Feat/cli (#6)

* feat: add model subcommands

* typo

* docs: update readme

README.md

@@ -15,7 +15,7 @@ Pydiffuser is a numerical simulation framework for nonequilibrium statistical ph
 
 This package mainly aims:
 - to share code to implement a numerical simulation on physical models written in various forms of [stochastic differential equations](https://en.wikipedia.org/wiki/Stochastic_differential_equation).
-- to revisit recent research highlights in non-equilibrium statistical physics.
+- to revisit recent research highlights in nonequilibrium statistical physics.
 - to reduce the repeated code on time-series data analysis, e.g., statistical analysis of [single-particle trajectory](https://en.wikipedia.org/wiki/Single-particle_trajectory) for [SPT](https://en.wikipedia.org/wiki/Single-particle_tracking) experiments.
 - to provide the skeleton of stochastic modeling for anyone interested in stochastic processes.
 
@@ -75,7 +75,7 @@ It is obtained by `matplotlib.pyplot.plot(tracer.position_x1, tracer.position_x2
 List all stochastic models supported by Pydiffuser.
 
 ```console
-$ pydiffuser list
+$ pydiffuser model list
 NAME            MODEL                           CONFIG                          DIMENSION       
 abp             ActiveBrownianParticle          ActiveBrownianParticleConfig    2d              
 aoup            ActiveOUParticle                ActiveOUParticleConfig          1d, 2d, 3d      

pydiffuser/_cli/cli.py

@@ -1,21 +1,15 @@
 import click
 
-from pydiffuser._cli.cli_utils import get_model_info
+from pydiffuser._cli.cli_utils import add_model_subcommands
 
 
 def create():
     @click.group()
     @click.version_option()
     def pydiffuser_cli():
-        """Pydiffuser CLI"""
+        """Pydiffuser CLI."""
 
-    @pydiffuser_cli.command()
-    def list():
-        """List all models defined in Pydiffuser."""
-
-        info = get_model_info()
-        for name, model, config, dimension in info:
-            click.echo(f"{name:16}{model:32}{config:32}{dimension:16}")
+    add_model_subcommands(pydiffuser_cli)
 
     return pydiffuser_cli
 

pydiffuser/_cli/cli_utils.py

@@ -1,3 +1,5 @@
+import click
+
 from pydiffuser.models import CONFIG_REGISTRY, MODEL_REGISTRY
 
 
@@ -17,3 +19,17 @@ def get_model_info():
         for k, dim in dims.items()
     ]
     return info
+
+
+def add_model_subcommands(cli: click.Group) -> None:
+    @cli.group(name="model")
+    def model_cli():
+        """Subcommands related to model."""
+
+    @model_cli.command()
+    def list():
+        """List all models defined in Pydiffuser."""
+
+        info = get_model_info()  # type: ignore[no-untyped-call]
+        for name, model, config, dimension in info:
+            click.echo(f"{name:16}{model:32}{config:32}{dimension:16}")

pydiffuser/mech/fields.py

@@ -15,7 +15,7 @@ def register(potential: Any) -> Any:
     def decorator() -> Any:
         if not isinstance(potential, PjitFunction):
             raise RuntimeError(
-                "Potential must be transformed via 'jax.jit' to register"
+                "Potential must be transformed via `jax.jit` to register"
             )
         FIELD_REGISTRY[f"{potential.__name__}"] = potential
         return potential