
+            optionally move to frame number *frame*
 
         The GRO format only allows 5 digits for resid and atom
         number. If these number become larger than 99,999 then this

package/MDAnalysis/coordinates/MOL2.py

@@ -242,12 +242,13 @@ def __init__(self, filename, n_atoms=None,
                  convert_units=None):
         """Create a new MOL2Writer
 
-        :Arguments:
-         *filename*
-           name of output file
-         *convert_units*
-           units are converted to the MDAnalysis base format; ``None`` selects
-           the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
+        Parameters
+        ----------
+        filename: str
+            name of output file
+        convert_units: bool
+            units are converted to the MDAnalysis base format; ``None`` selects
+            the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
         """
         self.filename = filename
         if convert_units is None: