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doc: fixed documentation for missing space
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Signed-off-by: Nick Papior <[email protected]>
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zerothi committed Jun 16, 2019
1 parent 91ce726 commit cc0e705
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Showing 27 changed files with 133 additions and 133 deletions.
2 changes: 1 addition & 1 deletion sisl/_help.py
Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@ def array_replace(array, *replace, **kwargs):
----------
array : ndarray
array in which to replace values from `replace`
replace: tuple
replace : tuple
replacement values, if `replace` is a tuple, it will be interpreted as
``array[replace[0]] = replace[1]``.
other : val
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2 changes: 1 addition & 1 deletion sisl/_namedindex.py
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ def merge(self, other, offset=0, duplicate="raise"):
the object to merge names(+indices) with
offset : int, optional
`other` will have `offset` added to all indices before merge is done.
duplicate: {"raise", "union", "left", "right", "omit"}
duplicate : {"raise", "union", "left", "right", "omit"}
Selects the default behaviour in case of name conflict.
Default ("raise") is to raise a ValueError in the case of conflict.
If "union", each name will contain indices from both `self` and `other`.
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6 changes: 3 additions & 3 deletions sisl/geom/nanotube.py
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Expand Up @@ -14,11 +14,11 @@ def nanotube(bond, atom=None, chirality=(1, 1)):
Parameters
----------
bond: float
bond : float
length between atoms in nano-tube
atom: Atom(6)
atom : Atom(6)
nanotube atoms
chirality: (int, int)
chirality : (int, int)
chirality of nanotube (n, m)
"""
if atom is None:
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14 changes: 7 additions & 7 deletions sisl/geometry.py
Original file line number Diff line number Diff line change
Expand Up @@ -72,9 +72,9 @@ class Geometry(SuperCellChild):
the supercell describing the periodicity of the
geometry
no
n_s: int
n_s : int
total number of supercells in the supercell
no_s: int
no_s : int
total number of orbitals in the geometry times number of supercells
Parameters
Expand Down Expand Up @@ -2907,7 +2907,7 @@ def o2a(self, io, unique=False):
Parameters
----------
io: array_like
io : array_like
List of indices to return the atoms for
unique : bool, optional
If True only return the unique atoms.
Expand Down Expand Up @@ -3482,16 +3482,16 @@ def ArgumentParser(self, p=None, *args, **kwargs):
Parameters
----------
parser: ArgumentParser, optional
parser : ArgumentParser, optional
in case the arguments should be added to a specific parser. It defaults
to create a new.
limit_arguments: bool, optional
limit_arguments : bool, optional
If ``False`` additional options will be created which are similar to other options.
For instance ``--repeat-x`` which is equivalent to ``--repeat x``.
Default `True`.
short: bool, optional
short : bool, optional
Create short options for a selected range of options.
positional_out: bool, optional
positional_out : bool, optional
If ``True``, adds a positional argument which acts as --out. This may be handy if only the geometry is in the argument list.
"""
limit_args = kwargs.get('limit_arguments', True)
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20 changes: 10 additions & 10 deletions sisl/grid.py
Original file line number Diff line number Diff line change
Expand Up @@ -215,13 +215,13 @@ def set_bc(self, boundary=None, a=None, b=None, c=None):
Parameters
----------
boundary: (3, 2) or (3, ) or int, optional
boundary : (3, 2) or (3, ) or int, optional
boundary condition for all boundaries (or the same for all)
a: int or list of int, optional
a : int or list of int, optional
boundary condition for the first unit-cell vector direction
b: int or list of int, optional
b : int or list of int, optional
boundary condition for the second unit-cell vector direction
c: int or list of int, optional
c : int or list of int, optional
boundary condition for the third unit-cell vector direction
Raises
Expand Down Expand Up @@ -400,7 +400,7 @@ def remove_part(self, idx, axis, above):
for ``above=False`` grid[idx:,...]
axis : int
the axis segment from which we retain the indices `idx`
above: bool
above : bool
if ``True`` will retain the grid:
``grid[:idx,...]``
else it will retain the grid:
Expand All @@ -421,7 +421,7 @@ def sub_part(self, idx, axis, above):
for ``above=False`` grid[:idx,...]
axis : int
the axis segment from which we retain the indices `idx`
above: bool
above : bool
if ``True`` will retain the grid:
``grid[idx:,...]``
else it will retain the grid:
Expand Down Expand Up @@ -1180,15 +1180,15 @@ def ArgumentParser(self, p=None, *args, **kwargs):
Parameters
----------
p: ArgumentParser, None
p : ArgumentParser, None
in case the arguments should be added to a specific parser. It defaults
to create a new.
limit_arguments: bool, True
limit_arguments : bool, True
If `False` additional options will be created which are similar to other options.
