Merge pull request #355 from tovrstra/optional-keyword

Require optional arguments of iodata.api functions to be specified with keywords

docs/example_scripts/load_water_foo.py

@@ -2,5 +2,5 @@
 
 from iodata import load_one
 
-mol = load_one("water.foo", "xyz")  # XYZ file with unusual extension
+mol = load_one("water.foo", fmt="xyz")  # XYZ file with unusual extension
 print(mol.atcoords)

iodata/api.py

@@ -151,7 +151,7 @@ def inner(*args, **kwargs):
 
 
 @_reissue_warnings
-def load_one(filename: str, fmt: Optional[str] = None, **kwargs) -> IOData:
+def load_one(filename: str, *, fmt: Optional[str] = None, **kwargs) -> IOData:
     """Load data from a file.
 
     This function uses the extension or prefix of the filename to determine the
@@ -186,7 +186,7 @@ def load_one(filename: str, fmt: Optional[str] = None, **kwargs) -> IOData:
 
 
 @_reissue_warnings
-def load_many(filename: str, fmt: Optional[str] = None, **kwargs) -> Iterator[IOData]:
+def load_many(filename: str, *, fmt: Optional[str] = None, **kwargs) -> Iterator[IOData]:
     """Load multiple IOData instances from a file.
 
     This function uses the extension or prefix of the filename to determine the
@@ -408,6 +408,7 @@ def write_input(
     data: IOData,
     filename: str,
     fmt: str,
+    *,
     template: Optional[str] = None,
     atom_line: Optional[Callable] = None,
     **kwargs,

iodata/test/common.py

@@ -171,7 +171,7 @@ def check_orthonormal(mo_coeffs: NDArray[float], ao_overlap: NDArray[float], ato
 
 
 def load_one_warning(
-    filename: str, fmt: Optional[str] = None, match: Optional[str] = None, **kwargs
+    filename: str, *, fmt: Optional[str] = None, match: Optional[str] = None, **kwargs
 ) -> IOData:
     """Call load_one, catching expected LoadWarning.
 
@@ -195,9 +195,9 @@ def load_one_warning(
     """
     with as_file(files("iodata.test.data").joinpath(filename)) as fn:
         if match is None:
-            return load_one(str(fn), fmt, **kwargs)
+            return load_one(str(fn), fmt=fmt, **kwargs)
         with pytest.warns(LoadWarning, match=match):
-            return load_one(str(fn), fmt, **kwargs)
+            return load_one(str(fn), fmt=fmt, **kwargs)
 
 
 def create_generalized() -> IOData:

iodata/test/test_inputs.py

@@ -135,10 +135,10 @@ def atom_line(data, iatom):
         return f"{symbol}(Fragment={fid}) {atcoord[0]:10.6f} {atcoord[1]:10.6f} {atcoord[2]:10.6f}"
 
     with as_file(files("iodata.test.data").joinpath("s66_4114_02WaterMeOH.xyz")) as fn:
-        mol = load_one(fn, "extxyz")
+        mol = load_one(fn, fmt="extxyz")
 
     fn_com = os.path.join(tmpdir, "input_bsse.com")
-    write_input(mol, fn_com, "gaussian", template, atom_line)
+    write_input(mol, fn_com, fmt="gaussian", template=template, atom_line=atom_line)
     with as_file(files("iodata.test.data").joinpath("input_gaussian_bsse.com")) as fn_expected:
         check_load_input_and_compare(fn_com, fn_expected)
 
@@ -175,7 +175,9 @@ def atom_line(data, iatom):
         return f"        {symbol:3s} {atcoord[0]:10.6f} {atcoord[1]:10.6f} {atcoord[2]:10.6f}"
 
     grid_stuff = "Grid4 TightSCF NOFINALGRID"
-    write_input(mol, fname, "orca", template, atom_line, grid_stuff=grid_stuff)
+    write_input(
+        mol, fname, fmt="orca", template=template, atom_line=atom_line, grid_stuff=grid_stuff
+    )
     # compare saved input to expected input
     source = files("iodata.test.data").joinpath("input_orca_h2o_sp_b3lyp.txt")
     with as_file(source) as fname_expected: