From 6ee7d8ee12356bb645b5368bd23d1ef5c37c2136 Mon Sep 17 00:00:00 2001
From: Anto01 <antoine.letarte@gmail.com>
Date: Wed, 7 Jan 2026 09:02:36 -0500
Subject: [PATCH] build: Add optional dependency groups and clean up
 pyproject.toml
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- Add neural optional group (torch, torch-geometric, tensorboard)
- Add gnn optional group (torch, torch-geometric)
- Add all optional group for convenience
- Remove mcp optional group (not implemented)
- Remove mcp_server from packages.find
- Update pytest coverage config

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 pyproject.toml | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f5f22b06..a1898248 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,8 +35,15 @@ dev = [
     "pre-commit>=3.6.0",
 ]
 
-mcp = [
-    "mcp>=0.1.0",
+neural = [
+    "torch>=2.0.0",
+    "torch-geometric>=2.3.0",
+    "tensorboard>=2.13.0",
+]
+
+gnn = [
+    "torch>=2.0.0",
+    "torch-geometric>=2.3.0",
 ]
 
 dashboard = [
@@ -44,13 +51,17 @@ dashboard = [
     "dash-bootstrap-components>=1.5.0",
 ]
 
+all = [
+    "atomizer[neural,gnn,dev,dashboard]",
+]
+
 [build-system]
 requires = ["setuptools>=68.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["mcp_server*", "optimization_engine*", "nx_journals*"]
+include = ["optimization_engine*", "nx_journals*"]
 
 [tool.black]
 line-length = 100
@@ -73,4 +84,4 @@ testpaths = ["tests"]
 python_files = ["test_*.py"]
 python_classes = ["Test*"]
 python_functions = ["test_*"]
-addopts = "-v --cov=mcp_server --cov=optimization_engine --cov-report=html --cov-report=term"
+addopts = "-v --cov=optimization_engine --cov-report=html --cov-report=term"