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osteosarc 0.9.0

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@iskandr iskandr released this 26 Sep 00:28
· 27 commits to main since this release
v0.9.0
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Learn about vigilant mode.

The command line and the Python API now use the same two nouns, samples and files, and every command prints something a person can read. See the changelog for details.

  • Samples.
    • data.samples / osteosarc samples list tumor, organoid and blood samples.
    • data.samples["T1_tumor"] / osteosarc samples T1_tumor show that sample's BAMs and FASTQ folders, with commands that fetch them.
    • Sequencing now also comes from the site's FASTQ table, so the 2026 blood draws no longer show "unknown".
  • Files.
    • Assets are renamed files: data.files, data.file(), File, Files, osteosarc files.
    • With no filters, osteosarc files summarizes the bucket by kind and folder.
  • Downloads.
    • osteosarc downloads and data.downloads() list what's on this computer.
    • data.local_path(file) finds a local copy.
    • download --to DIR puts a file and its index in a folder as read-only hard links.
  • Timeline. One row per named treatment over a month axis. Frequent records are hidden unless --all.
  • Command line.
    • Commands are grouped in help.
    • Every command prints text by default, with --json for scripts.
    • variants ID and corrections ID show one record.
    • curation is renamed corrections.
    • osteosarc repl replaces the explore shell.
  • Breaking renames. data.assets, data.asset(), Asset, Assets, data.specimens, describe_samples(), assets_for_sample(), data.explore() and the old data.samples (now data.claims) are gone. See migration.
Assets 5
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