Update output file CLI options (#89)

Co-authored-by: ElliottKasoar <ElliottKasoar@users.noreply.github.com>
stfc · Mar 22, 2024 · 7090317 · 7090317
1 parent b9d05bb
commit 7090317
Show file tree

Hide file tree

Showing 3 changed files with 44 additions and 23 deletions.
diff --git a/janus_core/cli.py b/janus_core/cli.py
@@ -155,6 +155,16 @@ def singlepoint(
             ),
         ),
     ] = None,
+    out_file: Annotated[
+        Path,
+        typer.Option(
+            "--out",
+            help=(
+                "Path to save structure with calculated results. Default is inferred "
+                "from name of structure file."
+            ),
+        ),
+    ] = None,
     read_kwargs: ReadKwargs = None,
     calc_kwargs: CalcKwargs = None,
     write_kwargs: WriteKwargs = None,
@@ -174,6 +184,9 @@ def singlepoint(
         Device to run model on. Default is "cpu".
     properties : Optional[str]
         Physical properties to calculate. Default is "energy".
+    out_file : Optional[Path]
+        Path to save structure with calculated results. Default is inferred from name
+        of the structure file.
     read_kwargs : Optional[dict[str, Any]]
         Keyword arguments to pass to ase.io.read. Default is {}.
     calc_kwargs : Optional[dict[str, Any]]
@@ -187,6 +200,14 @@ def singlepoint(
         [read_kwargs, calc_kwargs, write_kwargs]
     )
 
+    # Check filename for results not duplicated
+    if "filename" in write_kwargs:
+        raise ValueError("'filename' must be passed through the --out option")
+
+    # Default filname for saving results determined in SinglePoint if not specified
+    if out_file:
+        write_kwargs["filename"] = out_file
+
     s_point = SinglePoint(
         struct_path=struct_path,
         architecture=architecture,
@@ -225,10 +246,10 @@ def geomopt(  # pylint: disable=too-many-arguments,too-many-locals
             help="Fully optimize the cell vectors, angles, and atomic positions.",
         ),
     ] = False,
-    opt_file: Annotated[
+    out_file: Annotated[
         Path,
         typer.Option(
-            "--opt",
+            "--out",
             help=(
                 "Path to save optimized structure. Default is inferred from name "
                 "of structure file."
@@ -282,7 +303,7 @@ def geomopt(  # pylint: disable=too-many-arguments,too-many-locals
     fully_opt : bool
         Whether to fully optimize the cell vectors, angles, and atomic positions.
         Default is False.
-    opt_file : Optional[Path]
+    out_file : Optional[Path]
         Path to save optimized structure, or last structure if optimization did not
         converge. Default is inferred from name of structure file.
     traj_file : Optional[str]
@@ -315,15 +336,15 @@ def geomopt(  # pylint: disable=too-many-arguments,too-many-locals
 
     # Check optimized structure path not duplicated
     if "filename" in write_kwargs:
-        raise ValueError("'filename' must be passed through the --opt option")
+        raise ValueError("'filename' must be passed through the --out option")
 
     # Check trajectory path not duplicated
     if "trajectory" in opt_kwargs:
         raise ValueError("'trajectory' must be passed through the --traj option")
 
     # Set default filname for writing optimized structure if not specified
-    if opt_file:
-        write_kwargs["filename"] = opt_file
+    if out_file:
+        write_kwargs["filename"] = out_file
     else:
         write_kwargs["filename"] = f"{s_point.struct_name}-opt.xyz"
 

diff --git a/tests/test_geomopt_cli.py b/tests/test_geomopt_cli.py
@@ -53,7 +53,7 @@ def test_geomopt_log(tmp_path, caplog):
                 "geomopt",
                 "--struct",
                 DATA_PATH / "NaCl.cif",
-                "--opt",
+                "--out",
                 results_path,
                 "--log",
                 f"{tmp_path}/test.log",
@@ -75,7 +75,7 @@ def test_geomopt_traj(tmp_path):
             "geomopt",
             "--struct",
             DATA_PATH / "NaCl.cif",
-            "--opt",
+            "--out",
             results_path,
             "--traj",
             traj_path,
@@ -97,7 +97,7 @@ def test_fully_opt(tmp_path, caplog):
                 "geomopt",
                 "--struct",
                 DATA_PATH / "NaCl-deformed.cif",
-                "--opt",
+                "--out",
                 results_path,
                 "--fully-opt",
             ],
@@ -123,7 +123,7 @@ def test_fully_opt_and_vectors(tmp_path, caplog):
                 DATA_PATH / "NaCl-deformed.cif",
                 "--fully-opt",
                 "--vectors-only",
-                "--opt",
+                "--out",
                 results_path,
                 "--log",
                 f"{tmp_path}/test.log",
@@ -148,7 +148,7 @@ def test_vectors_not_fully_opt(tmp_path, caplog):
                 "geomopt",
                 "--struct",
                 DATA_PATH / "NaCl.cif",
-                "--opt",
+                "--out",
                 results_path,
                 "--vectors-only",
             ],
@@ -186,7 +186,7 @@ def test_restart(tmp_path):
             "geomopt",
             "--struct",
             data_path,
-            "--opt",
+            "--out",
             results_path,
             "--opt-kwargs",
             f"{{'restart': '{str(restart_path)}'}}",
@@ -204,7 +204,7 @@ def test_restart(tmp_path):
             "geomopt",
             "--struct",
             DATA_PATH / "NaCl.cif",
-            "--opt",
+            "--out",
             results_path,
             "--opt-kwargs",
             f"{{'restart': '{str(restart_path)}'}}",

diff --git a/tests/test_singlepoint_cli.py b/tests/test_singlepoint_cli.py
@@ -62,8 +62,8 @@ def test_singlepoint_properties(tmp_path):
             DATA_PATH / "H2O.cif",
             "--property",
             "energy",
-            "--write-kwargs",
-            f"{{'filename': '{str(results_path_1)}'}}",
+            "--out",
+            results_path_1,
         ],
     )
     assert result.exit_code == 0
@@ -79,8 +79,8 @@ def test_singlepoint_properties(tmp_path):
             DATA_PATH / "H2O.cif",
             "--property",
             "stress",
-            "--write-kwargs",
-            f"{{'filename': '{str(results_path_2)}'}}",
+            "--out",
+            results_path_2,
         ],
     )
     assert result.exit_code == 1
@@ -100,8 +100,8 @@ def test_singlepoint_read_kwargs(tmp_path):
             DATA_PATH / "benzene-traj.xyz",
             "--read-kwargs",
             "{'index': ':'}",
-            "--write-kwargs",
-            f"{{'filename': '{str(results_path)}'}}",
+            "--out",
+            results_path,
             "--property",
             "energy",
         ],
@@ -124,8 +124,8 @@ def test_singlepoint_calc_kwargs(tmp_path):
             DATA_PATH / "NaCl.cif",
             "--calc-kwargs",
             "{'default_dtype': 'float32'}",
-            "--write-kwargs",
-            f"{{'filename': '{str(results_path)}'}}",
+            "--out",
+            results_path,
             "--property",
             "energy",
         ],
@@ -146,8 +146,8 @@ def test_singlepoint_log(tmp_path, caplog):
                 DATA_PATH / "NaCl.cif",
                 "--property",
                 "energy",
-                "--write-kwargs",
-                f"{{'filename': '{str(results_path)}'}}",
+                "--out",
+                results_path,
                 "--log",
                 f"{tmp_path}/test.log",
             ],