Fix documentation warnings

docs/source/conf.py

@@ -198,18 +198,27 @@
 nitpicky = True
 nitpick_ignore = [
     ("py:class", "Logger"),
+    ("py:class", "float64"),
     ("py:class", "numpy.float64"),
+    ("py:class", "NDArray"),
+    ("py:class", "ndarray"),
     ("py:class", "typer.models.Context"),
     ("py:class", "ellipsis"),
     ("py:class", "janus_core.helpers.stats.T"),
+    ("py:class", "PhonopyAtoms"),
     ("py:class", "phonopy.structure.atoms.PhonopyAtoms"),
     ("py:class", "ase.optimize.optimize.Optimizer"),
-    ("py:class", "codecarbon.emissions_tracker.OfflineEmissionsTracker"),
-    ("py:class", "_io.StringIO"),
+    ("py:class", "Dynamics"),
+    ("py:class", "OfflineEmissionsTracker"),
+    ("py:class", "StringIO"),
     ("py:class", "Architectures"),
     ("py:class", "Devices"),
+    ("py:class", "Properties"),
+    ("py:class", "PhononCalcs"),
+    ("py:class", "MaybeList"),
     ("py:class", "MaybeSequence"),
     ("py:class", "SliceLike"),
+    ("py:class", "StartStopStep"),
     ("py:class", "PathLike"),
     ("py:class", "Atoms"),
     ("py:class", "Calculator"),

janus_core/calculations/descriptors.py

@@ -68,11 +68,6 @@ class Descriptors(BaseCalculation):
     write_kwargs
         Keyword arguments to pass to ase.io.write if saving structure with
         results of calculations. Default is {}.
-
-    Methods
-    -------
-    run()
-        Calculate descriptors for structure(s)
     """
 
     def __init__(

janus_core/calculations/eos.py

@@ -100,11 +100,6 @@ class EoS(BaseCalculation):
         List of energies of generated structures.
     lattice_scalars : NDArray[float64]
         Lattice scalars of generated structures.
-
-    Methods
-    -------
-    run()
-        Calculate equation of state.
     """
 
     def __init__(

janus_core/calculations/geom_opt.py

@@ -91,13 +91,6 @@ class GeomOpt(BaseCalculation):
     traj_kwargs
         Keyword arguments to pass to ase.io.write to save optimization trajectory.
         Must include "filename" keyword. Default is {}.
-
-    Methods
-    -------
-    set_optimizer()
-        Set optimizer for geometry optimization.
-    run()
-        Run geometry optimization.
     """
 
     def __init__(

janus_core/calculations/md.py

@@ -172,13 +172,6 @@ class MolecularDynamics(BaseCalculation):
         Number of previous steps if restarting simulation.
     created_final : bool
         Whether the final structure file has been created.
-
-    Methods
-    -------
-    run()
-        Run molecular dynamics simulation and/or heating ramp.
-    get_stats()
-        Get thermodynamical statistics to be written to file.
     """
 
     def __init__(
@@ -1169,11 +1162,6 @@ class NPT(MolecularDynamics):
         Keyword arguments to pass to ensemble initialization. Default is {}.
     **kwargs
         Additional keyword arguments.
-
-    Attributes
-    ----------
-    dyn : Dynamics
-        Configured NPT dynamics.
     """
 
     def __init__(
@@ -1316,11 +1304,6 @@ class NVT(MolecularDynamics):
         Keyword arguments to pass to ensemble initialization. Default is {}.
     **kwargs
         Additional keyword arguments.
-
-    Attributes
-    ----------
-    dyn : Dynamics
-        Configured NVT dynamics.
     """
 
     def __init__(
@@ -1411,11 +1394,6 @@ class NVE(MolecularDynamics):
         Keyword arguments to pass to ensemble initialization. Default is {}.
     **kwargs
         Additional keyword arguments.
-
-    Attributes
-    ----------
-    dyn : Dynamics
-        Configured NVE dynamics.
     """
 
     def __init__(
@@ -1624,11 +1602,6 @@ class NPH(NPT):
         Keyword arguments to pass to ensemble initialization. Default is {}.
     **kwargs
         Additional keyword arguments.
-
-    Attributes
-    ----------
-    dyn : Dynamics
-        Configured NVE dynamics.
     """
 
     def __init__(

janus_core/calculations/phonons.py

@@ -128,31 +128,6 @@ class Phonons(BaseCalculation):
         ASE Calculator attached to structure.
     results : dict
         Results of phonon calculations.
-
-    Methods
-    -------
-    calc_force_constants(write_force_consts)
-        Calculate force constants and optionally write results.
-    write_force_constants(phonopy_file, force_consts_to_hdf5, force_consts_file)
-        Write results of force constants calculations.
-    calc_bands(write_bands)
-        Calculate band structure and optionally write and plot results.
-    write_bands(bands_file, save_plots, plot_file)
-        Write results of band structure calculations.
-    calc_thermal_props(mesh, write_thermal)
-        Calculate thermal properties and optionally write results.
-    write_thermal_props(thermal_file)
-        Write results of thermal properties calculations.
-    calc_dos(mesh, write_dos)
-        Calculate density of states and optionally write results.
-    write_dos(dos_file, plot_to_file, plot_file, plot_bands, plot_bands_file)
-        Write results of DOS calculation.
-    calc_pdos(mesh, write_pdos)
-        Calculate projected density of states and optionally write results.
-    write_pdos(pdos_file, plot_to_file, plot_file)
-        Write results of PDOS calculation.
-    run()
-        Run phonon calculations.
     """
 
     def __init__(

janus_core/calculations/single_point.py

@@ -74,11 +74,6 @@ class SinglePoint(BaseCalculation):
     ----------
     results : CalcResults
         Dictionary of calculated results, with keys from `properties`.
-
-    Methods
-    -------
-    run()
-        Run single point calculations.
     """
 
     def __init__(

janus_core/helpers/utils.py

@@ -41,14 +41,6 @@ class FileNameMixin(ABC):  # noqa: B024 (abstract-base-class-without-abstract-me
         Default prefix to use.
     *additional
         Components to add to default file_prefix (joined by hyphens).
-
-    Methods
-    -------
-    _get_default_prefix(file_prefix, struct)
-        Return a prefix from the provided file_prefix or from chemical formula of
-        struct.
-    _build_filename(suffix, *additional, filename, prefix_override)
-         Return a standard format filename if filename not provided.
     """
 
     def __init__(