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Changelog

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

[0.9.0] - 2025-08-13

  • performance fix for calculating jaccard similarties
  • add human_readable_name list as an attribute to SequenceCollection for displaying similarity results
  • adding SequenceCollections via PEP will now add associated sample_name as a human_readable_name
  • add wrapper for gtars GlobalRefgetStore so it can be called directly from refget

[0.8.3] - 2025-07-31

  • adds API endpoints for jaccard similarity calculations
  • some refactoring for newest gtars, v0.3.0
  • add class method from_PySequenceCollection for creating SequenceCollection from a gtars-created SequenceCollection
  • adds Similarity UI to frontend

[0.8.2] - 2025-03-26

  • updated add method to use boolean for updating SequenceCollection if already exists

[0.8.1] - 2025-03-21

  • addition of SCIM

[0.8.0] - 2025-03-05

  • Complete rewrite of the clients and agents.
  • New SequenceAgent class allows using the RefgetDBAgent class to store sequences. This is meant for testing purposes.
  • Completely refactored Clients work adds mature SequenceClient and SequenceCollectionClient classes.
  • Fix issues with rust digest calculations to improve flexibilty, using latest update to gtars interface.
  • Updates to latest ga4gh paging guidance
  • Add a beta CLI with digest-fasta and add-fasta functionality.
  • Remove some old stuff based on henge backend

[0.7.0] - 2025-01-11

  • Major revamp to RefGetClient object, which now works with either sequences or seqcol servers, and can handle any of the seqcol API endpoints.
  • Better integration of rust digest calculations built on gtars
  • switch back-end to use JSON instead of str
  • implement name_length_pairs and sorted_sequences attrs
  • improve some SeqCol object representations

[0.6.0] - 2024-08-08

  • Change paging style of list endpoints to match latest GA4GH pagination guide
  • Implement new /list/attribute endpoint on back-end, and add to demo
  • Update endpoint paths slightly after discussion for the /list and /attribute endpoints
  • Remove some of the duplicate endpoints to solidify to one API

[0.5.0] - 2024-07-06

  • Work on deployment, container building, configuration
  • Add some work toward pangenomes
  • Various misc improvements

[0.4.0] - 2024-06-26

  • Implement new sqlmodel and agent for new database backend
  • Add new React interface

[0.3.0] - 2024-02-23

  • Add seqcolapi router

[0.2.0] - 2024-02-03

  • Integrate seqcol into refget package.

[0.1.0] - 2021-06-17

  • First public version, backed by henge version 0.1.1.

[0.0.1] - 2020-06-25

Beta version for testing