Release 0.11.0

[khoroshevskyi]

Changes:

• Added CLI commands for efficient upload of BED files to the database, including indexing and upload to Qdrant
• Fixed download of Refgenie sequence, chromosome size, and column files

TODO:

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

[Copilot]

Pull request overview

Release 0.11.0 focuses on HPC-friendly workflows (chunking + SLURM orchestration) for both PEP processing and Qdrant reindexing, along with UMAP output format changes and a more robust Refgenie chrom-sizes fallback.

Changes:

• Added HPC/SLURM orchestration commands for run-pep and Qdrant reindexing (vectorize → upload → status).
• Refactored UMAP outputs to write a single parquet (and optional JSON) with updated column set.
• Bumped project version to 0.11.0 and updated changelog; improved Refgenie seqcol download fallback.

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
scripts/encode_processing/encode_into_parts.py	Adds a utility script to split a CSV into parts (currently hard-coded and fragile).
pyproject.toml	Bumps package version to 0.11.0.
docs/changelog.md	Adds 0.11.0 changelog entry.
bedboss/scripts/make_umap.py	Refactors UMAP export logic (single parquet + optional JSON) and CLI-facing output options.
bedboss/refgenome_validator/refgenie_chrom_sizes.py	Adds URL-based fallback for seqcol JSON when Refgenie fetch fails.
bedboss/qdrant_index/vectorize.py	Adds connection-free (DB-free) vectorization workers for HPC jobs.
bedboss/qdrant_index/upload.py	Adds uploader that reads parquet vectors and upserts to Qdrant + updates DB flags.
bedboss/qdrant_index/qdrant_index.py	Defers BedBaseAgent import to reduce import-time side effects.
bedboss/qdrant_index/qdrant_hpc.py	Adds SLURM chunking/orchestration + status reporting for Qdrant reindex jobs.
bedboss/qdrant_index/qdrant_cli.py	Introduces bedboss qdrant ... Typer subcommands for HPC reindex workflows.
bedboss/qdrant_index/init.py	Switches to lazy export of add_to_qdrant via __getattr__.
bedboss/const.py	Replaces tiered parquet column constants with a single UMAP_PARQUET_COLUMNS list.
bedboss/cli.py	Registers new qdrant subapp and adds run-pep-hpc / status commands; updates UMAP CLI options.
bedboss/bedclassifier/bedclassifier.py	Normalizes column indices after dropping NaN columns to prevent indexing errors.
bedboss/bedboss_hpc.py	Adds SLURM orchestration implementation for bedboss run-pep chunking/resume.

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