Fix format and warnings for docs

docs/conf.py

@@ -1,7 +1,7 @@
 # Configuration file for the Sphinx documentation builder.
+import os
 import pathlib
 import sys
-import os
 
 # -- Version information
 

src/jaxsim/high_level/model.py

@@ -137,8 +137,7 @@ def build_from_model_description(
         Build a Model object from a model description.
 
         Args:
-            model_description: A path to an SDF/URDF file, a string containing its content,
-                or a pre-parsed/pre-built rod model.
+            model_description: A path to an SDF/URDF file, a string containing its content, or a pre-parsed/pre-built rod model.
             model_name: The optional name of the model that overrides the one in the description.
             vel_repr: The velocity representation to use.
             gravity: The 3D gravity vector.

src/jaxsim/math/adjoint.py

@@ -1,9 +1,12 @@
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
 from jaxsim.sixd import so3
+
 from .quaternion import Quaternion
 from .skew import Skew
 
+
 class Adjoint:
     @staticmethod
     def from_quaternion_and_translation(

src/jaxsim/math/conv.py

@@ -1,7 +1,10 @@
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
+
 from .skew import Skew
 
+
 class Convert:
     @staticmethod
     def coordinates_tf(X: jtp.Matrix, p: jtp.Matrix) -> jtp.Matrix:

src/jaxsim/math/cross.py

@@ -1,7 +1,10 @@
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
+
 from .skew import Skew
 
+
 class Cross:
     @staticmethod
     def vx(velocity_sixd: jtp.Vector) -> jtp.Matrix:

src/jaxsim/math/inertia.py

@@ -1,8 +1,12 @@
 from typing import Tuple
+
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
+
 from .skew import Skew
 
+
 class Inertia:
     @staticmethod
     def to_sixd(mass: jtp.Float, com: jtp.Vector, I: jtp.Matrix) -> jtp.Matrix:

src/jaxsim/math/joint.py

@@ -1,10 +1,14 @@
 from typing import Tuple, Union
+
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
 from jaxsim.parsers.descriptions import JointDescriptor, JointGenericAxis, JointType
+
 from .adjoint import Adjoint
 from .rotation import Rotation
 
+
 def jcalc(
     jtyp: Union[JointType, JointDescriptor], q: jtp.Float
 ) -> Tuple[jtp.Matrix, jtp.Vector]:

src/jaxsim/math/quaternion.py

@@ -1,8 +1,10 @@
 import jax.lax
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
 from jaxsim.sixd import so3
 
+
 class Quaternion:
     @staticmethod
     def to_xyzw(wxyz: jtp.Vector) -> jtp.Vector:

src/jaxsim/math/rotation.py

@@ -1,10 +1,14 @@
 from typing import Tuple
+
 import jax
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
 from jaxsim.sixd import so3
+
 from .skew import Skew
 
+
 class Rotation:
     @staticmethod
     def x(theta: jtp.Float) -> jtp.Matrix:

src/jaxsim/math/skew.py

@@ -1,6 +1,8 @@
 import jax.numpy as jnp
+
 import jaxsim.typing as jtp
 
+
 class Skew:
     """
     A utility class for skew-symmetric matrix operations.

src/jaxsim/parsers/descriptions/collision.py

@@ -10,6 +10,7 @@
 
 from .link import LinkDescription
 
+
 @dataclasses.dataclass
 class CollidablePoint:
     """
@@ -58,6 +59,7 @@ def __str__(self):
             + ")"
         )
 
+
 @dataclasses.dataclass
 class CollisionShape(abc.ABC):
     """
@@ -78,6 +80,7 @@ def __str__(self):
             + "\n])"
         )
 
+
 @dataclasses.dataclass
 class BoxCollision(CollisionShape):
     """
@@ -90,6 +93,7 @@ class BoxCollision(CollisionShape):
 
     center: npt.NDArray
 
+
 @dataclasses.dataclass
 class SphereCollision(CollisionShape):
     """

src/jaxsim/parsers/descriptions/joint.py

@@ -7,6 +7,7 @@
 
 from .link import LinkDescription
 
+
 class JointType(enum.IntEnum):
     """
     Enumeration of joint types for robot joints.
@@ -31,12 +32,13 @@ class JointType(enum.IntEnum):
     Rx = enum.auto()
     Ry = enum.auto()
     Rz = enum.auto()
-    
+
     # Prismatic joints, single axis
     Px = enum.auto()
     Py = enum.auto()
     Pz = enum.auto()
 
+
 @dataclasses.dataclass
 class JointDescriptor:
     """
@@ -52,6 +54,7 @@ class JointDescriptor:
     def __hash__(self) -> int:
         return hash(self.__repr__())
 
+
 @dataclasses.dataclass
 class JointGenericAxis(JointDescriptor):
     """
@@ -74,6 +77,7 @@ def __eq__(self, other):
     def __hash__(self) -> int:
         return hash(self.__repr__())
 
+
 @dataclasses.dataclass
 class JointDescription:
     """

src/jaxsim/parsers/descriptions/link.py

@@ -10,6 +10,7 @@
 from jaxsim.sixd import se3
 from jaxsim.utils import JaxsimDataclass
 
+
 @jax_dataclasses.pytree_dataclass
 class LinkDescription(JaxsimDataclass):
     """

src/jaxsim/parsers/descriptions/model.py

@@ -3,12 +3,15 @@
 from typing import List
 
 import numpy.typing as npt
+
 import jaxsim.logging as logging
+
 from ..kinematic_graph import KinematicGraph, RootPose
 from .collision import CollidablePoint, CollisionShape
 from .joint import JointDescription
 from .link import LinkDescription
 