For instance `--repeat-x` which is equivalent to `--repeat x`.
short: bool, False
short : bool, False
Create short options for a selected range of options
positional_out: bool, False
positional_out : bool, False
If `True`, adds a positional argument which acts as --out. This may be handy if only the geometry is in the argument list.
"""
limit_args = kwargs.get('limit_arguments', True)
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2 changes: 1 addition & 1 deletion sisl/io/ham.py
Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ def write_geometry(self, geom, fmt='.8f', **kwargs):
Parameters
----------
geom: Geometry
geom : Geometry
The geometry we wish to write
"""

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4 changes: 2 additions & 2 deletions sisl/io/sile.py
Original file line number Diff line number Diff line change
Expand Up @@ -440,7 +440,7 @@ def ArgumentParser(self, p=None, *args, **kwargs):
Parameters
----------
p: ArgumentParser
p : ArgumentParser
the argument parser to add the arguments to.
"""
raise NotImplementedError("The ArgumentParser of '"+self.__class__.__name__+"' has not been implemented yet.")
Expand All @@ -450,7 +450,7 @@ def ArgumentParser_out(self, p=None, *args, **kwargs):
Parameters
----------
p: ArgumentParser
p : ArgumentParser
the argument parser to add the arguments to.
"""
pass
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2 changes: 1 addition & 1 deletion sisl/io/xsf.py
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ def read_geometry(self, data=False):
Parameters
----------
data: bool, optional
data : bool, optional
in case the XSF file has auxiliary data, return that as well.
"""
# Prepare containers...
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14 changes: 7 additions & 7 deletions sisl/messages.py
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def deprecate(message):
Parameters
----------
message: str
message : str
"""
warnings.warn_explicit(message, SislDeprecation, 'dep', 0, registry=_sisl_warn_registry)

Expand All @@ -68,12 +68,12 @@ def warn(message, category=None, register=False):
Parameters
----------
message: str, Warning
message : str, Warning
the warning to issue, default to issue a `SislWarning`
category: Warning, optional
category : Warning, optional
the category of the warning to issue. Default to `SislWarning', unless `message` is
a subclass of `Warning`
register: bool, optional
register : bool, optional
whether the warning is registered to limit the number of times this is output
"""
if isinstance(message, Warning):
Expand All @@ -91,12 +91,12 @@ def info(message, category=None, register=False):
Parameters
----------
message: str, Warning
message : str, Warning
the information to issue, default to issue a `SislInfo`
category: Warning, optional
category : Warning, optional
the category of the warning to issue. Default to `SislInfo', unless `message` is
a subclass of `Warning`
register: bool, optional
register : bool, optional
whether the information is registered to limit the number of times this is output
"""
if isinstance(message, Warning):
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2 changes: 1 addition & 1 deletion sisl/physics/bloch.py
Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ def __call__(self, func, k, *args, **kwargs):
k-point to be unfolded
*args : list
arguments passed directly to `func`
**kwargs: dict
**kwargs : dict
keyword arguments passed directly to `func`
Returns
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4 changes: 2 additions & 2 deletions sisl/physics/brillouinzone.py
Original file line number Diff line number Diff line change
Expand Up @@ -220,9 +220,9 @@ def parametrize(self, sc, func, N, *args, **kwargs):
a k-point in 3 dimensions.
