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Osteosarc 0.5.0

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@iskandr iskandr released this 24 Sep 19:58
· 41 commits to main since this release
v0.5.0
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Learn about vigilant mode.

Makes the command line easier for exploring samples and their files.

python -m pip install --upgrade osteosarc==0.5.0
osteosarc samples --assay scrna-seq --platform ont     # Samples with single-cell Nanopore data
osteosarc assets --sample T1_tumor --kind alignment    # Their files, with complete keys
  • Sequencing uses the filter names. samples and specimens show sequencing as the names the filters take, such as rna-seq; wes; wgs; scrna-seq (ont, pacbio). Before, they showed registry labels like scRNA_ONT that the filters don't accept.
  • Filter the overview by sequencing. samples --assay / --platform list the samples with that sequencing, and describe_samples() takes the same filters.
  • assets prints a table. It shows complete file keys (what reads takes) and a hint when rows are cut off. --json prints the full records.
  • Bad filter values are errors. An assay, platform or tissue that no file uses now fails with a list of the valid values instead of returning nothing. A registry label names the filters to use: 'scRNA_ONT' is a registry label; select assay 'scrna-seq' with platform 'ont'.
  • Tables: keys are never cut off, cells wrap without splitting hyphenated names, and sizes show in KB, MB or GB.

Validation:

  • CI passes on Python 3.9–3.13, including Varcode 7/9 consumer checks.
  • 250 tests pass against the built wheel in a clean virtualenv.
  • The changed documentation examples pass against live osteosarc.com.

#39 · Changelog · PyPI

https://claude.ai/code/session_01CcNHdiWgNhPGLmd4kDvG9G

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