Release 0.11.4

[khoroshevskyi]

Changes:

• Search improvements

TODO:

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

[Copilot]

Pull Request Overview

Implements search improvements and adds genome filtering capabilities, along with a new manual test helper and version bump to 0.11.4

• Added genome filter parameter and metadata‐based search fields in sql_search for bed files
• Introduced get_list_genomes ordering change and a get_genomes helper in manual_testing.py
• Bumped version and updated query stripping in bedset ID listing

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
manual_testing.py	Updated sql_search example to include a genome filter; added get_genomes helper
bbconf/modules/bedsets.py	Trim whitespace from query in get_ids_list
bbconf/modules/bedfiles.py	Enhanced sql_search and _sql_search_count with genome support and extra metadata fields; updated text‐to‐bed search count logic
bbconf/bbagent.py	Changed get_list_genomes to group/order rather than distinct; filtered out empty aliases
bbconf/_version.py	Bumped package version to 0.11.4