+
 @dataclasses.dataclass(frozen=True)
 class ModelDescription(KinematicGraph):
     """
@@ -30,7 +33,6 @@ class ModelDescription(KinematicGraph):
         update_collision_shape_of_link(...): Enable or disable collision shapes associated with a link.
         collision_shape_of_link(...): Get the collision shape associated with a specific link.
         all_enabled_collidable_points(...): Get all enabled collidable points in the model.
-
     """
 
     name: str = None
@@ -66,7 +68,6 @@ def build_model_from(
 
         Raises:
             ValueError: If invalid or missing input data.
-
         """
 
         # Create the full kinematic graph
@@ -164,8 +165,8 @@ def reduce(self, considered_joints: List[str]) -> "ModelDescription":
 
         Raises:
             ValueError: If the specified joints are not part of the model.
-
         """
+
         msg = "The model reduction logic assumes that removed joints have zero angles"
         logging.info(msg=msg)
 

src/jaxsim/parsers/kinematic_graph.py

@@ -29,6 +29,7 @@ class RootPose(NamedTuple):
         root_position (npt.NDArray): A NumPy array of shape (3,) representing the root's position.
         root_quaternion (npt.NDArray): A NumPy array of shape (4,) representing the root's quaternion.
     """
+
     root_position: npt.NDArray = np.zeros(3)
     root_quaternion: npt.NDArray = np.array([1.0, 0, 0, 0])
 

src/jaxsim/physics/algos/crba.py

@@ -21,7 +21,7 @@ def crba(model: PhysicsModel, q: jtp.Vector) -> jtp.Matrix:
     Returns:
         jtp.Matrix: The Composite Rigid-Body Inertia Matrix (CRBA) of the articulated body or robot.
     """
-    
+
     _, q, _, _, _, _ = utils.process_inputs(
         physics_model=model, xfb=None, q=q, qd=None, tau=None, f_ext=None
     )

src/jaxsim/physics/algos/forward_kinematics.py

@@ -25,7 +25,7 @@ def forward_kinematics_model(
     Returns:
         jtp.Array: A 3D array containing the forward kinematics transformations for all links.
     """
-    
+
     x_fb, q, _, _, _, _ = utils.process_inputs(
         physics_model=model, xfb=xfb, q=q, qd=None, tau=None, f_ext=None
     )

src/jaxsim/physics/algos/soft_contacts.py

@@ -20,7 +20,22 @@
 
 @jax_dataclasses.pytree_dataclass
 class SoftContactsState:
-    """State of the soft contacts model."""
+    """
+    State of the soft contacts model.
+
+    Attributes:
+        tangential_deformation (jtp.Matrix): The tangential deformation of the material at each collidable point.
+
+    Methods:
+        zero(physics_model: "jaxsim.physics.model.physics_model.PhysicsModel") -> SoftContactsState:
+            Modify the SoftContactsState instance imposing zero tangential deformation.
+
+        valid(physics_model: "jaxsim.physics.model.physics_model.PhysicsModel") -> bool:
+            Check if the soft contacts state has valid shape.
+
+        replace(validate: bool = True, kwargs) -> SoftContactsState:
+            Replace attributes of the soft contacts state.
+    """
 
     tangential_deformation: jtp.Matrix
 
@@ -37,7 +52,7 @@ def zero(
         Returns:
             SoftContactsState: A SoftContactsState instance with zero tangential deformation.
         """
-        
+
         return SoftContactsState(
             tangential_deformation=jnp.zeros(shape=(3, physics_model.gc.body.size))
         )
@@ -54,7 +69,7 @@ def valid(
         Returns:
             bool: True if the state has a valid shape, otherwise False.
         """
-        
+
         from jaxsim.simulation.utils import check_valid_shape
 
         return check_valid_shape(
@@ -70,7 +85,6 @@ def replace(self, validate: bool = True, **kwargs) -> "SoftContactsState":
 
         Args:
             validate (bool, optional): Whether to validate the state after replacement. Defaults to True.
-            **kwargs: Keyword arguments for attribute replacement.
 
         Returns:
             SoftContactsState: A new SoftContactsState instance with replaced attributes.

src/jaxsim/physics/algos/terrain.py

@@ -75,6 +75,6 @@ def height(self, x: float, y: float) -> float:
         Returns:
             float: The height of the terrain at the specified location on the plane.
         """
-        
+
         a, b, c = self.plane_normal
-        return -(a * x + b * x) / c
+        return -(a * x + b * x) / c

src/jaxsim/physics/model/ground_contact.py

@@ -19,8 +19,7 @@ class GroundContact:
 
     Attributes:
         point (npt.NDArray): An array of shape (3, N) representing the 3D positions of collidable points.
-        body (Static[npt.NDArray]): An array of integers representing the indices of the bodies (links)
-            associated with each collidable point.
+        body (Static[npt.NDArray]): An array of integers representing the indices of the bodies (links) associated with each collidable point.
 
     Methods:
         build_from(model_description: ModelDescription) -> GroundContact:

src/jaxsim/simulation/simulator.py

@@ -235,8 +235,7 @@ def insert_model_from_description(
         Insert a model from a model description.
 
         Args:
-            model_description: A path to an SDF/URDF file, a string containing its content,
-                or a pre-parsed/pre-built rod model.
+            model_description: A path to an SDF/URDF file, a string containing its content, or a pre-parsed/pre-built rod model.
             model_name: The optional name of the model that overrides the one in the description.
             considered_joints: Optional list of joints to consider. It is also useful to specify the joint serialization.