Remove pyembree (#252)

* remove collada and pyembree

* remove default options from config

* re-add collada to Ingredient.py

examples/packing-configs/peroxisome_packing_config.json

@@ -1,19 +1,10 @@
 {
     "name": "analyze",
-    "format": "simularium",
-    "inner_grid_method": "trimesh",
-    "live_packing": false,
-    "ordered_packing": false,
     "number_of_packings": 1,
     "out": "out/analyze",
-    "overwrite_place_method": true,
-    "place_method": "spheresSST",
     "save_analyze_result": true,
-    "show_grid_plot": false,
     "save_plot_figures": true,
     "spacing": 2.5,
-    "use_periodicity": false,
-    "show_sphere_trees": false,
-    "load_from_grid_file": true,
+    "load_from_grid_file": false,
     "upload_results": false
 }

setup.py

@@ -53,13 +53,12 @@
     "firebase_admin>=6.0.1",
     "matplotlib>=3.3.4",
     "numpy>=1.19.2",
-    "pmw==2.0.1",
     "scipy>=1.6.2",
     "simulariumio>=1.6.3",
     "plotly>=5.3.1",
-    "pycollada==0.7.2",
-    "pyembree>=0.1.8",
+    "pycollada>=0.7.1",
     "pymunk>=6.2.0",
+    "rtree",
     "trimesh>=3.9.34",
     "deepdiff>=5.5.0",
     "python-dotenv>=1.0.0",