enabled ellipsis here and there

Should be improved so None fully gets removed.

Signed-off-by: Nick Papior <[email protected]>

CHANGELOG.md

@@ -8,6 +8,12 @@ we hit release version 1.0.0.
 
 ## [0.15.3] - YYYY-MM-DD
 
+### Added
+- 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/io/_multiple.py

@@ -109,6 +109,10 @@ def __call__(self, *args, **kwargs):
         start = 0
         stop = inf
 
+        if key is Ellipsis:
+            # Allow [...] to extract all"
+            key = slice(None)
+
         if isinstance(key, Integral):
             if key >= 0:
                 start = key

src/sisl/io/siesta/stdout.py

@@ -828,7 +828,7 @@ 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,
     ):
@@ -840,7 +840,7 @@ 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
@@ -854,7 +854,9 @@ 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!"
@@ -1084,8 +1086,8 @@ 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,
     ):
@@ -1127,15 +1129,15 @@ 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.
@@ -1568,9 +1570,9 @@ 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"),
                 )
@@ -1605,6 +1607,9 @@ 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/io/siesta/tests/test_stdout.py

@@ -40,6 +40,8 @@ def test_mgco3_md_out(sisl_files):
     assert len(out.read_geometry[:]()) == nOutputs
     assert len(out.read_force[:]()) == nOutputs
     assert len(out.read_stress[:]()) == nOutputs
+    # slicing using ellipsis (same as above)
+    assert len(out.read_stress[...]()) == nOutputs
 
     f0 = out.read_force()
     f = out.read_force[-1]()