chore: refactored layouts of code

Signed-off-by: Nick Papior <nickpapior@gmail.com>

src/sisl/io/tbtrans/pht.py

@@ -55,6 +55,8 @@ def kT(self, elec: ElecType) -> float:
  "shot_noise",
  "noise_power",
 ):
+ # TODO change this such that the intrinsic details
+ # are separated.
  setattr(phtncSilePHtrans, _name, None)
  setattr(phtavncSilePHtrans, _name, None)
 

src/sisl/io/tbtrans/tbt.py

@@ -117,7 +117,7 @@ class tbtncSileTBtrans(_devncSileTBtrans):
  are in fortran indexing (1-based), everything is returned as Python indexing (0-based)
  when using Python scripts.
 
- The mathematical notation described in :ref:`this document <math_convention>`
+ The mathematical notation described :ref:`here <math_convention>`
  will be used throughout.
 
  A word on DOS normalization:

src/sisl/physics/_brillouinzone_apply.py

@@ -12,15 +12,9 @@
 from itertools import zip_longest
 
 import numpy as np
+import xarray
 from numpy import cross, pi
 
-try:
- import xarray
-
- _has_xarray = True
-except ImportError:
- _has_xarray = False
-
 try:
  import pathos
 
@@ -196,6 +190,8 @@ def __getattr__(self, key):
 
 @set_module("sisl.physics")
 class IteratorApply(BrillouinZoneParentApply):
+ """Iterator for calculations *while iterating*."""
+
  def __str__(self, message="iter"):
  return super().__str__(message)
 
@@ -280,7 +276,6 @@ def dispatch(self, method):
  def func(*args, **kwargs):
  for _ in iter_func(*args, **kwargs):
  pass
- return None
 
  return func
 
@@ -303,7 +298,7 @@ def func(*args, **kwargs):
 
  @wraps(method)
  def func(*args, **kwargs):
- return [v for v in iter_func(*args, **kwargs)]
+ return list(iter_func(*args, **kwargs))
 
  return func
 
@@ -602,9 +597,8 @@ def func(*args, coords=None, dims=None, name=method.__name__, **kwargs):
 apply_dispatch.register("none", NoneApply)
 apply_dispatch.register("list", ListApply)
 apply_dispatch.register("oplist", OpListApply)
-if _has_xarray:
- apply_dispatch.register("dataarray", XArrayApply)
- apply_dispatch.register("xarray", XArrayApply)
+apply_dispatch.register("dataarray", XArrayApply)
+apply_dispatch.register("xarray", XArrayApply)
 
 # Remove refernce
 del apply_dispatch

src/sisl/physics/brillouinzone.py

@@ -266,15 +266,23 @@ class BrillouinZone:
 
  Parameters
  ----------
- parent : object or array_like
+ parent : object or array-like
  An object with associated ``parent.cell`` and ``parent.rcell`` or
  an array of floats which may be turned into a `Lattice`
- k : array_like, optional
+ k : array-like, optional
  k-points that this Brillouin zone represents
- weight : scalar or array_like, optional
+ weight : scalar or array-like, optional
  weights for the k-points.
+
  """
 
+ apply = BrillouinZoneDispatcher(
+ "apply",
+ # Do not allow class dispatching
+ type_dispatcher=None,
+ obj_getattr=lambda obj, key: getattr(obj.parent, key),
+ )
+
  def __init__(self, parent, k=None, weight=None):
  self.set_parent(parent)
  # define a bz_attr as though it has not been set
@@ -291,13 +299,6 @@ def __init__(self, parent, k=None, weight=None):
  weight = 1.0 / len(self._k)
  self._w[:] = weight
 
- apply = BrillouinZoneDispatcher(
- "apply",
- # Do not allow class dispatching
- type_dispatcher=None,
- obj_getattr=lambda obj, key: getattr(obj.parent, key),
- )
-
  def set_parent(self, parent) -> None:
  """Update the parent associated to this object
 

src/sisl/physics/densitymatrix.py

@@ -370,7 +370,7 @@ def spin_align(self, vec: SeqFloat, atoms: AtomsIndex = None):
  def mulliken(self, projection: Literal["orbital", "atom"] = "orbital"):
  r""" Calculate Mulliken charges from the density matrix
 
- See :ref:`this document <math_convention>` for details on the mathematical notation.
+ See :ref:`here <math_convention>` for details on the mathematical notation.
  Matrices :math:`\boldsymbol\rho` and :math:`\mathbf S` are density
  and overlap matrices, respectively.