From e3f32147270ee7aebfd3220e2a53adf0ddf36465 Mon Sep 17 00:00:00 2001
From: Nick Papior <nickpapior@gmail.com>
Date: Thu, 10 Oct 2024 22:42:44 +0200
Subject: [PATCH] chore: refactored layouts of code

Signed-off-by: Nick Papior <nickpapior@gmail.com>
---
 src/sisl/io/tbtrans/pht.py               |  2 ++
 src/sisl/io/tbtrans/tbt.py               |  2 +-
 src/sisl/physics/_brillouinzone_apply.py | 18 ++++++------------
 src/sisl/physics/brillouinzone.py        | 21 +++++++++++----------
 src/sisl/physics/densitymatrix.py        |  2 +-
 5 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/src/sisl/io/tbtrans/pht.py b/src/sisl/io/tbtrans/pht.py
index 40f4479d5..842c80e75 100644
--- a/src/sisl/io/tbtrans/pht.py
+++ b/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)
 
diff --git a/src/sisl/io/tbtrans/tbt.py b/src/sisl/io/tbtrans/tbt.py
index 6b08381cd..f5f13c0a9 100644
--- a/src/sisl/io/tbtrans/tbt.py
+++ b/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:
diff --git a/src/sisl/physics/_brillouinzone_apply.py b/src/sisl/physics/_brillouinzone_apply.py
index 64a103e56..53dec1b3c 100644
--- a/src/sisl/physics/_brillouinzone_apply.py
+++ b/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
diff --git a/src/sisl/physics/brillouinzone.py b/src/sisl/physics/brillouinzone.py
index da3fa8545..4c7ad1711 100644
--- a/src/sisl/physics/brillouinzone.py
+++ b/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
 
diff --git a/src/sisl/physics/densitymatrix.py b/src/sisl/physics/densitymatrix.py
index 87b216e41..eddab3586 100644
--- a/src/sisl/physics/densitymatrix.py
+++ b/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.