Refactor contact dynamics and detection logic to use signed distance functions

.gitignore

@@ -151,3 +151,6 @@ src/jaxsim/_version.py
 # data
 .mp4
 .png
+
+# macOS
+.DS_Store

docs/guide/configuration.rst

@@ -9,21 +9,10 @@ Collision Dynamics
 
 Environment variables starting with ``JAXSIM_COLLISION_`` are used to configure collision dynamics. The available variables are:
 
-- ``JAXSIM_COLLISION_SPHERE_POINTS``: Specifies the number of collision points to approximate the sphere.
-
-  *Default:* ``50``.
-
-- ``JAXSIM_COLLISION_MESH_ENABLED``: Enables or disables mesh-based collision detection.
+- ``JAXSIM_COLLISION_ENABLE_CYLINDER``: Enables collision dynamics for cylindrical geometries.
 
   *Default:* ``False``.
 
-- ``JAXSIM_COLLISION_USE_BOTTOM_ONLY``: Limits collision detection to only the bottom half of the box or sphere.
-
-  *Default:* ``False``.
-
-.. note::
-  The bottom half is defined as the half of the box or sphere with the lowest z-coordinate in the collision link frame.
-
 
 Testing
 ~~~~~~~

environment.yml

@@ -15,7 +15,6 @@ dependencies:
   - pptree
   - qpax
   - rod >= 0.3.3
-  - trimesh
   - typing_extensions # python<3.12
   # ====================================
   # Optional dependencies from setup.cfg

examples/jaxsim_as_physics_engine_advanced.ipynb

@@ -130,10 +130,7 @@
     "# JaxSim currently only supports collisions between points attached to bodies\n",
     "# and a ground surface modeled as a heightmap sampled from a smooth function.\n",
     "# While this approach is universal as it applies to generic meshes, the number\n",
-    "# of considered points greatly affects the performance. Spheres, by default,\n",
-    "# are discretized with 250 points. It's too much for this simple example.\n",
-    "# This number can be decreased with the following environment variable.\n",
-    "os.environ[\"JAXSIM_COLLISION_SPHERE_POINTS\"] = \"50\""
+    "# of considered points greatly affects the performance."
    ]
   },
   {

pyproject.toml

@@ -55,7 +55,6 @@ dependencies = [
     "qpax",
     "rod >= 0.4.1",
     "typing_extensions ; python_version < '3.12'",
-    "trimesh",
 ]
 
 [project.optional-dependencies]
@@ -223,8 +222,7 @@ jax-dataclasses = "*"
 pptree = "*"
 optax = "*"
 qpax = "*"
-rod = ">=0.4.1"
-trimesh = "*"
+rod = "*"
 typing_extensions = "*"
 #
 # Optional dependencies.