more bug fixes (#533)

Co-authored-by: John Wu <[email protected]>

More dependency fixes such that readthedocs can install dependencies properly.

Author: jhnwu3

pyproject.toml

@@ -25,9 +25,9 @@ dependencies = [
   "torch~=2.7.1",
   "torchvision",
   "transformers~=4.53.2",
-  "rdkit==2025.3.3",
+  "rdkit",
   "scikit-learn~=1.7.0",
-  "networkx==3.5",
+  "networkx",
   "mne~=1.10.0",
   "urllib3~=2.5.0",
   "numpy~=1.26.4",