Pepdbagent

- Fixed project.update function

- Transitioned to SQLAlchemy ORM.
- Added a pep_schema column to the database.
- Implemented a new testing approach.
- Integrated sorting functionality into the annotations module.
- Temporarily disabled description-based searches to mitigate long processing times and reduce database load.
- Included timezone support in the database.
- Standardized namespace and names to lowercase for case-insensitivity.
- Streamlined the database schema creation process, with tables now created dynamically as needed.

- Fixed bug with peppy const dependencies

- Restructured pepdbagent:
- Renamed `Agent` class to `PEPDatabaseAgent`
- created subclasses (project, annotation, namespace).
- Merged methods that have similar use case.
- Removed unused methods.
- Simplified pepdbagent API
- Restructured database (added columns: `private`, `number_of_samples`, `submission_date`, `last_update_date`)
- Improved logging
- Added new tests
- Improved documentation

- Added more logging information in uploading project methods
- Added `update_only` argument `upload_project` method

- Fixed error in pepannotation (privacy error)