Refactor non-standard object identity test

changes/996.dev.rst

@@ -0,0 +1,3 @@
+Refactor non-standard object identity tests.
+
+Refactors `not object is None` to `object is not None` to improve readability and adhere to the standard.

src/sisl/_category.py

@@ -371,7 +371,7 @@ def _(self, other):
 
 def _composite_name(sep):
     def getter(self):
-        if not self._name is None:
+        if self._name is not None:
             return self._name
 
         # Name is unset, we simply return the other parts

src/sisl/_core/_ufuncs_geometry.py

@@ -395,7 +395,7 @@ class NestedList:
 
         def __init__(geometry, idx=None, sort=False):
             geometry._idx = []
-            if not idx is None:
+            if idx is not None:
                 geometry.append(idx, sort)
 
         def append(geometry, idx, sort=False):

src/sisl/_core/_ufuncs_grid.py

@@ -147,7 +147,7 @@ def sub(grid: Grid, idx: Union[int, Sequence[int]], axis: CellAxis) -> Grid:
     shift_geometry = False
     if len(idx) > 1:
         if np.allclose(np.diff(idx), 1):
-            shift_geometry = not grid.geometry is None
+            shift_geometry = grid.geometry is not None
 
     if shift_geometry:
         out = grid._copy_sub(len(idx), axis)
@@ -193,7 +193,7 @@ def append(grid: Grid, other: GridLike, axis: CellAxis) -> Grid:
     shape[axis] += other.shape[axis]
     d = grid._sc_geometry_dict()
     if "geometry" in d:
-        if not other.geometry is None:
+        if other.geometry is not None:
             d["geometry"] = d["geometry"].append(other.geometry, axis)
     else:
         d["geometry"] = other.geometry

src/sisl/_core/grid.py

@@ -402,7 +402,7 @@ def _sc_geometry_dict(self):
         """Internal routine for copying the Lattice and Geometry"""
         d = dict()
         d["lattice"] = self.lattice.copy()
-        if not self.geometry is None:
+        if self.geometry is not None:
             d["geometry"] = self.geometry.copy()
         return d
 
@@ -429,7 +429,7 @@ def _copy_sub(self, n, axis, scale_geometry=False):
         grid = self.__class__(shape, dtype=self.dtype, **self._sc_geometry_dict())
         # Update cell shape (the cell is smaller now)
         grid.set_lattice(cell)
-        if scale_geometry and not self.geometry is None:
+        if scale_geometry and self.geometry is not None:
             geom = self.geometry.copy()
             fxyz = geom.fxyz.copy()
             geom.set_lattice(grid.lattice)
@@ -847,7 +847,7 @@ def __str__(self):
             s += f"commensurate: [{l[0]} {l[1]} {l[2]}]"
         else:
             s += "{}".format(str(self.lattice).replace("\n", "\n "))
-        if not self.geometry is None:
+        if self.geometry is not None:
             s += ",\n {}".format(str(self.geometry).replace("\n", "\n "))
         return f"{s}\n}}"
 

src/sisl/_core/lattice.py

@@ -313,7 +313,7 @@ def conv(v):
             self._bc = _a.fulli([3, 2], getitem("Unknown"))
         old = self._bc.copy()
 
-        if not boundary is None:
+        if boundary is not None:
             if isinstance(boundary, (Integral, str, bool)):
                 try:
                     getitem(boundary)
@@ -450,9 +450,9 @@ def set_nsc(
         c : int, optional
            number of supercells in the third unit-cell vector direction
         """
-        if not nsc is None:
+        if nsc is not None:
             for i in range(3):
-                if not nsc[i] is None:
+                if nsc[i] is not None:
                     self.nsc[i] = nsc[i]
         if a:
             self.nsc[0] = a
@@ -601,7 +601,7 @@ def fit(self, xyz, axes: CellAxes = (0, 1, 2), atol: float = 0.05) -> Lattice:
         ireps = np.amax(ix, axis=0) - np.amin(ix, axis=0) + 1
 
         # Reduce the non-set axis
-        if not axes is None:
+        if axes is not None:
             axes = map(direction, listify(axes))
             for ax in (0, 1, 2):
                 if ax not in axes:
@@ -857,10 +857,10 @@ def _assert(m, v):
         else:
             idx = (self.sc_off[:, 0] == sc_off[0]).nonzero()[0]
 
-        if not sc_off[1] is None:
+        if sc_off[1] is not None:
             idx = idx[(self.sc_off[idx, 1] == sc_off[1]).nonzero()[0]]
 
-        if not sc_off[2] is None:
+        if sc_off[2] is not None:
             idx = idx[(self.sc_off[idx, 2] == sc_off[2]).nonzero()[0]]
 
         return idx

src/sisl/_core/sparse_geometry.py

@@ -1497,7 +1497,7 @@ def iter_nnz(self, atoms: AtomsIndex = None, orbitals=None):
         """
         if atoms is not None:
             orbitals = self.geometry.a2o(atoms, all=True)
-        elif not orbitals is None:
+        elif orbitals is not None:
             orbitals = _a.asarrayi(orbitals)
         if orbitals is None:
             yield from self._csr
@@ -1890,7 +1890,7 @@ def add(self, other, axis: Optional[int] = None, offset: Coord = (0, 0, 0)):
         transfer_idx = _a.arangei(self.geometry.no_s).reshape(-1, self.geometry.no)
         transfer_idx += _a.arangei(self.geometry.n_s).reshape(-1, 1) * other.geometry.no
         # Remove couplings along axis
-        if not axis is None:
+        if axis is not None:
             idx = (self.geometry.lattice.sc_off[:, axis] != 0).nonzero()[0]
             # Tell the routine to delete these indices
             transfer_idx[idx, :] = full_no_s + 1

src/sisl/_help.py

@@ -231,7 +231,7 @@ def array_replace(array, *replace, **kwargs):
     others = []
 
     for idx, val in replace:
-        if not val is None:
+        if val is not None:
             ar[idx] = val
         others.append(np.asarray(idx).ravel())
 

src/sisl/_namedindex.py

@@ -35,7 +35,7 @@ def __init__(self, name=None, index=None):
 
         if isinstance(name, str):
             self.add_name(name, index)
-        elif not name is None:
+        elif name is not None:
             for n, i in zip(name, index):
                 self.add_name(n, i)
 

src/sisl/geom/_category/_coord.py

@@ -247,11 +247,11 @@ def func(a, b):
             # Now we are ready to build our scheme
             if value.size == 2:
                 # do it twice
-                if not value[0] is None:
+                if value[0] is not None:
                     coord_ops.append(
                         create2(is_frac, is_abs, operator.ge, sdir, value[0])
                     )
-                if not value[1] is None:
+                if value[1] is not None:
                     coord_ops.append(
                         create2(is_frac, is_abs, operator.le, sdir, value[1])
                     )

src/sisl/geom/_category/_neighbors.py

@@ -113,7 +113,7 @@ def categorize(self, geometry: Geometry, atoms: AtomsIndex = None):
             return NullCategory()
 
         # Check if we have a condition
-        if not self._in is None:
+        if self._in is not None:
             # Get category of neighbors
             cat = self._in.categorize(geometry, geometry.asc2uc(idx))
             idx = [i for i, c in zip(idx, cat) if not isinstance(c, NullCategory)]

src/sisl/io/cube.py

@@ -298,7 +298,7 @@ def read_grid(self, imag=None) -> Grid:
             the imaginary part of the grid. If the geometries does not match
             an error will be raised.
         """
-        if not imag is None:
+        if imag is not None:
             if not isinstance(imag, Grid):
                 imag = Grid.read(imag)
 

src/sisl/io/openmx/omx.py

@@ -392,7 +392,7 @@ def _r_lattice_omx(self, *args, **kwargs):
         cell = np.empty([3, 3], np.float64)
 
         lc = self.get("Atoms.UnitVectors")
-        if not lc is None:
+        if lc is not None:
             for i in range(3):
                 cell[i, :] = [float(k) for k in lc[i].split()[:3]]
         else:

src/sisl/io/scaleup/ref.py

@@ -162,7 +162,7 @@ def read_geometry(self, *args, **kwargs) -> Geometry:
             ref = None
 
         restart = super().read_geometry()
-        if not ref is None:
+        if ref is not None:
             restart.lattice = Lattice(
                 np.dot(ref.lattice.cell, restart.lattice.cell.T), nsc=restart.nsc
             )

src/sisl/io/siesta/bands.py

@@ -164,7 +164,7 @@ def myplot(ax, title, x, y, E):
                         ax.plot(x, y[ib, :])
                     ax.set_ylabel("E-Ef [eV]")
                     ax.set_xlim(x.min(), x.max())
-                    if not E is None:
+                    if E is not None:
                         ax.set_ylim(E[0], E[1])
 
                 if b.shape[1] == 2:

src/sisl/io/siesta/binaries.py

@@ -836,7 +836,7 @@ def _xij2system(self, xij, geometry=None, **kwargs):
 
         def get_geom_handle(xij):
             atoms = self.read_basis(geometry=geometry, **kwargs)
-            if not atoms is None:
+            if atoms is not None:
                 return Geometry(np.zeros([len(atoms), 3]), atoms)
 
             N = len(xij)

src/sisl/io/siesta/eig.py

@@ -359,7 +359,7 @@ def myplot(ax, title, y, E, s):
                         ax.scatter(ik, y[:, ib], s=s)
                     ax.set_xlabel("k-index")
                     ax.set_xlim(-0.5, len(y) + 0.5)
-                    if not E is None:
+                    if E is not None:
                         ax.set_ylim(E[0], E[1])
 
                 if E.shape[0] == 2:

src/sisl/io/siesta/stdout.py

@@ -1732,15 +1732,15 @@ def _p(flag, found):
         if not (FOUND_SCF or FOUND_MD):
             # none of these are found
             # we request that user does not request any input
-            if (opt_iscf or (not iscf is None)) or (opt_imd or (not imd is None)):
+            if (opt_iscf or (iscf is not None)) or (opt_imd or (imd is not None)):
                 raise SileError(f"{self!s} does not contain MD/SCF charges")
 
         elif not FOUND_SCF:
-            if opt_iscf or (not iscf is None):
+            if opt_iscf or (iscf is not None):
                 raise SileError(f"{self!s} does not contain SCF charges")
 
         elif not FOUND_MD:
-            if opt_imd or (not imd is None):
+            if opt_imd or (imd is not None):
                 raise SileError(f"{self!s} does not contain MD charges")
 
         # if either are options they may hold

src/sisl/io/sile.py

@@ -258,7 +258,7 @@ def get_sile_class(filename, *args, **kwargs):
 
     # searchable rules
     eligible_rules = []
-    if cls is None and not cls_search is None:
+    if cls is None and cls_search is not None:
         # cls has not been set, and fcls is found
         # Figure out if fcls is a valid sile, if not
         # do nothing (it may be part of the file name)
@@ -1378,7 +1378,7 @@ def __init__(self, filename, mode="r", *args, **kwargs):
         comment = kwargs.pop("comment", None)
         if isinstance(comment, (list, tuple)):
             self._comment = list(comment)
-        elif not comment is None:
+        elif comment is not None:
             self._comment = [comment]
         else:
             self._comment = []

src/sisl/io/tbtrans/se.py

@@ -195,7 +195,7 @@ def info(self, elec=None):
         elec : str or int
            the electrode to request information from
         """
-        if not elec is None:
+        if elec is not None:
             elec = self._elec(elec)
 
         # Create a StringIO object to retain the information

src/sisl/io/tbtrans/tbt.py

@@ -484,7 +484,7 @@ def norm(self, atoms=None, orbitals=None, norm: NormType = "none") -> int:
                 NORM = geom.orbitals[a].sum()
             return NORM
 
-        if not orbitals is None:
+        if orbitals is not None:
             raise ValueError(
                 f"{self.__class__.__name__}.norm both atom and orbital cannot be specified!"
             )
@@ -528,7 +528,7 @@ def _DOS(self, DOS, atoms, orbitals, sum, norm) -> ndarray:
         if isinstance(orbitals, bool):
             if not orbitals:
                 orbitals = None
-        if not atoms is None and not orbitals is None:
+        if atoms is not None and orbitals is not None:
             raise ValueError(
                 "Both atoms and orbitals keyword in DOS request "
                 "cannot be specified, only one at a time."
@@ -1174,7 +1174,7 @@ def _sparse_data_to_matrix(self, data, isc=None, orbitals=None) -> csr_matrix:
         col = self._value("list_col") - 1
 
         # get subset orbitals
-        if not orbitals is None:
+        if orbitals is not None:
             orbitals = geom._sanitize_orbs(orbitals)
 
