Pepdbagent

- 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)

- Fixed error with namespace user if user is unknown

- Added limits and offset to function: `get_projects_in_namespace()`
- Annotation changed to BaseModel from pydantic
- Added privacy information in annotations
- Added update feature to `upload_project` method with `overwrite` argument
- Added mock tests
- Deleted unused functions:
- `get_projects_in_list`
- `get_projects_annotation_by_namespace`
- `project_status`
- `project_status_by_registry`
- `get_registry_paths_by_digest`

- Changed method names:
- `get_project_by_registry` --> `get_project_by_registry_path`
- `get_project_annotation_by_registry` --> `get_project_annotation_by_registry_path`

- 🎉 first release!