feat: Consolidate code structure

[pesap]

Code Structure Changes

• Reorganized methods fromapi.py and sqlite.py to plexosdb.py and db_manager.py. plexosdb.py includes only the API to the application, e.g., get_object, add_object and db_manager the API to SQLite only.
• Enhanced documentation to all the methods
• Database Interface Improvements with accurate transaction handling, context manager and rollbacks
• Added class factory method for PlexosDB from_xml() for easier instantiation from an XML file,
• Added plexos version property,
• Consistent parameter naming and method signatures
• Chunked data processing for large datasets
• Memory-efficient iterators for large result sets

Remaining methods to migrate

• version
• backup_database - Backup the in-memory database to a file
• add_memberships_from_records - Bulk insert multiple memberships
• add_properties_from_records - Bulk insert multiple properties
• update_property - Update property values for objects
• get_scenario_id - Get scenario ID by name
• export_to_xml - Export database to XML format
• copy_object - Copy an object with its properties
• delete_object - Delete an object from the database
• update_object - Update object attributes
• get_objects - Get objects with filtering options
• check_membership_exists - Check if membership exists
• add_band - Add a band to a property data record
• add_text - Add text data to a property
• delete_property - Delete properties from objects
• update_properties - Update multiple properties
• get_property_unit - Get unit for a property
• add_attribute - Add attribute to an object
• add_metadata - Add metadata to entities
• get_attribute - Get attribute details
• get_attributes - Get all attributes for an object
• check_attribute_exists - Check attribute existence
• add_report - Add a report configuration
• list_reports - List all defined reports
• export_to_csv - Export tables to CSV files
• add_time_slice - Add time slice definition
• validate_database - Validate database integrity
• list_scenarios - List all scenarios
• list_models - List all models
• list_units - List all available units
• list_classes - List available classes
• list_collections - List available collections
• iterate_properties - Iterator for properties
• add_custom_column - Add custom columns
• add_datafile_tag - Add file tags
• add_variable_tag - Add variable tags
• set_date_range - Set date range for data

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 85.13120% with 102 lines in your changes missing coverage. Please review.

Project coverage is 90.14%. Comparing base (b4cfc1f) to head (abd4aad).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
src/plexosdb/plexosdb.py	80.41%	85 Missing ⚠️
src/plexosdb/xml_handler.py	81.57%	7 Missing ⚠️
src/plexosdb/db_manager.py	97.89%	4 Missing ⚠️
src/plexosdb/utils.py	72.72%	3 Missing ⚠️
src/plexosdb/sqlite.py	50.00%	2 Missing ⚠️
src/plexosdb/enums.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #26      +/-   ##
==========================================
- Coverage   93.97%   90.14%   -3.84%     
==========================================
  Files           7        9       +2     
  Lines         880     1552     +672     
==========================================
+ Hits          827     1399     +572     
- Misses         53      153     +100     

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[daniel-thom]

This except clause is a no-op.