             # select values for all supercells
@@ -1222,7 +1222,7 @@ def _sparse_data_to_matrix(self, data, isc=None, orbitals=None) -> csr_matrix:
             for i in (0, 1, 2):
                 if nsc[i] == 1:
                     isc[i] = 0
-                if not isc[i] is None:
+                if isc[i] is not None:
                     nsc[i] = 1
 
             # Small function for creating the supercells allowed
@@ -2777,7 +2777,7 @@ def info(self, elec: Optional[ElecType] = None):
         elec : str or int
            the electrode to request information from
         """
-        if not elec is None:
+        if elec is not None:
             elec = self._elec(elec)
 
         # Create a StringIO object to retain the information
@@ -3234,7 +3234,7 @@ class DataDOS(argparse.Action):
             @collect_action
             @ensure_E
             def __call__(self, parser, ns, value, option_string=None):
-                if not value is None:
+                if value is not None:
                     # we are storing the spectral DOS
                     e = ns._tbt._elec(value)
                     if e not in ns._tbt.elecs:

src/sisl/io/tests/test_cube.py

@@ -46,16 +46,16 @@ def test_geometry(sisl_tmp):
     grid.write(f)
     read = grid.read(f)
     assert np.allclose(grid.grid, read.grid)
-    assert not grid.geometry is None
-    assert not read.geometry is None
+    assert grid.geometry is not None
+    assert read.geometry is not None
     assert grid.geometry == read.geometry
 
     # write in another unit
     grid.write(f, unit="nm")
     read = grid.read(f)
     assert np.allclose(grid.grid, read.grid)
-    assert not grid.geometry is None
-    assert not read.geometry is None
+    assert grid.geometry is not None
+    assert read.geometry is not None
     assert grid.geometry == read.geometry
 
 
@@ -75,8 +75,8 @@ def test_imaginary(sisl_tmp):
     read_i = grid.read(fi)
     read.grid = read.grid + 1j * read_i.grid
     assert np.allclose(grid.grid, read.grid)
-    assert not grid.geometry is None
-    assert not read.geometry is None
+    assert grid.geometry is not None
+    assert read.geometry is not None
     assert grid.geometry == read.geometry
 
     read = grid.read(fr, imag=fi)

src/sisl/io/tests/test_xsf.py

@@ -60,7 +60,7 @@ def test_xsf_geometry(sisl_tmp):
     grid = Grid(0.2, geometry=geom)
     grid.grid = np.random.rand(*grid.shape)
     grid.write(f)
-    assert not grid.geometry is None
+    assert grid.geometry is not None
 
 
 def test_xsf_imaginary(sisl_tmp):
@@ -73,7 +73,7 @@ def test_xsf_imaginary(sisl_tmp):
     grid = Grid(0.2, geometry=geom, dtype=np.complex128)
     grid.grid = np.random.rand(*grid.shape) + 1j * np.random.rand(*grid.shape)
     grid.write(f)
-    assert not grid.geometry is None
+    assert grid.geometry is not None
 
 
 def test_axsf_geoms(sisl_tmp):

src/sisl/physics/electron.py

@@ -1762,7 +1762,7 @@ def Sk(self, format=None):
                 }
                 for key in ("gauge",):
                     val = self.info.get(key, None)
-                    if not val is None:
+                    if val is not None:
                         opt[key] = val
                 return self.parent.Sk(**opt)
 

src/sisl/physics/hamiltonian.py

@@ -372,7 +372,7 @@ def eigenvalue(self, k: KPoint = (0, 0, 0), gauge: GaugeType = "lattice", **kwar
         for name in ("spin",):
             if name in kwargs:
                 info[name] = kwargs[name]
-        if not format is None:
+        if format is not None:
             info["format"] = format
         return EigenvalueElectron(e, self, **info)
 
@@ -413,7 +413,7 @@ def eigenstate(self, k: KPoint = (0, 0, 0), gauge: GaugeType = "lattice", **kwar
         for name in ("spin",):
             if name in kwargs:
                 info[name] = kwargs[name]
-        if not format is None:
+        if format is not None:
             info["format"] = format
         # Since eigh returns the eigenvectors [:, i] we have to transpose
         return EigenstateElectron(v.T, e, self, **info)