feat(GridFire): Added a number of python hooks

python hooks to make getting base composition more reliable; further, a number of small changes made to aid in my analysis in response to ref report 1

tests/python/logger.py

@@ -0,0 +1,80 @@
+from enum import Enum
+
+from typing import Dict, List, Any, SupportsFloat
+import json
+from datetime import datetime
+import os
+import sys
+
+from gridfire.solver import PointSolverTimestepContext
+from gridfire._gridfire.engine.scratchpads import StateBlob
+import gridfire
+
+class LogEntries(Enum):
+    Step = "Step"
+    t = "t"
+    dt = "dt"
+    eps = "eps"
+    Composition = "Composition"
+    ReactionContributions = "ReactionContributions"
+
+
+class StepLogger:
+    def __init__(self):
+        self.num_steps : int = 0
+        self.steps : List[Dict[LogEntries, Any]] = []
+
+    def log_step(self, ctx: PointSolverTimestepContext):
+        comp_data: Dict[str, SupportsFloat] = {}
+        for species in ctx.engine.getNetworkSpecies(ctx.state_ctx):
+            sid = ctx.engine.getSpeciesIndex(ctx.state_ctx, species)
+            comp_data[species.name()] = ctx.state[sid]
+        entry : Dict[LogEntries, Any] = {
+            LogEntries.Step: ctx.num_steps,
+            LogEntries.t: ctx.t,
+            LogEntries.dt: ctx.dt,
+            LogEntries.eps: ctx.state[-1],
+            LogEntries.Composition: comp_data,
+        }
+        self.steps.append(entry)
+        self.num_steps += 1
+
+    def to_json(self, filename: str, **kwargs):
+        serializable_steps : List[Dict[str, Any]] = [
+            {
+                LogEntries.Step.value: step[LogEntries.Step],
+                LogEntries.t.value: step[LogEntries.t],
+                LogEntries.dt.value: step[LogEntries.dt],
+                LogEntries.eps.value: step[LogEntries.eps],
+                LogEntries.Composition.value: step[LogEntries.Composition],
+            }
+            for step in self.steps
+        ]
+        out_data : Dict[str, Any] = {
+            "Metadata": {
+                "NumSteps": self.num_steps,
+                **kwargs,
+                "DateCreated": datetime.now().isoformat(),
+                "GridFireVersion": gridfire.__version__,
+                "Author": "Emily M. Boudreaux",
+                "OS": os.uname().sysname,
+                "ClangVersion": os.popen("clang --version").read().strip(),
+                "GccVersion": os.popen("gcc --version").read().strip(),
+                "PythonVersion": sys.version,
+            },
+            "Steps": serializable_steps
+        }
+        with open(filename, 'w') as f:
+            json.dump(out_data, f, indent=4)
+
+
+    def summary(self) -> Dict[str, Any]:
+        if not self.steps:
+            return {}
+        final_step = self.steps[-1]
+        summary_data : Dict[str, Any] = {
+            "TotalSteps": self.num_steps,
+            "FinalTime": final_step[LogEntries.t],
+            "FinalComposition": final_step[LogEntries.Composition],
+        }
+        return summary_data