Changelog

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

[0.4.2] -- 2024-10-07

• Cleaned dependencies and separated into 2 groups: basic and ml.
• Improved efficiency of CLI
• Fixed bbcache incorrectly saving files from url #175

[0.4.1] -- 2024-09-18

• Fixed: bbclient ignores --cache-folder on CLI #164
• Fixed bug in opening bed files

[0.4.0] -- 2024-06-04

• Added bed tokens caching to bbclient [bbclient] Add tokenized file cache and download #153
• Added pyBiocFileCache for bedfiles to support R caching [bbclient] Integrate bedbase caching with R #151
• Added support of Python3.12
• Optimized encoding of regions for Region2Vec models
• Added updates to the new Atacformer
• Renamed tokenizers to TreeTokenizer and AnnDataTokenizer
• Bump genimtools which includes performance upgrades and stability updates to the tokenizers

[0.3.0] -- 2024-04-04

• Added S3 uploading to bbclient
• Added and cleaned tests
• Added bed2bed search interface

[0.2.0] -- 2024-02-20

• Fixed a bug with pydantic
• Integrate lightning for easier training of models with SLURM and the DDP framework
• New datasets for streaming .gtok files to models
• New tutorials for updated ScEmbed
• Start working on Atacformer

[0.1.0] -- 2023-12-18

• First official released version of geniml
• Integrated bedshift 1.1.1 into geniml (excluding intersection support)

[bedshift 1.1.1] - 2021-04-15

• Updated documentation
• Fixed dependencies packaging for building documentation

[bedshift 1.1.0] - 2021-04-02

• Added ability to specify chrom sizes file, or refgenie genome.
• Add perturbation will create regions proportional to chromosome size
• Improve performance of perturbations
• Add --dropfile, --addfile, and --shiftfile options
• Add --add_valid option
• Add --yaml-config option
• Improved testing framework
• Improved logging messages

[bedshift 1.0.0] - 2020-05-20

• Add, shift, drop, cut, and merge perturbations.
• Basic documentation
• Basic tests