Group CLI options (#497)

* Group janus commands

* Group janus options

* Add epilogue for janus CLI

* Tidy janus subcommand help

* Expand config help text

* Group CLI subcommand options

* Update MD CLI groupings

* Move remove extra MD grouping

* Reorder MD help

* Tidy CLI help and docstrings

Author: ElliottKasoar

janus_core/cli/descriptors.py

@@ -18,6 +18,7 @@
     ReadKwargsAll,
     StructPath,
     Summary,
+    Tracker,
     WriteKwargs,
 )
 from janus_core.cli.utils import yaml_converter_callback
@@ -26,43 +27,53 @@
 
 
 @app.command()
-@use_config(yaml_converter_callback)
+@use_config(yaml_converter_callback, param_help="Path to configuration file.")
 def descriptors(
     # numpydoc ignore=PR02
     ctx: Context,
+    # Calculation
     struct: StructPath,
     invariants_only: Annotated[
         bool,
-        Option(help="Only calculate invariant descriptors."),
+        Option(
+            help="Only calculate invariant descriptors.", rich_help_panel="Calculation"
+        ),
     ] = True,
     calc_per_element: Annotated[
         bool,
-        Option(help="Calculate mean descriptors for each element."),
+        Option(
+            help="Calculate mean descriptors for each element.",
+            rich_help_panel="Calculation",
+        ),
     ] = False,
     calc_per_atom: Annotated[
         bool,
-        Option(help="Calculate descriptors for each atom."),
+        Option(
+            help="Calculate descriptors for each atom.", rich_help_panel="Calculation"
+        ),
     ] = False,
-    arch: Architecture = "mace_mp",
-    device: Device = "cpu",
-    model_path: ModelPath = None,
-    file_prefix: FilePrefix = None,
     out: Annotated[
         Path | None,
         Option(
             help=(
                 "Path to save structure with calculated descriptors. Default is "
                 "inferred from name of structure file."
             ),
+            rich_help_panel="Calculation",
         ),
     ] = None,
-    read_kwargs: ReadKwargsAll = None,
+    # MLIP Calculator
+    arch: Architecture = "mace_mp",
+    device: Device = "cpu",
+    model_path: ModelPath = None,
     calc_kwargs: CalcKwargs = None,
+    # Structure I/O
+    file_prefix: FilePrefix = None,
+    read_kwargs: ReadKwargsAll = None,
     write_kwargs: WriteKwargs = None,
+    # Logging/summary
     log: LogPath = None,
-    tracker: Annotated[
-        bool, Option(help="Whether to save carbon emissions of calculation")
-    ] = True,
+    tracker: Tracker = True,
     summary: Summary = None,
 ) -> None:
     """
@@ -80,24 +91,24 @@ def descriptors(
         Whether to calculate mean descriptors for each element. Default is False.
     calc_per_atom
         Whether to calculate descriptors for each atom. Default is False.
+    out
+        Path to save structure with calculated results. Default is inferred
+        `file_prefix`.
     arch
         MLIP architecture to use for calculations. Default is "mace_mp".
     device
         Device to run model on. Default is "cpu".
     model_path
         Path to MLIP model. Default is `None`.
+    calc_kwargs
+        Keyword arguments to pass to the selected calculator. Default is {}.
     file_prefix
         Prefix for output files, including directories. Default directory is
         ./janus_results, and default filename prefix is inferred from the input
         stucture filename.
-    out
-        Path to save structure with calculated results. Default is inferred
-        `file_prefix`.
     read_kwargs
         Keyword arguments to pass to ase.io.read. By default,
             read_kwargs["index"] is ":".
-    calc_kwargs
-        Keyword arguments to pass to the selected calculator. Default is {}.
     write_kwargs
         Keyword arguments to pass to ase.io.write when saving results. Default is {}.
     log

janus_core/cli/eos.py

@@ -19,6 +19,7 @@
     ReadKwargsLast,
     StructPath,
     Summary,
+    Tracker,
     WriteKwargs,
 )
 from janus_core.cli.utils import yaml_converter_callback
@@ -28,51 +29,79 @@
 
