Fix test failures after rebase

Author: ajjackson

janus_core/calculations/geom_opt.py

@@ -5,8 +5,7 @@
 from collections.abc import Callable
 import inspect
 from pathlib import Path
-from typing import Any, Callable
-
+from typing import Any
 import warnings
 
 from ase import Atoms, constraints, filters, units
@@ -125,10 +124,10 @@ def __init__(
         filter_class: Callable | str | None = FrechetCellFilter,
         filter_func: Callable | str | None = None,
         filter_kwargs: dict[str, Any] | None = None,
-        optimizer: Callable | str = LBFGS,
-        opt_kwargs: ASEOptArgs | None = None,
         constraint_func: Callable | str | None = None,
         constraint_kwargs: dict[str, Any] | None = None,
+        optimizer: Callable | str = LBFGS,
+        opt_kwargs: ASEOptArgs | None = None,
         write_results: bool = False,
         write_kwargs: OutputKwargs | None = None,
         write_traj: bool = False,
@@ -185,6 +184,11 @@ def __init__(
             Deprecated. Please use `filter_class`.
         filter_kwargs
             Keyword arguments to pass to filter_class. Default is {}.
+        constraint_func
+            Constraint function, or name of function from ase.constraints. Default is
+            None.
+        constraint_kwargs
+            Keyword arguments to pass to constraint_func. Default is {}.
         optimizer
             Optimization function, or name of function from ase.optimize. Default is
             `LBFGS`.
@@ -202,9 +206,21 @@ def __init__(
             "filename" keyword is inferred from `file_prefix` if not given.
             Default is {}.
         """
-        read_kwargs, constraint_kwargs, filter_kwargs, opt_kwargs, write_kwargs, traj_kwargs = (
+        (
+            read_kwargs,
+            constraint_kwargs,
+            filter_kwargs,
+            opt_kwargs,
+            write_kwargs,
+            traj_kwargs,
+        ) = list(
             none_to_dict(
-                (read_kwargs, constraint_kwargs, filter_kwargs, opt_kwargs, write_kwargs, traj_kwargs)
+                read_kwargs,
+                constraint_kwargs,
+                filter_kwargs,
+                opt_kwargs,
+                write_kwargs,
+                traj_kwargs,
             )
         )
 
@@ -220,7 +236,7 @@ def __init__(
         self.filter_class = filter_class
         self.filter_kwargs = filter_kwargs
         self.constraint_func = constraint_func
-        self.constraint_kwargs = constraint_kwargs        
+        self.constraint_kwargs = constraint_kwargs
         self.optimizer = optimizer
         self.opt_kwargs = opt_kwargs
         self.write_results = write_results
@@ -312,7 +328,8 @@ def output_files(self) -> None:
         }
 
     def _set_mandatory_constraint_kwargs(self) -> None:
-        """Inspect constraint class for mandatory arguments
+        """
+        Inspect constraint class for mandatory arguments.
 
         For now we are just looking for the "atoms" parameter of FixSymmetry
         """
@@ -369,9 +386,11 @@ def _set_functions(self) -> None:
             try:
                 self.constraint_func = getattr(constraints, self.constraint_func)
             except AttributeError as e:
-                raise AttributeError(f"No such constraint: {self.constraint_func}") from e
+                raise AttributeError(
+                    f"No such constraint: {self.constraint_func}"
+                ) from e
 
-        if self.filter_class is not None and isinstance(self.filter_func, str):
+        if self.filter_class is not None and isinstance(self.filter_class, str):
             try:
                 self.filter_class = getattr(filters, self.filter_class)
             except AttributeError as e:

janus_core/cli/geomopt.py

@@ -125,11 +125,13 @@ def geomopt(
             rich_help_panel="Calculation",
         ),
     ] = None,
+    filter_func: Annotated[
+        str | None,
+        Option(help="Deprecated. Please use --filter", rich_help_panel="Calculation"),
+    ] = None,
     constraint_func: Annotated[
         str,
-        Option(
-            help="Name of ASE constraint function to use."
-        ),
+        Option(help="Name of ASE constraint function to use."),
     ] = None,
     pressure: Annotated[
         float,
@@ -213,10 +215,12 @@ def geomopt(
     filter_class
         Name of filter from ase.filters to wrap around atoms. If using
         --opt-cell-lengths or --opt-cell-fully, defaults to `FrechetCellFilter`.
+    filter_func
+        Deprecated. Please use --filter.
     constraint_func
         Name of constraint function from ase.constraints, to apply constraints
         to atoms. Parameters should be included as a "constraint_kwargs" dict
-        within "minimize_kwargs". Default is None
+        within "minimize_kwargs". Default is None.
     pressure
         Scalar pressure when optimizing cell geometry, in GPa. Passed to the filter
         function if either `opt_cell_lengths` or `opt_cell_fully` is True. Default is
@@ -340,7 +344,7 @@ def geomopt(
         "track_carbon": tracker,
         "optimizer": optimizer,
         "fmax": fmax,
-        "steps": steps,<<<<<< HEAD
+        "steps": steps,
         "symmetrize": symmetrize,
         "symmetry_tolerance": symmetry_tolerance,
         "file_prefix": file_prefix,