Merge pull request #21 from gperdrizet/dev

General clean up

Author: gperdrizet

docs/source/api.rst

@@ -68,10 +68,3 @@ Core functions
 .. automodule:: hill_climber.climber_functions
    :members:
    :undoc-members:
-
-Plotting functions
-------------------
-
-.. automodule:: hill_climber.plotting_functions
-   :members:
-   :undoc-members:

docs/source/index.rst

@@ -48,7 +48,6 @@ Features
 - **Multi-column data**: Optimize datasets with any number of features
 - **Structured state management**: ReplicaState dataclass with type hints for clarity and IDE support
 - **Checkpointing**: Save and resume long-running optimizations with configurable checkpoint intervals
-- **Rich visualization**: Built-in plotting functions for results analysis
 - **JIT compilation**: Numba-optimized core functions for performance
 
 Data format

hill_climber/__init__.py

@@ -10,7 +10,6 @@
     ReplicaState: State container for individual replicas
     OptimizerConfig: Type-safe configuration dataclass
     Helper functions: Data manipulation and objective calculation utilities
-    Plotting functions: Visualization tools for input data and results
 
 Example:
     >>> from hill_climber import HillClimber
@@ -54,9 +53,6 @@
     extract_columns,
     calculate_objective
 )
-from .plotting_functions import (
-    plot_input_data
-)
 
 __all__ = [
     'HillClimber',
@@ -68,5 +64,4 @@
     'perturb_vectors',
     'extract_columns',
     'calculate_objective',
-    'plot_input_data',
 ]

hill_climber/database.py

@@ -337,6 +337,17 @@ def set_run_end_time(self):
             """, (time.time(),))
 
 
+    def checkpoint_database(self):
+        """Checkpoint the database to consolidate WAL files.
+        
+        Merges all Write-Ahead Log (WAL) changes back into the main database
+        file and removes the auxiliary .db-shm and .db-wal files. This should
+        be called when the optimization is complete to clean up temporary files.
+        """
+        with self.get_connection() as conn:
+            conn.execute("PRAGMA wal_checkpoint(TRUNCATE)")
+
+
     def update_replica_status(self, replica_id: int, current_perturbation_num: int,
                              num_accepted: int, num_improvements: int,
                              temperature: float, best_objective: float,

hill_climber/optimizer.py

@@ -565,6 +565,9 @@ def _finalize_results(self) -> np.ndarray:
 
             # Mark run as complete
             self.db_writer.set_run_end_time()
+            
+            # Checkpoint database to consolidate WAL files and remove auxiliary files
+            self.db_writer.checkpoint_database()
 
         # Final checkpoint
         if self.checkpoint_file: