Release 0.8.0

[khoroshevskyi]

Changes:

• Changed data source of chrom sizes in bed reference validator to new refgenie.
• Added CLI for automatic UMAP generation from qdrant
• Fixed bedboss logger
• Improved reindexing
• Added "generate UMAP" cli command
• Improved efficiency of bdd Reference validator function
• Added script for search evaluation

TODO:

• Version of pepdbagent updated in __version__.py file
• Changelog updated
• Wait for Release 0.12.0 bbconf#92

[Copilot]

Pull Request Overview

This release (0.8.0) enhances BedBoss with improved reference genome validation, new CLI tools for UMAP generation, and better vector database functionality. The primary focus is migrating from local genome files to RefGenie for chromosome size data, improving search capabilities, and adding visualization tools.

• Migrated reference genome validation to use RefGenie API for chromosome sizes instead of local files
• Added CLI commands for UMAP generation, semantic search reindexing, and genome database updates
• Improved logger configuration and vector database reindexing functionality

Reviewed Changes

Copilot reviewed 24 out of 33 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
bedboss/_version.py	Version bump to 0.8.0
bedboss/refgenome_validator/main.py	Updated to use RefGenie chromosome sizes and genome digests
bedboss/refgenome_validator/refgenie_chrom_sizes.py	New module for fetching genome data from RefGenie API
bedboss/cli.py	Added new CLI commands for UMAP, reindexing, and genome updates
bedboss/scripts/make_umap.py	New script for generating UMAP visualizations from vector embeddings
scripts/	Added utility scripts for database operations and evaluation
docs/changelog.md	Updated changelog for 0.8.0 release

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