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genomehubs / data Public

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historical assembly version backfill (phase 0)#3

Merged

rjchallis merged 18 commits into

genomehubs:maingenomehubs/data:mainfrom

fchen13:fang-assembliesfchen13/genomehubs-data:fang-assembliesCopy head branch name to clipboard

Apr 2, 2026

Conversation Commits18 (18)Checks Files changed

Merged

historical assembly version backfill (phase 0)#3
rjchallis merged 18 commits into
genomehubs:mainfrom
fchen13:fang-assemblies

Commits

Commits on Dec 19, 2025

one-time backfill process to populate historical assembly versions.
fchen13
committed
Add version status column to the existing parser
fchen13
committed
Phase 0 summary
fchen13
committed
Merge upstream/main: resolve conflict in parse_ncbi_assemblies.py
fchen13
committed
Add strict accession validation as suggested by reviewer

fchen13
and
claude
committed
Merge remote-tracking branch 'upstream/main' into fang-assemblies
fchen13
committed
Remove parse_s3_file stub, use existing implementation

fchen13
and
claude
committed
Update documentation to run parser as module

fchen13
and
claude
committed
Fix YAML config as suggested by reviewer

fchen13
and
claude
committed
Simplify cache key format to use accession only

fchen13
and
claude
committed
Use shared argument parser from flows.parsers.args

fchen13
and
claude
committed

Commits on Mar 19, 2026

update on Phase 0 scripts and test
fchen13
committed
Merge upstream/main: keep version_status param in process_assembly_report
fchen13
committed
update on flake8 import
fchen13
committed
Fix flake8: remove unused imports, add noqa for E402
fchen13
committed

Commits on Apr 1, 2026

Merge remote-tracking branch 'upstream/main' into feature/assembly-history
fchen13
committed
fix: rename yaml to .types.yaml, taxon_names field, and checkpoint re-run bug
fchen13
committed
untrack backfill test file
fchen13
committed

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