Tidy code (stfc#81)

* Simplify run_single_point function name

* Tidy CLI help, docstrings and tests

---------

Co-authored-by: ElliottKasoar <ElliottKasoar@users.noreply.github.com>

janus_core/cli.py

@@ -82,7 +82,11 @@ def parse_dict_class(value: str):
     TyperDict,
     typer.Option(
         parser=parse_dict_class,
-        help="Keyword arguments to pass to selected calculator  [default: {}]",
+        help=(
+            "Keyword arguments to pass to selected calculator. For the default "
+            "architecture ('mace_mp'), {'model':'small'} is set by default  "
+            "[default: {}]"
+        ),
         metavar="DICT",
     ),
 ]
@@ -92,7 +96,7 @@ def parse_dict_class(value: str):
         parser=parse_dict_class,
         help=(
             "Keyword arguments to pass to ase.io.write when saving "
-            "results [default: {}]"
+            "results  [default: {}]"
         ),
         metavar="DICT",
     ),
@@ -162,9 +166,7 @@ def singlepoint(
         calc_kwargs=calc_kwargs,
         log_kwargs={"filename": log_file, "filemode": "w"},
     )
-    s_point.run_single_point(
-        properties=properties, write_results=True, write_kwargs=write_kwargs
-    )
+    s_point.run(properties=properties, write_results=True, write_kwargs=write_kwargs)
 
 
 @app.command()
@@ -184,7 +186,13 @@ def geomopt(  # pylint: disable=too-many-arguments,too-many-locals
     ] = False,
     vectors_only: Annotated[
         bool,
-        typer.Option("--vectors-only", help="Allow only cell vectors to change"),
+        typer.Option(
+            "--vectors-only",
+            help=(
+                "Disable optimizing cell angles, so only cell vectors and atomic "
+                "positions are optimized. Requires --fully-opt to be set"
+            ),
+        ),
     ] = False,
     read_kwargs: ReadKwargs = None,
     calc_kwargs: CalcKwargs = None,

janus_core/single_point.py

@@ -69,7 +69,7 @@ class SinglePoint:
         Read structure and structure name.
     set_calculator(**kwargs)
         Configure calculator and attach to structure.
-    run_single_point(properties=None)
+    run(properties=None)
         Run single point calculations.
     """
 
@@ -298,7 +298,7 @@ def _clean_results(
         else:
             self._remove_invalid_props(self.struct, results, properties)
 
-    def run_single_point(
+    def run(
         self,
         properties: MaybeSequence[str] = (),
         write_results: bool = False,

tests/test_geom_opt.py

@@ -46,7 +46,7 @@ def test_optimize(architecture, struct_path, expected, kwargs):
         calc_kwargs={"model": MODEL_PATH},
     )
 
-    init_energy = single_point.run_single_point("energy")["energy"]
+    init_energy = single_point.run("energy")["energy"]
 
     atoms = optimize(single_point.struct, **kwargs)
 
@@ -64,7 +64,7 @@ def test_saving_struct(tmp_path):
         calc_kwargs={"model": MODEL_PATH},
     )
 
-    init_energy = single_point.run_single_point("energy")["energy"]
+    init_energy = single_point.run("energy")["energy"]
 
     optimize(
         single_point.struct,

tests/test_mlip_calculators.py

@@ -52,15 +52,3 @@ def test_model_model_paths():
             model=MODEL_PATH,
             model_paths=MODEL_PATH,
         )
-    with pytest.raises(ValueError):
-        choose_calculator(
-            architecture="mace_mp",
-            model=MODEL_PATH,
-            model_paths=MODEL_PATH,
-        )
-    with pytest.raises(ValueError):
-        choose_calculator(
-            architecture="mace_off",
-            model=MODEL_PATH,
-            model_paths=MODEL_PATH,
-        )

tests/test_single_point.py

@@ -38,7 +38,7 @@ def test_potential_energy(
     single_point = SinglePoint(
         struct_path=struct_path, architecture="mace", calc_kwargs=calc_kwargs
     )
-    results = single_point.run_single_point(properties)[prop_key]
+    results = single_point.run(properties)[prop_key]
 
     # Check correct values returned
     if idx is not None:
@@ -60,7 +60,7 @@ def test_single_point_none():
         calc_kwargs={"model": MODEL_PATH},
     )
 
-    results = single_point.run_single_point()
+    results = single_point.run()
     for prop in ["energy", "forces", "stress"]:
         assert prop in results
 
@@ -73,7 +73,7 @@ def test_single_point_clean():
         calc_kwargs={"model": MODEL_PATH},
     )
 
-    results = single_point.run_single_point()
+    results = single_point.run()
     for prop in ["energy", "forces"]:
         assert prop in results
     assert "stress" not in results
@@ -89,7 +89,7 @@ def test_single_point_traj():
     )
 
     assert len(single_point.struct) == 2
-    results = single_point.run_single_point("energy")
+    results = single_point.run("energy")
     assert results["energy"][0] == pytest.approx(-76.0605725422795)
     assert results["energy"][1] == pytest.approx(-74.80419118083256)
 
@@ -107,7 +107,7 @@ def test_single_point_write():
     )
     assert "forces" not in single_point.struct.arrays
 
-    single_point.run_single_point(write_results=True)
+    single_point.run(write_results=True)
 
     atoms = read_atoms(results_path)
     assert atoms.get_potential_energy() is not None
@@ -126,9 +126,7 @@ def test_single_point_write_kwargs(tmp_path):
     )
     assert "forces" not in single_point.struct.arrays
 
-    single_point.run_single_point(
-        write_results=True, write_kwargs={"filename": results_path}
-    )
+    single_point.run(write_results=True, write_kwargs={"filename": results_path})
     atoms = read(results_path)
     assert atoms.get_potential_energy() is not None
     assert "forces" in atoms.arrays
@@ -144,13 +142,11 @@ def test_single_point_write_nan(tmp_path):
         calc_kwargs={"model": MODEL_PATH},
     )
 
-    assert isfinite(single_point.run_single_point("energy")["energy"]).all()
+    assert isfinite(single_point.run("energy")["energy"]).all()
     with pytest.raises(ValueError):
-        single_point.run_single_point("stress")
+        single_point.run("stress")
 
-    single_point.run_single_point(
-        write_results=True, write_kwargs={"filename": results_path}
-    )
+    single_point.run(write_results=True, write_kwargs={"filename": results_path})
     atoms = read(results_path)
     assert atoms.get_potential_energy() is not None
     assert "forces" in atoms.calc.results
@@ -165,7 +161,7 @@ def test_invalid_prop():
         calc_kwargs={"model": MODEL_PATH},
     )
     with pytest.raises(NotImplementedError):
-        single_point.run_single_point("invalid")
+        single_point.run("invalid")
 
 
 def test_atoms():
@@ -178,7 +174,7 @@ def test_atoms():
         calc_kwargs={"model": MODEL_PATH},
     )
     assert single_point.struct_name == "NaCl"
-    assert single_point.run_single_point("energy")["energy"] < 0
+    assert single_point.run("energy")["energy"] < 0
 
 
 def test_default_atoms_name():

tests/utils.py

@@ -1,4 +1,4 @@
-"""Utility functions for tests"""
+"""Utility functions for tests."""
 
 from pathlib import Path
 from typing import Union