This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) 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