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Merge pull request #80 from KohlbacherLab/release/3.3.0
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Release 3.3.0
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@christopher-mohr
christopher-mohr authored Dec 2, 2022
2 parents 56eaa93 + 5021d12 commit 4e36404
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10 changes: 10 additions & 0 deletions CHANGELOG.md
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v3.3.0 - 2022-12-01

### `Added`

### `Changed`

- Switch from [PyVCF](https://github.com/jamescasbon/PyVCF) to [PyVCF3](https://github.com/dridk/PyVCF3) as dependency

### `Fixed`

## v3.2.0 - 2022-11-02

### `Added`
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2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netMHCstabpan_1_0.py
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'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07',
'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd',
'H-2-Kk', 'H-2-Ld', 'H-2-Qa2', 'H-2-Qa1', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03',
'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netctlpan_1_1.py
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'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07', 'HLA-C*18:01', 'HLA-C*18:02',
'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd', 'H-2-Kk', 'H-2-Ld',
'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08',
'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:09', 'HLA-E*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhcII_2_2.py
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netmhcII_2_2 = frozenset(['H-2-IAb', 'H-2-IAd', 'HLA-DPA1*01:-DPB104*01:', 'HLA-DPA1*01:03-DPB1*02:01', 'HLA-DPA1*02:01-DPB1*01:01', 'HLA-DPA1*02:01-DPB1*05:01', 'HLA-DPA1*03:01-DPB1*04:02',
'HLA-DPB1*03:01-DPB1*04:01', 'HLA-DQA1*01:01-DQB1*05:01', 'HLA-DQA1*01:02-DQB1*06:02', 'HLA-DQA1*03:01-DQB1*03:02', 'HLA-DQA1*04:01-DQB1*04:02', 'HLA-DQA1*05:01-DQB1*02:01', 'HLA-DQA1*05:01-DQB1*03:01',
'HLA-DRB1*01:01', 'HLA-DRB1*03:01', 'HLA-DRB1*04:01', 'HLA-DRB1*04:04', 'HLA-DRB1*04:05', 'HLA-DRB1*07:01', 'HLA-DRB1*08:02',
'HLA-DRB1*09:01', 'HLA-DRB1*11:01', 'HLA-DRB1*13:02', 'HLA-DRB1*15:01', 'HLA-DRB3*01:01', 'HLA-DRB4*01:01', 'HLA-DRB5*01:01'])
'HLA-DRB1*09:01', 'HLA-DRB1*11:01', 'HLA-DRB1*13:02', 'HLA-DRB1*15:01', 'HLA-DRB3*01:01', 'HLA-DRB4*01:01', 'HLA-DRB5*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhc_4_0.py
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'HLA-B*45:06', 'HLA-B*46:01', 'HLA-B*48:01', 'HLA-B*51:01', 'HLA-B*53:01', 'HLA-B*54:01', 'HLA-B*57:01',
'HLA-B*57:03', 'HLA-B*58:01', 'HLA-B*58:02', 'HLA-B*73:01', 'HLA-B*81:01', 'HLA-B*83:01', 'HLA-C*03:03',
'HLA-C*04:01', 'HLA-C*05:01', 'HLA-C*06:02', 'HLA-C*07:01', 'HLA-C*07:02', 'HLA-C*08:02', 'HLA-C*12:03',
'HLA-C*14:02', 'HLA-C*15:02', 'HLA-E*01:01', 'HLA-E*01:03'])
'HLA-C*14:02', 'HLA-C*15:02', 'HLA-E*01:01', 'HLA-E*01:03'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhcpan_2_4.py
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'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07',
'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd',
'H-2-Kk', 'H-2-Ld', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06',
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhcpan_2_8.py
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'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07',
'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd',
'H-2-Kk', 'H-2-Ld', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06',
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhcpan_3_0.py
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'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07',
'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd',
'H-2-Kk', 'H-2-Ld', 'H-2-Qa2', 'H-2-Qa1', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03',
'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/netmhcpan_4_0.py
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'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'HLA-E*01:01', 'HLA-E*01:03', 'HLA-E*01:01', 'HLA-E*01:03',
'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07', 'HLA-G*01:08',
'HLA-G*01:09', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06', 'HLA-G*01:07',
'HLA-G*01:08', 'HLA-G*01:09'])
'HLA-G*01:08', 'HLA-G*01:09'])
2 changes: 1 addition & 1 deletion epytope/Data/supportedAlleles/external/pickpocket_1_1.py
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'HLA-C*17:01', 'HLA-C*17:02', 'HLA-C*17:03', 'HLA-C*17:04', 'HLA-C*17:05', 'HLA-C*17:06', 'HLA-C*17:07',
'HLA-C*18:01', 'HLA-C*18:02', 'HLA-C*18:03', 'H-2-Db', 'H-2-Dd', 'H-2-Kb', 'H-2-Kd',
'H-2-Kk', 'H-2-Ld', 'HLA-G*01:01', 'HLA-G*01:02', 'HLA-G*01:03', 'HLA-G*01:04', 'HLA-G*01:06',
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
'HLA-G*01:07', 'HLA-G*01:08', 'HLA-G*01:09', 'HLA-E*01:01'])
1 change: 0 additions & 1 deletion epytope/EpitopePrediction/__init__.py
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.. moduleauthor:: schubert
"""

from epytope.Core.Base import AEpitopePrediction

from epytope.EpitopePrediction.External import *
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8 changes: 4 additions & 4 deletions setup.py
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name='epytope',

# Version:
version='3.2.0',
version='3.3.0',

description='A Framework for Epitope Detection and Vaccine Design',
long_description=long_description,
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# Run-time dependencies. (will be installed by pip when epytope is installed)
# TODO: find alternative for SMVlight scikitlearn
install_requires=[
'setuptools<=57',
'setuptools',
'pandas',
'pyomo>=4.0',
'PyMySQL',
'biopython',
'pyVCF',
'PyVCF3',
'mhcflurry<=1.4.3',
'mhcnuggets',
'mhcnuggets==2.3.2',
'keras<=2.3.1', # legacy tensorflow required by mhcnuggets resolves to incompatible keras version
'h5py<=2.10.0', # mhcnuggets fails to read model with newer versions
'requests',
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