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Fetch pinned predictor tools and weights - #272

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iskandr merged 1 commit into
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feature/fetch-open-tools
Sep 4, 2026
Merged

Fetch pinned predictor tools and weights#272
iskandr merged 1 commit into
masterfrom
feature/fetch-open-tools

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@iskandr iskandr commented Sep 4, 2026

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Summary

  • add atomic, commit-pinned sparse fetches for DeepTAP, DeepImmuno, ERAMER, TULIP-TCR, NetTCR, and BigMHC
  • require explicit license acceptance for NetTCR and BigMHC, and preserve repository, revision, sparse-path, and license provenance in each installation
  • teach wrapper constructors and class-level fetch() methods to use the managed snapshots automatically
  • expand mhctools ls to inventory bundled weights, MHCflurry-managed downloads, mhctools-managed snapshots, user checkouts, and manual licensed executables
  • add MHCTOOLS_DATA_DIR / --data-dir, JSON-safe fetch output, and TULIP setup-script integration

MixMHCpred, MixMHC2pred, PRIME, DTU tools, NetCleave, and TLimmuno2 remain inventory-only because mhctools cannot safely redistribute them under their current terms.

Verification

  • ./lint.sh
  • ./test.sh — 699 passed, 53 skipped, 2 xfailed
  • real ERAMER fetch and wrapper resolution
  • real NetTCR sparse fetch: 20 checkpoints, 7.9 MB installed, all checkpoints load
  • NetTCR upstream-reference regression: 28 passed, including all six published ensemble anchors

This builds on #271 and removes the artifact-acquisition part of iskandr/eureka-bench#159.

@iskandr
iskandr merged commit 47eca98 into master Sep 4, 2026
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@iskandr
iskandr deleted the feature/fetch-open-tools branch September 4, 2026 20:36
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