refactor(snomed): re-export from biodb.snomed instead of in-tree impl - #6
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The SNOMED downloader (and the GitHub Release asset it pulls) moved into bioDB on 2026-05-18. This commit: * Replaces synthlab/download_snomed.py with a thin re-export shim. All existing imports ``from synthlab.download_snomed import ...`` keep working; the actual implementation lives in biodb.snomed. * Adds ``biodb`` as a dep in pyproject.toml. The release URL hard-coded in the old code (synthlab/vocab-v1) is replaced by biodb's. If callers were passing ``url=`` to override for a private mirror, the wrapper raises a DeprecationWarning and tells them to set GITHUB_TOKEN instead — bioDB's token-auth path against the same release tag is the supported escape hatch now. Net diff: -304 lines of duplicated download/auth/decompress logic, +76 lines of compat shim. Downstream behaviour unchanged. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
The SNOMED downloader + its GitHub Release asset moved into bioDB on 2026-05-18 (bioDB PR #15). This PR makes synthlab consume it from there.
Changes
synthlab/download_snomed.py: 379 lines of in-tree download / auth / decompress / gzip logic → 76-line back-compat shim that re-exports the public names frombiodb.snomed. Every existingfrom synthlab.download_snomed import ...keeps working.pyproject.toml: addbiodb @ git+https://github.com/bschilder/bioDBas a dep.Net effect
url=kwarg ondownload_snomed_vocabularyis preserved but now ignored (with aDeprecationWarningpointing callers atGITHUB_TOKENfor private mirrors against the bioDB release URL).Asset relocation note
The GitHub Release asset itself was physically moved: same
vocab-v1tag, sameCONCEPT.csv.gzfilename, identical SHA-256 (ce9029c84f1f5a5e300353f2833a4735f40bdf57e64262d46f4d4bfe274a04b7). New canonical URL:https://github.com/bschilder/bioDB/releases/download/vocab-v1/CONCEPT.csv.gz
The
bschilder/synthlabvocab-v1release will be deleted as a follow-up step (per the original move plan) once this PR merges and the new flow is confirmed working.Test plan
from synthlab.download_snomed import download_snomed_vocabulary, get_concept_csv_path, is_snomed_availableround-trips.download_snomed_vocabulary(url=...)with a non-default URL emitsDeprecationWarning.tests/test_snomed.pyprovides full coverage).🤖 Generated with Claude Code