Added pip dependencies to pyproject.toml

pyproject.toml

@@ -18,11 +18,22 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.8"
+requires-python = "==3.11"
 # Declare any run-time dependencies that should be installed with the package.
-#dependencies = [
+dependencies = [
 #    "importlib-resources;python_version<'3.10'",
-#]
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "pillow",
+    "pandas",
+    "anytree",
+    "networkx",
+    "rdkit",
+    "openmm",
+    "lammps",
+    "mdtraj",
+]
 
 # Update the urls once the hosting is set up.
 #[project.urls]
@@ -32,7 +43,22 @@ requires-python = ">=3.8"
 [project.optional-dependencies]
 test = [
   "pytest>=6.1.2",
-  "pytest-runner"
+  "pytest-runner",
+  "pytest-cov",
+  "codecov",
+]
+jupyter = [
+    "jupyterlab",
+    "ipywidgets==8.0.4",
+]
+visuals = [
+    "rich",
+    "nglview",
+    "py3Dmol",
+]
+chemdb = [
+    "cirpy",
+    "chemspipy",
 ]
 
 [tool.setuptools]