Python maintenance

doc/sphinx/system_setup.rst

@@ -158,7 +158,7 @@ Lees--Edwards boundary conditions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Lees--Edwards boundary conditions (LEbc) are special periodic boundary
-conditions to simulation systems under shear stress :cite:`lees72a`.
+conditions to simulate systems under shear stress :cite:`lees72a`.
 Periodic images of particles across the shear boundary appear with a
 time-dependent position offset. When a particle crosses the shear boundary,
 it appears to the opposite side of the simulation box with a position offset
@@ -227,13 +227,13 @@ The properties of the cell system can be accessed by
 
 * :py:attr:`~espressomd.cellsystem.CellSystem.node_grid`
 
- (int[3]) 3D node grid for real space domain decomposition (optional, if
+ 3D node grid for real space domain decomposition (optional, if
  unset an optimal set is chosen automatically). The domain decomposition
  can be visualized with :file:`samples/visualization_cellsystem.py`.
 
 * :py:attr:`~espressomd.cellsystem.CellSystem.skin`
 
- (float) Skin for the Verlet list. This value has to be set, otherwise the simulation will not start.
+ Skin for the Verlet list. This value has to be set, otherwise the simulation will not start.
 
 Details about the cell system can be obtained by :meth:`espressomd.system.System.cell_system.get_state() <espressomd.cellsystem.CellSystem.get_state>`:
 

src/python/espressomd/lees_edwards.py

@@ -22,9 +22,23 @@
 @script_interface_register
 class LeesEdwards(ScriptInterfaceHelper):
 
- """Interface to the Lees-Edwards boundary conditions.
+ """
+ Interface to the :ref:`Lees-Edwards boundary conditions`.
 
- See documentation.
+ Attributes
+ ----------
+ protocol : :obj:`object`
+ Lees--Edwards protocol.
+ shear_velocity: :obj:`float`
+ Current shear velocity.
+ pos_offset : :obj:`float`
+ Current position offset
+ shear_direction : :obj:`int`
+ Shear direction: 0 for the *x*-axis, 1 for the *y*-axis,
+ 2 for the *z*-axis.
+ shear_plane_normal : :obj:`int`
+ Shear plane normal: 0 for the *x*-axis, 1 for the *y*-axis,
+ 2 for the *z*-axis.
 
  """
 
@@ -34,25 +48,21 @@ class LeesEdwards(ScriptInterfaceHelper):
 @script_interface_register
 class Off(ScriptInterfaceHelper):
 
- """Lees-Edwards protocol resulting in un-shifted boundaries."""
+ """Lees--Edwards protocol resulting in un-shifted boundaries."""
  _so_name = "LeesEdwards::Off"
 
 
 @script_interface_register
 class LinearShear(ScriptInterfaceHelper):
 
- """Lees-Edwards protocol for linear shear.
+ """Lees--Edwards protocol for linear shear.
 
  Parameters
  ----------
- shear_direction
- Cartesian coordinate of the shear direction (0=x, 1=y, 2=z)
- shear_plane_normal
- Cartesian coordinate of the shear plane normal
- initial_pos_offset
- Positional offset at the Lees-Edwards boundary at t=0
- shear_velocity
- Shear velocity (velocity jump) across the Lees-Edwards boundary
+ initial_pos_offset : :obj:`float`
+ Positional offset at the Lees--Edwards boundary at t=0.
+ shear_velocity : :obj:`float`
+ Shear velocity (velocity jump) across the Lees--Edwards boundary.
 
  """
  _so_name = "LeesEdwards::LinearShear"
@@ -61,21 +71,16 @@ class LinearShear(ScriptInterfaceHelper):
 @script_interface_register
 class OscillatoryShear(ScriptInterfaceHelper):
 
- """Lees-Edwards protocol for oscillatory shear.
+ """Lees--Edwards protocol for oscillatory shear.
 
  Parameters
  ----------
- shear_direction
- Cartesian coordinate of the shear direction (0=x, 1=y, 2=z)
- shear_plane_normal
- Cartesian coordinate of the shear plane normal
- amplitude
- Maximum amplitude of the positional offset at the Lees-Edwards boundary
- frequency
- Frequency of the shear
- time_0
- Time offset of the oscillation
-
+ amplitude : :obj:`float`
+ Maximum amplitude of the positional offset at the Lees--Edwards boundary.
+ omega : :obj:`float`
+ Radian frequency of the oscillation.
+ time_0 : :obj:`float`
+ Time offset of the oscillation.
 
  """
  _so_name = "LeesEdwards::OscillatoryShear"

testsuite/scripts/importlib_wrapper.py

@@ -52,23 +52,23 @@ def configure_and_import(filepath,
 
  Parameters
  ----------
- filepath : str
+ filepath : :obj:`str`
  python script to import
- gpu : bool
+ gpu : :obj:`bool`
  whether GPU is necessary or not
- substitutions : function
+ substitutions : :obj:`function`
  custom text replacement operation (useful to edit out calls to the
  OpenGL or Mayavi visualizers' ``run()`` method)
- cmd_arguments : list
+ cmd_arguments : :obj:`list`
  command line arguments, i.e. sys.argv without the script path
- script_suffix : str
+ script_suffix : :obj:`str`
  suffix to append to the configured script (useful when a single
  module is being tested by multiple tests in parallel)
- mock_visualizers : bool
- if ``True``, substitute ES visualizers with `Mock()` classes in case
- of `ImportError()` (use ``False`` if an `ImportError()` is relevant
+ mock_visualizers : :obj:`bool`
+ if ``True``, substitute ES visualizers with ``Mock`` classes in case
+ of ``ImportError`` (use ``False`` if an ``ImportError`` is relevant
  to your test)
- move_to_script_dir : bool
+ move_to_script_dir : :obj:`bool`
  if ``True``, move to the script's directory (useful when the script
  needs to load files hardcoded as relative paths, or when files are
  generated and need cleanup); this is enabled by default
@@ -203,12 +203,12 @@ def substitute_variable_values(code, strings_as_is=False, keep_original=True,
 
  Parameters
  ----------
- code : str
+ code : :obj:`str`
  Source code to edit.
- strings_as_is : bool
+ strings_as_is : :obj:`bool`
  If ``True``, consider all values in \*\*parameters are strings and
  substitute them in-place without formatting by ``repr()``.
- keep_original : bool
+ keep_original : :obj:`bool`
  Keep the original value (e.g. ``N = 10; _N__original = 1000``), helps
  with debugging.
  \*\*parameters :
@@ -569,9 +569,9 @@ def visit_ImportFrom(self, node):
 
 def mock_es_visualization(code):
  """
- Replace ``import espressomd.visualization_<backend>`` by a ``MagicMock()``
+ Replace ``import espressomd.visualization_<backend>`` by a ``MagicMock``
  when the visualization module is unavailable, by catching the
- ``ImportError()`` exception. Please note that ``espressomd.visualization``
+ ``ImportError`` exception. Please note that ``espressomd.visualization``
  is deferring the exception, thus requiring additional checks.
 
  Import aliases are supported, however please don't use