From b244761db1783619331f2e732069196da6f52c51 Mon Sep 17 00:00:00 2001
From: Robin Meersman <echteenrobin@gmail.com>
Date: Mon, 4 May 2026 22:39:33 +0200
Subject: [PATCH] cleanup(MLPs): moved build adjacency to own file, made MLPs a
 full python package

---
 src/brittle_star_project/MLPs/__init__.py     | 19 ++++++
 .../MLPs/adjancency_builder.py                | 67 +++++++++++++++++++
 2 files changed, 86 insertions(+)
 create mode 100644 src/brittle_star_project/MLPs/__init__.py
 create mode 100644 src/brittle_star_project/MLPs/adjancency_builder.py

diff --git a/src/brittle_star_project/MLPs/__init__.py b/src/brittle_star_project/MLPs/__init__.py
new file mode 100644
index 0000000..8f9c7f7
--- /dev/null
+++ b/src/brittle_star_project/MLPs/__init__.py
@@ -0,0 +1,19 @@
+from .mlps import (
+    GenericDenseLayersWithActivation,
+    OneDenseLayerMLP,
+    Actor,
+    MessagePasser,
+    AgentParams,
+    Storage,
+)
+from .adjancency_builder import build_adjacency
+
+__all__ = [
+    "GenericDenseLayersWithActivation",
+    "OneDenseLayerMLP",
+    "Actor",
+    "MessagePasser",
+    "AgentParams",
+    "Storage",
+    "build_adjacency",
+]
diff --git a/src/brittle_star_project/MLPs/adjancency_builder.py b/src/brittle_star_project/MLPs/adjancency_builder.py
new file mode 100644
index 0000000..878a02c
--- /dev/null
+++ b/src/brittle_star_project/MLPs/adjancency_builder.py
@@ -0,0 +1,67 @@
+from brittle_star_project.environment.env_config import MorphMode
+import jax.numpy as jnp
+
+
+def build_adjacency(segments_per_arm, mode: MorphMode):
+    num_arms = sum(1 for s in segments_per_arm if s > 0)
+    num_segments = sum(segments_per_arm)
+
+    # FOR NOW SEMI HARDCODE:
+    # CENTRALIZED: 1 agent, no stress, adja = 1,1 = [[1]]
+    # FULLY CONNECTED: 5 agents: adj = alle 1
+    # CENTRAL DISK:#arms= 5 agents, only neighbor as adjacent so diagonal kinda..
+    # ARM = #segments agents: diago kinda, but extra, center ring too, put center mlps first or..
+
+    if mode == MorphMode.CENTRALIZED:
+        return jnp.ones((1, 1))
+
+    if mode == MorphMode.FULLY_CONNECTED:
+        adj = jnp.ones((num_arms, num_arms))  # everybody adjacent everybody
+        return adj
+
+    if mode == MorphMode.RING:  # ring
+        adj = jnp.zeros((num_arms, num_arms))
+        for i in range(num_arms):
+            adj = adj.at[i, i].set(1)  # self
+            adj = adj.at[i, (i - 1) % num_arms].set(1)
+            adj = adj.at[i, (i + 1) % num_arms].set(1)  # left and right..
+        return adj
+
+    if mode == MorphMode.SEGMENT:
+        num_nodes = num_arms + num_segments
+        adj = jnp.zeros((num_nodes, num_nodes))
+
+        # first ring
+        for i in range(num_arms):
+            # self
+            adj = adj.at[i, i].set(1)
+
+            # ring neighbors
+            adj = adj.at[i, (i - 1) % num_arms].set(1)
+            adj = adj.at[i, (i + 1) % num_arms].set(1)
+
+        # then segment chains
+        idx = 0
+        for arm_idx, seg_count in enumerate(segments_per_arm):
+            for i in range(seg_count):
+                seg_node = num_arms + idx + i
+
+                adj = adj.at[seg_node, seg_node].set(1)
+                if i > 0:
+                    adj = adj.at[seg_node, seg_node - 1].set(1)
+                if i < seg_count - 1:
+                    adj = adj.at[seg_node, seg_node + 1].set(1)
+
+            idx += seg_count
+
+        idx = 0
+        for arm_idx, seg_count in enumerate(segments_per_arm):
+            first_seg = num_arms + idx  # first segment of this arm
+
+            # connect ring node first segment
+            adj = adj.at[arm_idx, first_seg].set(1)
+            adj = adj.at[first_seg, arm_idx].set(1)
+
+            idx += seg_count
+
+        return adj