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vdjtools 5.2.0 — configured corpora and bounded fitting

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@mikessh mikessh released this 17 Oct 18:53
· 70 commits to master since this release
3ac89a6

Configured statistical features and reproducible named corpus projection:

  • Basic/joint feature sets with frozen motif and V-gene definitions.
  • 70 configured real-corpus models plus nine preserved legacy models; list names with vdjtools corpus --list and fetch only the model needed. All 158 public parameter files have verified SHA256 identities and exact byte counts.
  • Bounded sparse/centered fitting, joined feature workers before numerical fitting, and compatible SciPy column-vector handling.
  • Shared TRA/TRD germline membership repairs, bounded unseen-taxon bootstrap memory, closed-form richness rarefaction, and impossible V/J suffix pruning.
  • Correct download-size diagnostics after partial-file cleanup.

Requires arda-mapper >=2.36.2 and seqtree >=1.2.0,<2. Both upstream versions are published and verified. Configured synthetic models remain deferred; existing model parameters were not refitted during this release work.

Validation: exact integration-head CI is green across Python 3.10/3.12 on Linux/macOS, native C++ and strict docs. A full Linux gate passed 1,385 tests plus the bounded-resource regression. Compatibility checks pass in both the normal and CI-pinned environments. Public named corpus fetch/load/projection passes from an empty cache.