N : int
number of k-points generated using the parameterization
args: list of arguments
args : list of arguments
arguments passed directly to `func`
kwargs: dictionary of arguments
kwargs : dictionary of arguments
keyword arguments passed directly to `func`
"""
k = np.empty([N, 3], np.float64)
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2 changes: 1 addition & 1 deletion sisl/physics/densitymatrix.py
Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def density(self, grid, spinor=None, tol=1e-7, eta=False):
tol : float, optional
DM tolerance for accepted values. For all density matrix elements with absolute values below
the tolerance, they will be treated as strictly zeros.
eta: bool, optional
eta : bool, optional
show a progressbar on stdout
"""
try:
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44 changes: 22 additions & 22 deletions sisl/physics/distribution.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,11 +57,11 @@ def get_distribution(method, smearing=0.1, x0=0.):
Parameters
----------
method: {'gaussian', 'lorentzian', 'fermi_dirac', 'bose_einstein', 'step_function', 'heaviside'}
method : {'gaussian', 'lorentzian', 'fermi_dirac', 'bose_einstein', 'step_function', 'heaviside'}
distribution function
smearing: float, optional
smearing : float, optional
smearing parameter for methods that have a smearing
x0: float, optional
x0 : float, optional
maximum/middle of the distribution function
Returns
Expand Down Expand Up @@ -95,11 +95,11 @@ def gaussian(x, sigma=0.1, x0=0.):
Parameters
----------
x: array_like
x : array_like
points at which the Gaussian distribution is calculated
sigma: float, optional
sigma : float, optional
spread of the Gaussian
x0: float, optional
x0 : float, optional
maximum position of the Gaussian
Returns
Expand All @@ -119,11 +119,11 @@ def lorentzian(x, gamma=0.1, x0=0.):
Parameters
----------
x: array_like
x : array_like
points at which the Lorentzian distribution is calculated
gamma: float, optional
gamma : float, optional
spread of the Lorentzian
x0: float, optional
x0 : float, optional
maximum position of the Lorentzian
Returns
Expand All @@ -142,11 +142,11 @@ def fermi_dirac(E, kT=0.1, mu=0.):
Parameters
----------
E: array_like
E : array_like
energy evaluation points
kT: float, optional
kT : float, optional
temperature broadening
mu: float, optional
mu : float, optional
chemical potential
Returns
Expand All @@ -165,11 +165,11 @@ def bose_einstein(E, kT=0.1, mu=0.):
Parameters
----------
E: array_like
E : array_like
energy evaluation points
kT: float, optional
kT : float, optional
temperature broadening
mu: float, optional
mu : float, optional
chemical potential
Returns
Expand All @@ -190,11 +190,11 @@ def cold(E, kT=0.1, mu=0.):
Parameters
----------
E: array_like
E : array_like
energy evaluation points
kT: float, optional
kT : float, optional
temperature broadening
mu: float, optional
mu : float, optional
chemical potential
Returns
Expand Down Expand Up @@ -224,9 +224,9 @@ def heaviside(x, x0=0.):
Parameters
----------
x: array_like
x : array_like
points at which the Heaviside step distribution is calculated
x0: float, optional
x0 : float, optional
step position
Returns
Expand Down Expand Up @@ -260,9 +260,9 @@ def step_function(x, x0=0.):
Parameters
----------
x: array_like
x : array_like
points at which the step distribution is calculated
x0: float, optional
x0 : float, optional
step position
Returns
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8 changes: 4 additions & 4 deletions sisl/physics/dynamicalmatrix.py
Original file line number Diff line number Diff line change
Expand Up @@ -350,7 +350,7 @@ def velocity(self, k=(0, 0, 0), **kwargs):
----------
k : array_like, optional
k-point at which the velocities are calculated
**kwargs: optional
**kwargs : optional
additional parameters passed to the `eigenmode` routine
See Also
Expand All @@ -368,7 +368,7 @@ def displacement(self, k=(0, 0, 0), **kwargs):
----------
k : array_like, optional
k-point at which the displacement are calculated
**kwargs: optional
**kwargs : optional
additional parameters passed to the `eigenmode` routine
See Also
Expand All @@ -391,7 +391,7 @@ def DOS(self, E, k=(0, 0, 0), distribution='gaussian', **kwargs):
distribution : func or str, optional
a function that accepts :math:`E-\hbar\omega` as argument and calculates the
distribution function.
**kwargs: optional
**kwargs : optional
additional parameters passed to the `eigenvalue` routine
See Also
Expand All @@ -415,7 +415,7 @@ def PDOS(self, E, k=(0, 0, 0), distribution='gaussian', **kwargs):
distribution : func or str, optional
a function that accepts :math:`E-\epsilon` as argument and calculates the
distribution function.
**kwargs: optional
**kwargs : optional
additional parameters passed to the `eigenmode` routine
See Also
Expand Down
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