v2.1.3-post1

Releasing code state on publication of our manuscript "Contrastive learning of T cell receptor representations"

v2.1.3

What's Changed

• Update new MHC info from IMGT by @yutanagano in #77

Full Changelog: v2.1.2...v2.1.3

v2.1.2

What's Changed

• Update usage page on the docs by @yutanagano in #69
• Link to original publication from docs and README by @yutanagano in #71
• Migrate to pyproject toml by @yutanagano in #74
• Pull updated data from IMGT by @yutanagano in #75
• Bump version number by @yutanagano in #76

Full Changelog: v2.1.1...v2.1.2

v2.1.1

This is a patch to fix a broken link on the PyPI README page.

v2.1.0

This is a minor version upgrade which brings a few new goodies:

• Improved functionality of the tr.get_aa_sequence function:
  • Added support for Mus musculus
  • Added support for diversity and joining region TR genes
• A new pretty logo!
• Better metadata linking the documentation page, github page and PyPI page together more closely

What's Changed

• Add logo by @yutanagano in #62
• Addition of project and download urls to setup.py by @yutanagano in #63
• Improve tr module by @yutanagano in #64
• Minor update to v2.1.0 by @yutanagano in #65

Full Changelog: v2.0.2...v2.1.0

v2.0.2

What's Changed

• Improved standardization warnings that don't compare the input string and best attempted fix if they are the same (thank you @andim for the suggestion!)
• Updated TR/MH allele data
• Updated documentation page and README with quality of life improvements

• Patch 2.0.2 by @yutanagano in #55
• Update github workflows to work with new Node by @yutanagano in #56

Full Changelog: v2.0.1...v2.0.2

Release 2.0.1

This is a minor version update with updated TR/MH reference data.

What's Changed

• Updated TR/MH lists by @yutanagano in #50
• Update to patch 2.0.1 by @yutanagano in #51
• Update to patch 2.0.1 by @yutanagano in #52

Full Changelog: v2.0.0...v2.0.1

Release 2.0.0

Overview of changes in version 2

Version 2 of tidytcells comes with several breaking changes:

• Renaming of submodules (this was done in order to make the software consistently IMGT-compliant)
  • The tcr submodule is now tr
  • The mhc submodule is now mh
• Deprecations of functions
  • tidytcells.mh.classify is now deprecated in favour of tidytcells.mh.get_class
• Deprecation of function parameters
  • The legacy parameter gene_name is now deprecated in favour of gene in the following functions:
    • tidytcells.mh.get_chain
    • tidytcells.mh.get_class
    • tidytcells.mh.standardize
    • tidytcells.tr.standardize
  • The parameter contains is now deprecated in favour of contains_pattern in the following functions:
    • tidytcells.mh.query
    • tidytcells.tr.query

What's Changed

• Develop by @yutanagano in #33
• Update function docstrings to reflect on_fail setting by @yutanagano in #36
• Develop by @yutanagano in #39
• Make cleaner code by @yutanagano in #41
• Update to version 2.0.0 by @yutanagano in #42

Full Changelog: v1.8.4...v2.0.0

Release 1.8.6

Fixed bug in tcr.query where specifying both functionality as "NF" and precision as "gene" caused an error.

Release 1.8.5

Improve warning messages in aa and junction submodules.