[khoroshevskyi]

Changes:

• Updated all type annotations to modern Python 3.10+ syntax (Union → |, List → list, Dict → dict, Optional → | None)
• Fixed bug in UsageModel where type annotations were incorrectly used as default values
• Replaced print statements with proper logging calls (_LOGGER.info/error)
• Applied SQLAlchemy best practices using .is_(False) instead of == False for boolean comparisons
• Added missing return type annotations and parameter type annotations
• Removed unused imports and unnecessary f-string prefixes
• Minor code cleanup (blank lines, import ordering)

TODO:

• Version of pepdbagent updated in __version__.py file
• Changelog updated

[Copilot]

Pull request overview

This pull request modernizes type annotations across the bbconf codebase as part of a phased modernization effort. It updates all type hints to use Python 3.10+ syntax, replacing typing.Union with the pipe operator (|) and using built-in generic types (list, dict) instead of their typing module equivalents.

Changes:

• Updated all type annotations to modern Python 3.10+ syntax (Union → |, List → list, Dict → dict, Optional → | None)
• Fixed bug in UsageModel where type annotations were incorrectly used as default values
• Replaced print statements with proper logging calls (_LOGGER.info/error)
• Applied SQLAlchemy best practices using .is_(False) instead of == False for boolean comparisons
• Added missing return type annotations and parameter type annotations
• Removed unused imports and unnecessary f-string prefixes
• Minor code cleanup (blank lines, import ordering)

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
bbconf/models/drs_models.py	Updated DRS model type annotations to modern syntax
bbconf/models/bedset_models.py	Updated bedset model type annotations to modern syntax
bbconf/models/bed_models.py	Updated bed model type annotations to modern syntax
bbconf/models/base_models.py	Updated base model type annotations; fixed UsageModel default value bug
bbconf/db_utils.py	Updated function signature type annotations; kept Optional for SQLAlchemy Mapped types
bbconf/config_parser/models.py	Updated config model type annotations to modern syntax
bbconf/config_parser/bedbaseconfig.py	Updated type annotations, added BaseClient import, removed unnecessary f-strings
bbconf/config_parser/utils.py	Replaced print with _LOGGER calls, removed BedBaseConfError wrapper
bbconf/modules/objects.py	Updated type annotations, added missing return type annotation
bbconf/modules/bedsets.py	Updated type annotations, removed blank lines
bbconf/modules/bedfiles.py	Updated type annotations, applied .is_(False) pattern, replaced print with logging, added deletion success log
bbconf/bbagent.py	Updated type annotations, added return type for get_list_assays
bbconf/init.py	Added blank line for PEP 8 compliance
pyproject.toml	Added manual_testing.py to ruff exclude list
tests/conftest.py	Removed unused imports (subprocess, register)
tests/test_common.py	Removed unused BedBaseConfError import
tests/test_bedfile.py	Removed unnecessary blank line
tests/test_universes.py	Removed unnecessary blank line

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