Update mhcgnomes dependency to >=3.4.0#171
Merged
Merged
Conversation
Update minimum mhcgnomes version from 2.0.0 to 3.4.0 in both pyproject.toml and requirements.txt. Also include the unstaged NetMHCIIpan version detection fix that broadens support from 4.0-only to any 4.x release. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Replace `secrets.NETMHC_BUNDLE_ACCESS_TOKEN != ''` with a repository check since GitHub Actions doesn't allow the secrets context in job-level if expressions. The integration job only needs to run on the main repo anyway (forks won't have the secret). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Bump pylint minimum from >=1.4.4 to >=3.0 to fix astroid crashes on Python 3.12 - Install setuptools explicitly in integration job so mhcflurry can import pkg_resources on Python 3.12+ Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Move setuptools install to after pip install so it isn't removed during dependency resolution. mhcflurry needs pkg_resources at runtime but doesn't declare setuptools as a dependency. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
setuptools 82.x removed pkg_resources, which mhcflurry still imports. Pin to <81 until mhcflurry updates. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The netMHC wrapper scripts have hardcoded paths like /tools/src/netMHCIIpan-4.3. Create a symlink from /tools/src to the bundle checkout directory so these paths resolve correctly. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
netMHC-3.4 wrapper calls python2 which isn't available on Ubuntu 24.04. Create a symlink to python3 since the bundle's Python scripts are compatible with Python 3. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
netMHC-3.4/netMHC.py and netMHCcons-1.1/pseudofind use Python 2 print syntax. Run lib2to3 to patch them for Python 3 compatibility. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The netMHC bundle scripts (netMHC-3.4, netMHCcons) require Python 2 which is not available on Ubuntu 24.04. Pin the integration job to ubuntu-22.04 and install python2 via apt. Remove lib2to3 workaround. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
mhcgnomesversion from>=2.0.0to>=3.4.0in bothpyproject.tomlandrequirements.txtfeature/newer-mhcgnomesbranch: migration topyproject.toml, replacement ofmhcnameswithmhcgnomes-backedallele_normalizationmodule, GitHub Actions CI, and NetMHCIIpan 4.x supportTest plan
mhcgnomes3.4.0 installs cleanly and all imports (Allele,Pair,ParseError,parse) work🤖 Generated with Claude Code