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osteosarc 0.13.0

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@iskandr iskandr released this 26 Sep 18:36
· 20 commits to main since this release
299454b

A simpler site, and less code (#75).

  • The home page is the overview. Concepts is folded into a short "How the data
    fits together" there, linking to each topic's page.
  • Removed, now that the OpenVax libraries take their reads from openvax-v1:
    • osteosarc.regional_corpus;
    • the generators in legacy_fixtures (generate, pack, verify, export_fixture and
      their helpers) and cohort_bundle (generate_cohort_bundle, retrieval_regions);
      the functions Isovar and Vaxrank import stay;
    • osteosarc.bundles.generate_panel; osteosarc test-data make --recipe, or
      generate_bundle, does the same;
    • osteosarc.records.sam_digest, and SAM-text record identities in recipes;
    • osteosarc.reads.subset_templates, a random sample that make_bundle's balanced
      sets replace;
    • reading bundles made by osteosarc 0.2 or earlier, which now says to make them
      again.
  • The frozen SV test recipe moves from the package into tests/data.