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Osteosarc 0.8.0

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@iskandr iskandr released this 25 Sep 23:19
· 30 commits to main since this release
v0.8.0
0a0affd
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Learn about vigilant mode.

A first look at the data is easier from both the command line and Python (#44).

python -m pip install --upgrade osteosarc==0.8.0
osteosarc              # Where to start
osteosarc explore      # Offers to download the metadata the first time
>>> data = Dataset.open()
>>> data
Osteosarc snapshot 2026-09-25 (dea7dd245659), downloaded 2026-09-25 23:00 UTC. Try data.summary() or data.explore().
>>> data.variants(gene="DYNC1H1")
2 variants, 2 ready
id                       gene     status  allele
DYNC1H1-chr14-101980529  DYNC1H1  ready   chr14:101980529 G>A
DYNC1H1-chr14-102030200  DYNC1H1  ready   chr14:102030200 G>T

Command line

  • osteosarc on its own suggests where to start.
  • Without a snapshot, commands say which cache they looked in and to run osteosarc sync. In a terminal, osteosarc explore offers to download one, and Ctrl-D at that prompt exits cleanly.

Python

  • Dataset objects, variants, files, tables and the timeline show readable previews instead of <object at 0x…>.
  • Text views such as describe_samples() display without quotes.
  • Single variants, files and events no longer print their full source records.
  • data.summary() shows what's in a snapshot and what to try next.
  • data.explore() opens the interactive explorer.
  • A new NoSnapshotsError (a FileNotFoundError) says which cache has no snapshots.

Docs: the README and docs home start with "Explore the data".

Validation:

  • CI passes on Python 3.9–3.13, including Varcode 7/9 consumer checks.
  • 257 tests pass against the built wheel in a clean virtualenv.
  • A code review's 10 findings were fixed before merging.

PR #45 · Documentation · PyPI

https://claude.ai/code/session_01CcNHdiWgNhPGLmd4kDvG9G

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