perf(graph_engine): finished sparsity system for jacobian, major preformance win, roughly 20x faster

essentially all callers can now inform the graph engine about which species they hold active and graph engine then uses those to define a sparsity pattern and only calculate the jacobian along that sparsity pattern

src/include/gridfire/engine/views/engine_priming.h

@@ -1,9 +1,7 @@
 #pragma once
 
-#include "gridfire/engine/engine_abstract.h"
 #include "gridfire/engine/views/engine_defined.h"
 
-
 #include "fourdst/logging/logging.h"
 #include "fourdst/composition/atomicSpecies.h"
 
@@ -51,7 +49,7 @@ namespace gridfire {
 
 
     private:
-        quill::Logger* m_logger = fourdst::logging::LogManager::getInstance().getLogger("log");
+        quill::Logger* m_logger = LogManager::getInstance().getLogger("log");
         fourdst::atomic::Species m_primingSpecies; ///< The priming species, if specified.
     private:
         /**