Release 0.12.0

[khoroshevskyi]

Changes:

• New qdrant semantic search added
• Improved reindexing methods
• Added more plots to bedbase summary page
• Fixed bedfile update method
• New reference genome compatibility that supports new refgenie
• Genomes table, with ability of automatic updates from refgenie
• Added filter in search (Assay and genome)

TODO:

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

[Copilot]

Pull Request Overview

This PR introduces version 0.12.0 with significant new features and improvements for the BedBase platform. The release focuses on enhancing search capabilities, improving data visualization, and expanding reference genome compatibility.

• Adds new qdrant semantic search functionality with advanced vector embeddings
• Implements comprehensive statistics and plotting features for the summary page
• Enhances reference genome compatibility to support new refgenie versions

Reviewed Changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
bbconf/_version.py	Version bump to 0.12.0
docs/changelog.md	Documents new features and fixes for 0.12.0 release
requirements/requirements-all.txt	Adds gtars dependency for genomic analysis
tests/test_bedfile.py	Disables PEPhub-related tests temporarily
manual_testing.py	Adds extensive plotting functions and search testing capabilities
bbconf/modules/bedfiles.py	Major updates for semantic search, reference validation, and vector operations
bbconf/models/bed_models.py	Updates model fields and adds VectorMetadata class
bbconf/models/base_models.py	Restructures statistics models and adds new data structures
bbconf/db_utils.py	Adds file indexing column and reference genome tables
bbconf/config_parser/	Implements advanced qdrant backend configuration
bbconf/bbagent.py	Extensive statistics and analysis functionality

Comments suppressed due to low confidence (1)

bbconf/modules/bedfiles.py:1

• Field name changed from exp_protocol to assay but the alias relationship should be maintained for backward compatibility. Consider adding alias='exp_protocol' to the Field definition.

import datetime

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