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Osteosarc 0.3.0

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@iskandr iskandr released this 24 Sep 19:19
· 45 commits to main since this release
v0.3.0
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Learn about vigilant mode.

Snapshots are indexed by download date, and the most recent is the default, so you no longer name one to use the dataset.

python -m pip install --upgrade osteosarc==0.3.0
osteosarc sync                 # Saves today's website metadata as a snapshot, e.g. 2026-09-24
osteosarc samples              # Every command uses the most recent snapshot
osteosarc snapshots            # Lists snapshots by download date
osteosarc variants --gene MAP2 --snapshot 2026-09   # Newest snapshot downloaded that month

The osteosarc.com metadata changes over time; on 2026-09-21 alone, five variants were renamed and two merged. A snapshot freezes what you analyzed (#35, #36).

  • Dataset.sync() / osteosarc sync need no name. The snapshot is named by its UTC download date and reopened for the rest of that day. refresh=True / --refresh saves another, such as 2026-09-24.2. Offline, a snapshot is built from source bytes already in the cache.
  • Dataset.open() and every CLI command use the most recently downloaded snapshot.
  • Dataset.snapshots() / osteosarc snapshots list snapshots with their download times and IDs.
  • Picking a snapshot:
    • Dataset.open(date="2026-09") or --snapshot 2026-09 picks the newest from a UTC download day, month or year.
    • Dataset.open(name) or --snapshot NAME pins one exactly, by name or ID prefix.
  • New data.name and data.downloaded. The explorer shows the snapshot and its download time.
  • Named snapshots keep working, but custom sources / --source-revision now require a name.
  • Deprecated: the CLI's leading snapshot argument (osteosarc samples baseline). It still works, with a warning on stderr.
  • The docs no longer use a baseline snapshot name, and they explain why snapshots exist.

Validation:

  • CI passes on Python 3.9–3.13, including Varcode 7/9 consumer checks.
  • 248 tests pass against the built wheel in a clean virtualenv.
  • All documentation examples pass against live osteosarc.com on a fresh, empty cache: 115 passed, 2 intentionally skipped.
  • The installed CLI was tested against real snapshots: the default, --snapshot by month, the deprecated positional form, and reads --variant.

Documentation · PyPI · Changelog

https://claude.ai/code/session_01CcNHdiWgNhPGLmd4kDvG9G

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