enabled ellipsis here and there (#863)

* enabled ellipsis here and there

Should be improved so None fully gets removed.

* Enabled ... for atoms, orbitals arguments

This seems a bit more natural than None.

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

---------

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

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/io/siesta/stdout.py

@@ -830,7 +830,7 @@ def read_data(self, *args, **kwargs) -> Any:
     def read_scf(
         self,
         key: str = "scf",
-        iscf: Optional[int] = -1,
+        iscf: Optional[Union[int, Ellipsis]] = -1,
         as_dataframe: bool = False,
         ret_header: bool = False,
     ):
@@ -842,7 +842,7 @@ def read_scf(
             parse SCF information from Siesta SCF or TranSiesta SCF
         iscf :
             which SCF cycle should be stored. If ``-1`` only the final SCF step is stored,
-            for None *all* SCF cycles are returned. When `iscf` values queried are not found they
+            for `...`/`None` *all* SCF cycles are returned. When `iscf` values queried are not found they
             will be truncated to the nearest SCF step.
         as_dataframe:
             whether the information should be returned as a `pandas.DataFrame`. The advantage of this
@@ -856,7 +856,9 @@ def read_scf(
         # These are the properties that are written in SIESTA scf
         props = ["iscf", "Eharris", "E_KS", "FreeEng", "dDmax", "Ef", "dHmax"]
 
-        if not iscf is None:
+        if iscf is Ellipsis:
+            iscf = None
+        elif iscf is not None:
             if iscf == 0:
                 raise ValueError(
                     f"{self.__class__.__name__}.read_scf requires iscf argument to *not* be 0!"
@@ -1086,8 +1088,8 @@ def construct_data(d, data):
     def read_charge(
         self,
         name: Literal["voronoi", "hirshfeld", "mulliken", "mulliken:<5.2"],
-        iscf=Opt.ANY,
-        imd=Opt.ANY,
+        iscf: Union[Opt, int, Ellipsis] = Opt.ANY,
+        imd: Union[Opt, int, Ellipsis] = Opt.ANY,
         key_scf: str = "scf",
         as_dataframe: bool = False,
     ):
@@ -1129,15 +1131,15 @@ def read_charge(
         ----------
         name:
             the name of the charges that you want to read
-        iscf: int or Opt, optional
+        iscf: int or Opt or `...`, optional
             index (0-based) of the scf iteration you want the charges for.
-            If the enum specifier `Opt.ANY` or `Opt.ALL` are used, then
+            If the enum specifier `Opt.ANY` or `Opt.ALL`/`...` are used, then
             the returned quantities depend on what is present.
             If ``None/Opt.NONE`` it will not return any SCF charges.
             If both `imd` and `iscf` are ``None`` then only the final charges will be returned.
         imd: int or Opt, optional
             index (0-based) of the md step you want the charges for.
-            If the enum specifier `Opt.ANY` or `Opt.ALL` are used, then
+            If the enum specifier `Opt.ANY` or `Opt.ALL`/`...` are used, then
             the returned quantities depend on what is present.
             If ``None/Opt.NONE`` it will not return any MD charges.
             If both `imd` and `iscf` are ``None`` then only the final charges will be returned.
@@ -1570,9 +1572,9 @@ def try_parse_int(s):
                 md_scf_charge = pd.concat(
                     [
                         pd.concat(
-                            iscf, keys=pd.RangeIndex(1, len(iscf) + 1, name="iscf")
+                            iscf_, keys=pd.RangeIndex(1, len(iscf_) + 1, name="iscf")
                         )
-                        for iscf in md_scf_charge
+                        for iscf_ in md_scf_charge
                     ],
                     keys=pd.RangeIndex(1, len(md_scf_charge) + 1, name="imd"),
                 )
@@ -1607,6 +1609,9 @@ def _p(flag, found):
             flag :
                 corrected flag
             """
+            if flag is Ellipsis:
+                flag = Opt.ALL
+
             if isinstance(flag, Opt):
                 # correct flag depending on what `found` is
                 # If the values have been found we

src/sisl/typing/_indices.py

@@ -94,3 +94,11 @@
     None,
 ]
 """Indexing orbitals via various construct methods"""
+
+try:
+    from types import EllipsisType
+
+    AtomsIndex = Union[AtomsIndex, EllipsisType]
+    OrbitalsIndex = Union[OrbitalsIndex, EllipsisType]
+except ImportError:
+    pass