Remove deprecated force_consts_to_hdf5 parameter (#642)

Author: ElliottKasoar

janus_core/calculations/phonons.py

@@ -4,7 +4,6 @@
 
 from collections.abc import Sequence
 from typing import Any, get_args
-from warnings import warn
 
 from ase import Atoms
 from numpy import ndarray
@@ -108,8 +107,6 @@ class Phonons(BaseCalculation):
         End temperature for thermal properties calculations, in K. Default is 1000.0.
     temp_step
         Temperature step for thermal properties calculations, in K. Default is 50.0.
-    force_consts_to_hdf5
-        Deprecated. Please use `hdf5`.
     hdf5
         Whether to write force constants and bands in hdf5 or not. Default is True.
     hdf5_compression
@@ -164,7 +161,6 @@ def __init__(
         temp_min: float = 0.0,
         temp_max: float = 1000.0,
         temp_step: float = 50.0,
-        force_consts_to_hdf5: bool | None = None,
         hdf5: bool = True,
         hdf5_compression: str | None = None,
         plot_to_file: bool = False,
@@ -244,8 +240,6 @@ def __init__(
             End temperature for thermal calculations, in K. Default is 1000.0.
         temp_step
             Temperature step for thermal calculations, in K. Default is 50.0.
-        force_consts_to_hdf5
-            Deprecated. Please use `hdf5`.
         hdf5
             Whether to write force constants and bands in hdf5 or not. Default is True.
         hdf5_compression
@@ -295,21 +289,6 @@ def __init__(
         self.write_full = write_full
         self.enable_progress_bar = enable_progress_bar
 
-        # Handle deprecation
-        if force_consts_to_hdf5 is not None:
-            if hdf5 is False:
-                raise ValueError(
-                    """`force_consts_to_hdf5`: has replaced `hdf5`.
-                     Please only use `hdf5`"""
-                )
-            self.hdf5 = force_consts_to_hdf5
-            warn(
-                """`force_consts_to_hdf5` has been deprecated.
-                Please use `hdf5`.""",
-                FutureWarning,
-                stacklevel=2,
-            )
-
         # Ensure supercell is a valid list
         self.supercell = [supercell] * 3 if isinstance(supercell, int) else supercell
         if len(self.supercell) not in [3, 9]:

janus_core/cli/phonons.py

@@ -26,7 +26,7 @@
     Summary,
     Tracker,
 )
-from janus_core.cli.utils import deprecated_option, yaml_converter_callback
+from janus_core.cli.utils import yaml_converter_callback
 
 app = Typer()
 
@@ -110,15 +110,6 @@ def phonons(
         ),
     ] = 0.1,
     minimize_kwargs: MinimizeKwargs = None,
-    force_consts_to_hdf5: Annotated[
-        bool,
-        Option(
-            help="Whether to save force constants in hdf5.",
-            rich_help_panel="Calculation",
-            callback=deprecated_option,
-            hidden=True,
-        ),
-    ] = None,
     hdf5: Annotated[
         bool,
         Option(
@@ -244,8 +235,6 @@ def phonons(
         Default is 0.1.
     minimize_kwargs
         Other keyword arguments to pass to geometry optimizer. Default is {}.
-    force_consts_to_hdf5
-        Deprecated. Please use `hdf5`.
     hdf5
         Whether to save force constants and bands in hdf5 format.
         Default is True.

tests/test_phonons.py

@@ -41,22 +41,6 @@ def test_calc_phonons():
     assert "phonon" in phonons.results
 
 
-def test_force_consts_to_hdf5_deprecation():
-    """Test deprecation of force-consts-to-hdf5."""
-    struct = read(DATA_PATH / "NaCl.cif")
-    struct.calc = choose_calculator(arch="mace_mp", model=MODEL_PATH)
-    with pytest.warns(
-        FutureWarning, match="`force_consts_to_hdf5` has been deprecated."
-    ):
-        phonons = Phonons(
-            struct=struct,
-            force_consts_to_hdf5=True,
-        )
-
-    phonons.calc_force_constants(write_force_consts=True)
-    assert "phonon" in phonons.results
-
-
 def test_force_consts_compression(tmp_path):
     """Test compression of force constants."""
     log_file = tmp_path / "phonons.log"

tests/test_phonons_cli.py

@@ -218,57 +218,6 @@ def test_hdf5(tmp_path, compression):
         assert h5f["force_constants"].compression == compression
 
 
-def test_force_consts_to_hdf5_deprecated(tmp_path):
-    """Test saving force constants to HDF5 deprecated."""
-    file_prefix = tmp_path / "test" / "NaCl"
-    phonon_results = tmp_path / "test" / "NaCl-phonopy.yml"
-    hdf5_results = tmp_path / "test" / "NaCl-force_constants.hdf5"
-    bands_results = tmp_path / "test" / "NaCl-auto_bands.hdf5"
-    summary_path = tmp_path / "test" / "NaCl-phonons-summary.yml"
-    log_path = tmp_path / "test" / "NaCl-phonons-log.yml"
-
-    result = runner.invoke(
-        app,
-        [
-            "phonons",
-            "--struct",
-            DATA_PATH / "NaCl.cif",
-            "--arch",
-            "mace_mp",
-            "--bands",
-            "--file-prefix",
-            file_prefix,
-            "--force-consts-to-hdf5",
-        ],
-    )
-
-    assert result.exit_code == 0
-    assert phonon_results.exists()
-    assert hdf5_results.exists()
-    assert bands_results.exists()
-
-    # Read phonons summary file
-    with open(summary_path, encoding="utf8") as file:
-        phonon_summary = yaml.safe_load(file)
-
-    output_files = {
-        "params": phonon_results,
-        "force_constants": hdf5_results,
-        "bands": bands_results,
-        "bands_plot": None,
-        "dos": None,
-        "dos_plot": None,
-        "band_dos_plot": None,
-        "pdos": None,
-        "pdos_plot": None,
-        "thermal": None,
-        "minimized_initial_structure": None,
-        "log": log_path,
-        "summary": summary_path,
-    }
-    check_output_files(summary=phonon_summary, output_files=output_files)
-
-
 def test_thermal_props(tmp_path):
     """Test calculating thermal properties."""
     file_prefix = tmp_path / "test" / "NaCl"