Enabled ... for atoms, orbitals arguments

This seems a bit more natural than None.

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

CHANGELOG.md

@@ -19,6 +19,12 @@ we hit release version 1.0.0.
       sisl.geom.graphene
 
 - added Nambu spin configuration, this is still experimental
+- enabled `...` when extracting slices of MD steps in siesta output
+  files.
+  Here it is the same as `:`. But it also allows
+  inline arguments: `read_scf(imd=...)` where `imd=:` is not
+  allowed, partly fixes #835
+- enabled `...` for `atoms=` arguments. Selects all atoms.
 
 ### Fixed
 - `projection` arguments of several functions has been streamlined
@@ -29,10 +35,6 @@ we hit release version 1.0.0.
   with *many* edges in the sparse matrix, but a perf. hit for very
   small TB matrices.
 - dtype removed from `Spin` class
-- enabled `...` when extracting slices of MD steps.
-  Here it is the same as `:`. But it also allows
-  inline arguments: `read_scf(imd=...)` where `imd=:` is not
-  allowed, partly fixes #835
 
 
 ## [0.15.2] - 2024-11-06

src/sisl/_core/geometry.py

@@ -366,9 +366,12 @@ def _sanitize_atoms(self, atoms) -> ndarray:
         - name -> self._names[name]
         - `Atom` -> self.atoms.index(atom)
         - range/list/ndarray -> ndarray
+        - `...` -> ndarray
         """
         if atoms is None:
             return np.arange(self.na)
+        elif atoms is Ellipsis:
+            return np.arange(self.na)
         atoms = _a.asarray(atoms)
         if atoms.size == 0:
             return _a.asarrayl([])
@@ -452,6 +455,8 @@ def _sanitize_orbs(self, orbitals) -> ndarray:
         """
         if orbitals is None:
             return np.arange(self.no)
+        elif orbitals is Ellipsis:
+            return np.arange(self.no)
         orbitals = _a.asarray(orbitals)
         if orbitals.size == 0:
             return _a.asarrayl([])

src/sisl/_core/tests/test_geometry.py

@@ -1654,6 +1654,11 @@ def test_geometry_sort_int():
         assert np.all(np.diff(bi.fxyz[ix, 1] * bi.lattice.length[i]) <= atol)
 
 
+def test_geometry_ellipsis():
+    gr = sisl_geom.graphene()
+    assert np.allclose(gr.axyz(...), gr.axyz(None))
+
+
 def test_geometry_sort_atom():
     bi = sisl_geom.bilayer().tile(2, 0).repeat(2, 1)
 

src/sisl/typing/_indices.py

@@ -78,6 +78,7 @@
     "GenericCategory",
     "Shape",
     bool,  # for all or none
+    Ellipsis,  # for all atoms
     None,  # typically used to default for all
 ]
 """Indexing atoms via various construct methods"""
@@ -91,6 +92,7 @@
     "AtomCategory",  # gets expended to orbitals on the atoms
     "Shape",
     bool,
+    Ellipsis,  # for all orbitals
     None,
 ]
 """Indexing orbitals via various construct methods"""