feat(python): Repaired python bindings

Python bindings have now been brought back up to feature pairity with
C++. Further, stubs have been added for all python features so that code
completion will work

src/lib/engine/diagnostics/dynamic_engine_diagnostics.cpp

@@ -15,7 +15,7 @@ namespace gridfire::engine::diagnostics {
         const double relTol,
         const double absTol,
         const size_t top_n,
-        bool json
+        const bool json
     ) {
         struct SpeciesError {
             std::string name;