Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.12.0] - 2026-08-18

Changes:

• All references to upload_pephub have been removed from function signatures, docstrings, and internal logic across the codebase, including in bedboss.py, bedbuncher.py, bbuploader/main.py, bedboss_hpc.py, and the CLI (cli.py). This means users can no longer upload to PEPHub using any part of the pipeline.
• Removed unused logging setup from bedboss/bbuploader/__init__.py and added logmuse import to cli.py for consistent logging across the CLI.
• Fixed a bug in _read_bed_file in bedclassifier.py to only drop columns that are entirely NA, instead of any column with any NA.
• Added import for snapshot_app in cli.py from bedboss.scripts.snapshot.
• Added Analysis files functionality.

[0.11.1] - 2026-04-22

Changed:

• Migrated to new yacman version 1.0.0

[0.11.0] - 2026-04-17

Added:

• HPC module for running bedboss on HPC
• CLI tool for bulk uploading files to Qdrant

Fixed:

• Bed classifier
• DB connection

[0.10.0] - 2026-04-05

Added:

• Creation of parquet file for umap with more metadata inside

Changed:

• Testing version of new peppy
• New project style
• Modernized docstrings and typing

[0.9.6] - 2026-02-18

Added:

• Added scripts for downloading and analyzing ENCODE metadata

Changed:

• Updated pep processing in GEO uploader and bedboss
• Updated UMAP creation

[0.9.5] - 2026-02-16

Changed:

• Improved metadata extractor with expanded cell line and assay extraction
• Updated UMAP creation scripts
• Updated requirements

[0.9.4] - 2026-02-06

Fixed:

• Fixed large downloads of embeddings from qdrant

[0.9.3] - 2026-02-04

Changed:

• Improved genome predictor
• Updated bbconf version requirement

Fixed:

• Added file check for GEO files that don't have size in their soft data

[0.9.2] - 2026-01-31

Added:

• Added file size check for project-level files in GEO uploader

[0.9.1] - 2026-01-31

Changed:

• Removed unpredictable cell lines from metadata extractor

[0.9.0] - 2026-01-31

Added:

• Processing of gse series bed files #143
• Added metadata extraction from description if cell line or assay is not avaliable

Changed:

• Improved reference genome predictor

Fixed:

• Fix reference genome update and upload in bedbase db #144

[0.8.2] - 2025-09-22

Fixed:

• Downloading Refgenie chrom sizes (due to endpoint change)

[0.8.1] - 2025-09-12

Fixed:

• Creation of UMAP

[0.8.0] - 2025-09-11

Added:

• Added CLI for automatic UMAP generation from qdrant
• Added "generate UMAP" cli command

Changed:

• Changed data source of chrom sizes in bed reference validator to new refgenie.

Fixed:

• Fixed bedboss logger
• Improved vector db reindexing
• Improved efficiency of bdd Reference validator function

[0.7.3] - 2025-06-28

Added:

• Added filter for rerunning unprocessed bed files based on genome

[0.7.2] - 2025-06-21

Changed:

• Updated path to the bigbed output folder
• Added update of metadata of the bed file
• Updated docker file
• Remove bedqc module

[0.7.1] - 2025-04-22

Fixed

• Minor bug fixes

[0.7.0] - 2025-04-21

Added

• Added dockerfile
• Added R processing as separate service
• Added initial qc for GEO data (QC, without loading full data)
• Refactored R code
• Added summary for bedsets #112
• Added original submission date of geo to the table #95

Changed:

• Improved logging
• Fixed python3.12 warnings
• Improved bedmaker. (identifier, bigbed, qc)
• Removed bedqc module - moved it to handle everything by RegionSet object
• Improved bedclasifier #101
• Fixed #97
• Fixed #110
• Fixed multiple bugs in geo uploader
• Switched RegionSet from geniml to RegionSet from Gtars

[0.6.0] - 2025-01-17

Added:

• Added open_chromatin plot back into processing.
• Added gtrs dependency, that calculates gc content.
• Added skipper that automatically skips samples in pep that were already processed.
• Added lite functionality to main functions that allows to run uploading without using any heavy processing.
• Added function that will reprocess files, if they were unprocessed in the bedbase.
• Added function that predicts genome if genome wasn't provided

Changed:

• Important speed improvements.

[0.5.0] - 2025-01-16

Added

• Added open_chromatin plot back into processing.
• Added gtrs dependency, that calculates gc content.
• Added skipper that automatically skips samples in pep that were already processed.
• Added lite functionality to main functions that allows to run uploading without using any heavy processing.
• Added function that will reprocess files, if they were unprocessed in the bedbase.
• Added function that predicts genome if genome wasn't provided.

Fixes

• Important speed improvements.
• Improved requirements checker.
• Minor bug fixes.

[0.4.1] - 2024-09-20

Added

• Standardization of peps using bedbase bedms schema
• Reference validator module

Fixed

• Pipeline failures (due to pipeline manager)
• Failure in cleaning temp files

[0.4.0] - 2024-08-26

Added

• Added bbuploader (GEO uploader)

[0.3.0] - 2024-08-21

Added

• Added classifier
• Added create universe uploader
• Added tokenization and token uploader

Changes

• Updated efficiency of CLI help

[0.2.1] - 2024-04-09

Changed

• small naming tweaks

Added

• added requirement check to cli

[0.2.0] - 2024-04-08

Changed

• moved all uploading functionality to the bbconf package

Added

• added commands for indexing bedfiles
• added commands for deleting bedfiles and bedsets

[0.1.0] - 2024-01-26

Added

• Initial alpha release