Remove ompl, collision detection (beta) and morphological descriptors

pyproject.toml

@@ -28,7 +28,6 @@ dependencies = [
   "numpy>=2.0.2",
   "numpy-quaternion>=2023.0.3",
   "omegaconf>=2.3.0",
-  "ompl>=1.7.0",
   "opencv-python>=4.11.0.86",
   "panel>=1.8.9",
   "pillow>=11.3.0",

src/ariel/ec/genotypes/nde/nde.py

@@ -121,19 +121,18 @@ def forward(
         self,
         genotype: list[npt.NDArray[np.float32]],
     ) -> list[npt.NDArray[np.float32]]:
-        """
-        Forward pass through the neural developmental encoder.
+        """Forward pass through the neural developmental encoder.
 
         Parameters
         ----------
         genotype : list[npt.NDArray[np.float32]]
             List of chromosomes (numpy arrays).
+
         Returns
         -------
         list[npt.NDArray[np.float32]]
             List of phenotype outputs (numpy arrays).
         """
-
         outputs: list[npt.NDArray[np.float32]] = []
         for idx, chromosome in enumerate(genotype):
             with torch.no_grad():  # double safety

src/ariel/ec/genotypes/tree/io.py

@@ -1,18 +1,49 @@
-"""I/O helpers for tree genomes (JSON load/save and networkx conversion).
-"""
+"""I/O helpers for tree genomes (JSON load/save and networkx conversion)."""
 from __future__ import annotations
 
-from typing import Dict, Any
+from typing import Any
+
 from .tree_genome import TreeGenome
 
 
 def load_genome(path: str) -> TreeGenome:
+    """Load a TreeGenome from a JSON file.
+
+    Parameters
+    ----------
+    path : str
+        Path to the JSON file containing the genome.
+
+    Returns
+    -------
+    TreeGenome
+        The loaded TreeGenome instance.
+    """
     return TreeGenome.load_json(path)
 
 
 def save_genome(genome: TreeGenome, path: str) -> None:
+    """Save a TreeGenome to a JSON file.
+
+    Parameters
+    ----------
+    genome : TreeGenome
+        The TreeGenome instance to save.
     genome.save_json(path)
+    """
 
 
 def genome_to_networkx_dict(genome: TreeGenome) -> dict[str, Any]:
+    """Convert a TreeGenome to a dictionary format compatible with networkx.
+
+    Parameters
+    ----------
+    genome : TreeGenome
+        The TreeGenome instance to convert.
+
+    Returns
+    -------
+    dict[str, Any]
+        A dictionary representation of the genome suitable for networkx.
+    """
     return genome.to_dict()