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osteosarc 0.11.3

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@iskandr iskandr released this 26 Sep 13:58
· 22 commits to main since this release
443f882

Follow-ups from moving Isovar, Topiary, Vaxrank and Varcode onto openvax-v1, which
all four now use.

  • Receipts and bundles hold no local paths
    (#65). Read receipts record a file
    by its place in the cache (objects/sha256/..., named by checksum) or else by its
    name, beside its checksum, and bundles leave out download times. So the same reads,
    extracted with the same tools from any cache, make the same bundle, and Isovar's and
    Vaxrank's recorded receipts lose their local paths too. Cache keys no longer depend
    on where the cache is, so reads extracted by earlier versions are fetched once more.
    openvax-v1 keeps its published bytes; the next version will be clean.
  • fetch_bundle(name, offline=True) never downloads, and raises OfflineError if the
    bundle isn't cached (#66).
  • osteosarc test-data check --help says fixture paths are relative to the fixtures
    file (#67).
  • check_fixtures is importable from osteosarc and takes a published bundle's name,
    and the Python API page shows it and osteosarc.shared.published
    (#68).
  • Export keeps the name of a member already named after its file: topiary/reads.bam
    is written as reads.bam, not reads.bam.bam; two members that would share a file
    are an error (#69).
  • The cross-library builder check is gone, with the builders it compared.