DOCS: use auto-generated module file for python API

Author: Puerling

conf.py

@@ -112,7 +112,6 @@
     ".venv",
     ".github",
     "_build",
-    "core/docs/python-api/apidoc/spirit.rst",
     "core/docs/python-api/apidoc/modules.rst",
     "core/thirdparty/toml++/README.md",
     "Thumbs.db",

core/docs/python-api/API_Reference.rst

@@ -2,19 +2,6 @@ Full API reference
 ==================================
 
 .. toctree::
-    :maxdepth: 4
+   :maxdepth: 5
 
-    spirit.chain            <apidoc/spirit.chain>
-    spirit.configuration    <apidoc/spirit.configuration>
-    spirit.constants        <apidoc/spirit.constants>
-    spirit.geometry         <apidoc/spirit.geometry>
-    spirit.hamiltonian      <apidoc/spirit.hamiltonian>
-    spirit.htst             <apidoc/spirit.htst>
-    spirit.io               <apidoc/spirit.io>
-    spirit.log              <apidoc/spirit.log>
-    spirit.parameters       <apidoc/spirit.parameters>
-    spirit.quantities       <apidoc/spirit.quantities>
-    spirit.simulation       <apidoc/spirit.simulation>
-    spirit.state            <apidoc/spirit.state>
-    spirit.system           <apidoc/spirit.system>
-    spirit.transition       <apidoc/spirit.transition>
+   apidoc/spirit