 
 @app.command()
-@use_config(yaml_converter_callback)
+@use_config(yaml_converter_callback, param_help="Path to configuration file.")
 def eos(
     # numpydoc ignore=PR02
     ctx: Context,
+    # Calculation
     struct: StructPath,
-    min_volume: Annotated[float, Option(help="Minimum volume scale factor.")] = 0.95,
-    max_volume: Annotated[float, Option(help="Maximum volume scale factor.")] = 1.05,
-    n_volumes: Annotated[int, Option(help="Number of volumes.")] = 7,
+    min_volume: Annotated[
+        float,
+        Option(help="Minimum volume scale factor.", rich_help_panel="Calculation"),
+    ] = 0.95,
+    max_volume: Annotated[
+        float,
+        Option(help="Maximum volume scale factor.", rich_help_panel="Calculation"),
+    ] = 1.05,
+    n_volumes: Annotated[
+        int, Option(help="Number of volumes.", rich_help_panel="Calculation")
+    ] = 7,
     eos_type: Annotated[
         str,
         Option(
             click_type=Choice(get_args(EoSNames)),
             help="Type of fit for equation of state.",
+            rich_help_panel="Calculation",
         ),
     ] = "birchmurnaghan",
     minimize: Annotated[
-        bool, Option(help="Whether to minimize initial structure before calculations.")
+        bool,
+        Option(
+            help="Whether to minimize initial structure before calculations.",
+            rich_help_panel="Calculation",
+        ),
     ] = True,
     minimize_all: Annotated[
         bool,
-        Option(help="Whether to minimize all generated structures for calculations."),
+        Option(
+            help="Whether to minimize all generated structures for calculations.",
+            rich_help_panel="Calculation",
+        ),
     ] = False,
     fmax: Annotated[
-        float, Option(help="Maximum force for optimization convergence.")
+        float,
+        Option(
+            help="Maximum force for optimization convergence.",
+            rich_help_panel="Calculation",
+        ),
     ] = 0.1,
     minimize_kwargs: MinimizeKwargs = None,
     write_structures: Annotated[
         bool,
-        Option(help="Whether to write out all genereated structures."),
+        Option(
+            help="Whether to write out all genereated structures.",
+            rich_help_panel="Calculation",
+        ),
     ] = False,
-    write_kwargs: WriteKwargs = None,
     plot_to_file: Annotated[
         bool,
-        Option(help="Whether to plot equation of state."),
+        Option(
+            help="Whether to plot equation of state.",
+            rich_help_panel="Calculation",
+        ),
     ] = False,
+    # MLIP Calculator
     arch: Architecture = "mace_mp",
     device: Device = "cpu",
     model_path: ModelPath = None,
-    read_kwargs: ReadKwargsLast = None,
     calc_kwargs: CalcKwargs = None,
+    # Structure I/O
     file_prefix: FilePrefix = None,
+    read_kwargs: ReadKwargsLast = None,
+    write_kwargs: WriteKwargs = None,
+    # Logging/summary
     log: LogPath = None,
-    tracker: Annotated[
-        bool, Option(help="Whether to save carbon emissions of calculation")
-    ] = True,
+    tracker: Tracker = True,
     summary: Summary = None,
 ) -> None:
     """
@@ -103,27 +132,26 @@ def eos(
         Other keyword arguments to pass to geometry optimizer. Default is {}.
     write_structures
         True to write out all genereated structures. Default is False.
-    write_kwargs
-        Keyword arguments to pass to ase.io.write to save generated structures.
-        Default is {}.
     plot_to_file
         Whether to save plot equation of state to svg. Default is False.
     arch
-        MLIP architecture to use for geometry optimization.
-        Default is "mace_mp".
+        MLIP architecture to use for geometry optimization. Default is "mace_mp".
     device
         Device to run model on. Default is "cpu".
     model_path
         Path to MLIP model. Default is `None`.
-    read_kwargs
-        Keyword arguments to pass to ase.io.read. By default,
-            read_kwargs["index"] is -1.
     calc_kwargs
         Keyword arguments to pass to the selected calculator. Default is {}.
     file_prefix
         Prefix for output files, including directories. Default directory is
         ./janus_results, and default filename prefix is inferred from the input
         stucture filename.
+    read_kwargs
+        Keyword arguments to pass to ase.io.read. By default,
+            read_kwargs["index"] is -1.
+    write_kwargs
+        Keyword arguments to pass to ase.io.write to save generated structures.
+        Default is {}.
     log
         Path to write logs to. Default is inferred from `file_prefix`.
     tracker