Remove deprecated filter_func parameter (#641)

Author: ElliottKasoar

janus_core/calculations/geom_opt.py

@@ -76,8 +76,6 @@ class GeomOpt(BaseCalculation):
     filter_class
         Filter class, or name of class from ase.filters to wrap around atoms.
         Default is `FrechetCellFilter`.
-    filter_func
-        Deprecated. Please use `filter_class`.
     filter_kwargs
         Keyword arguments to pass to filter_class. Default is {}.
     optimizer
@@ -117,7 +115,6 @@ def __init__(
         symmetry_tolerance: float = 0.001,
         angle_tolerance: float = -1.0,
         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,
@@ -173,8 +170,6 @@ def __init__(
         filter_class
             Filter class, or name of class from ase.filters to wrap around atoms.
             Default is `FrechetCellFilter`.
-        filter_func
-            Deprecated. Please use `filter_class`.
         filter_kwargs
             Keyword arguments to pass to filter_class. Default is {}.
         optimizer
@@ -200,10 +195,6 @@ def __init__(
             )
         )
 
-        # Handle deprecated filter_func, but warn later after logging is set up
-        if filter_func:
-            filter_class = filter_func
-
         self.fmax = fmax
         self.steps = steps
         self.symmetrize = symmetrize
@@ -242,15 +233,6 @@ def __init__(
         if not self.struct.calc:
             raise ValueError("Please attach a calculator to `struct`.")
 
-        # Warn for deprecated filter_func now that logging is set up
-        if filter_func:
-            warnings.warn(
-                "`filter_func` has been deprecated, but currently overrides "
-                "`filter_class`. Please only set `filter_class`.",
-                FutureWarning,
-                stacklevel=2,
-            )
-
         # Set output files
         self.write_kwargs["filename"] = self._build_filename(
             "opt.extxyz", filename=self.write_kwargs.get("filename")

janus_core/cli/geomopt.py

@@ -23,7 +23,7 @@
     Tracker,
     WriteKwargs,
 )
-from janus_core.cli.utils import deprecated_option, yaml_converter_callback
+from janus_core.cli.utils import yaml_converter_callback
 
 app = Typer()
 
@@ -125,15 +125,6 @@ def geomopt(
             rich_help_panel="Calculation",
         ),
     ] = None,
-    filter_func: Annotated[
-        str | None,
-        Option(
-            help="Deprecated. Please use --filter",
-            rich_help_panel="Calculation",
-            callback=deprecated_option,
-            hidden=True,
-        ),
-    ] = None,
     pressure: Annotated[
         float,
         Option(
@@ -216,8 +207,6 @@ 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_class`.
     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
@@ -303,19 +292,14 @@ def geomopt(
 
     _set_minimize_kwargs(minimize_kwargs, opt_cell_lengths, pressure)
 
-    if filter_func and filter_class:
-        raise ValueError("--filter-func is deprecated, please only use --filter")
-
     if opt_cell_fully or opt_cell_lengths:
         # Use default filter unless filter explicitly passed
         if filter_class:
             opt_cell_fully_dict = {"filter_class": filter_class}
-        elif filter_func:
-            opt_cell_fully_dict = {"filter_func": filter_func, "filter_class": None}
         else:
             opt_cell_fully_dict = {}
     else:
-        if filter_class or filter_func:
+        if filter_class:
             raise ValueError(
                 "--opt-cell-lengths or --opt-cell-fully must be set to use a filter"
             )

tests/test_geom_opt.py

@@ -416,16 +416,3 @@ def test_traj_kwargs_new_dir(tmp_path):
     assert traj_path.exists()
     traj = read(traj_path, index=":")
     assert len(traj) == 3
-
-
-def test_deprecation_filter_func(tmp_path):
-    """Test FutureWarning raised for model in calc_kwargs."""
-    with pytest.warns(FutureWarning, match="`filter_func` has been deprecated"):
-        geom_opt = GeomOpt(
-            struct=DATA_PATH / "NaCl.cif",
-            arch="mace_mp",
-            model=MODEL_PATH,
-            fmax=0.001,
-            filter_func="UnitCellFilter",
-        )
-    assert isinstance(geom_opt.filtered_struct, UnitCellFilter)

tests/test_geomopt_cli.py

@@ -999,63 +999,3 @@ def test_info(tmp_path):
     assert atoms.info["system_name"] == "NaCl"
     assert "config_type" in atoms.info
     assert atoms.info["config_type"] == "geom_opt"
-
-
-def test_filter_func_deprecated(tmp_path):
-    """Test filter_func sets filter."""
-    file_prefix = tmp_path / "NaCl"
-    log_path = tmp_path / "test.log"
-
-    result = runner.invoke(
-        app,
-        [
-            "geomopt",
-            "--struct",
-            DATA_PATH / "NaCl.cif",
-            "--arch",
-            "mace_mp",
-            "--model",
-            MACE_PATH,
-            "--opt-cell-fully",
-            "--filter-func",
-            "UnitCellFilter",
-            "--log",
-            log_path,
-            "--file-prefix",
-            file_prefix,
-            "--no-tracker",
-        ],
-    )
-    assert result.exit_code == 0
-    assert_log_contains(
-        log_path,
-        includes=["Starting geometry optimization", "Using filter: UnitCellFilter"],
-    )
-
-
-def test_filter_func_error(tmp_path):
-    """Test setting filter_func without --opt-cell-fully or --opt-cell-lengths."""
-    results_path = tmp_path / "NaCl-opt.extxyz"
-    log_path = tmp_path / "test.log"
-    summary_path = tmp_path / "summary.yml"
-
-    result = runner.invoke(
-        app,
-        [
-            "geomopt",
-            "--struct",
-            DATA_PATH / "NaCl-deformed.cif",
-            "--arch",
-            "mace_mp",
-            "--out",
-            results_path,
-            "--filter-func",
-            "UnitCellFilter",
-            "--log",
-            log_path,
-            "--summary",
-            summary_path,
-        ],
-    )
-    assert result.exit_code == 1
-    assert isinstance(result.exception, ValueError)