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Changelog

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

[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