epytope: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v3.4.0 - 2024-01-10

`Added`

#93 Added NetMHCIIpan version 4.2 interface #92
#96 Added NetMHCIIpan version 4.3 interface #95

`Changed`

`Fixed`

#93 Fixed length restriction of NetMHCIIpan interfaces #91

v3.3.1 - 2023-04-25

`Added`

`Changed`

#85 Pinned pandas version >= 1.3.5 as requested by @e-dorigatti #84.

`Fixed`

#83 Fixed erroneous mouse allele parsing for PSSM predictors #82

v3.3.0 - 2022-12-01

`Added`

`Changed`

Switch from PyVCF to PyVCF3 as dependency

`Fixed`

v3.2.0 - 2022-11-02

`Added`

#74 - Add function to Peptide class to determine if peptide originates from a variant

`Changed`

#63 - Outsource supported alleles of prediction tools #61
#69 - Improve Ensembl BioMart adapter #57

`Fixed`

#73 - Fix NetMHCII 4.0 parser #72

v3.1.0 - 2022-06-15

`Added`

#58 - Add check for BioMart transcript sequence availability #55
#59 - Add interface for NetMHCpan 4.1 #56
#66 - Add interface for NetMHCIIpan 4.1 #65

`Changed`

#62 - Update the supported alleles of syfpeithi #60

`Fixed`

#53 - Fix ANN predictor results #52

v3.0.0 - 2022-01-26

Initial release of epytope. epytope is the successor project of FRED2, which was renamed to a more versioning friendly base name.

`Added`

#6 - Add CI for external tools
#24 - Add keras dependency
#26 - Add a license file
#31 - Add deployment to PyPI
#42 - Add new Syfpeithi matrices
#46 - Add support for NetMHCII 2.3 and NetMHCIIpan 4.0

`Changed`

#1 - Switch CI/CD from Travis to GitHub Actions
#9 - Initial Python 2 to Python 3 conversion based on 2to3conv
#20 - Use logging module rather than print calls across the library
#23 - Rename the package from FRED-2 to epytope
#25 - Refactor CI to use more pip and less conda
#42 - Extend EpitopePredictionResult structure to store rank-based scores

`Fixed`

#11 - Fix Python version matrix in CI, remove versions that fail
#16 - Fix epitope prediction 2to3 bugs and tests
#17 - Fix Invalid subprocess handling and mhcflurry polluting stdout
#18 - Fix external (NetMHC tool family) epitope prediction error and temp file handling
#46 - Fix issues with MHC class-II CombinedAlleles #45
#46 - Do not override Allele objects #38