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Dev - #6

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ecrum19 merged 10 commits into
mainfrom
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Sep 11, 2026
Merged

Dev#6
ecrum19 merged 10 commits into
mainfrom
dev

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@ecrum19

@ecrum19 ecrum19 commented Sep 11, 2026

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Many large changes for v3.0.0

ecrum19 and others added 9 commits September 8, 2026 14:15
# Conflicts:
#	changelog.md
#	docs/conversion.md
#	docs/limitations.md
#	docs/roadmap.md
#	docs/vcf-coverage.md
#	test/test_vcf_rdfizer_unit.py
Partitioned compression works in a named volume and removes it in its own
`finally`. That is enough on the normal path but not on an interrupt: the
`finally` runs as the exception unwinds, which is before the handler kills the
containers, and Docker refuses to remove a volume a live container still
holds. Removal failed there, warned once, and nothing retried -- leaking
roughly 700 MB per interrupted run. Three had accumulated on the benchmark VM.

Volumes are now registered when created and swept by the interrupt path after
the containers are stopped, retrying while a just-killed container releases
its hold. A volume whose removal fails stays registered rather than being
forgotten, and `main`'s `finally` makes a last attempt so a failure on the
normal path is not left behind either. The checkpoint records the counts.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@codecov-commenter

codecov-commenter commented Sep 11, 2026 •

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⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 91.56171% with 335 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
src/validation/validation_runner.py 77.50% 135 Missing ⚠️
vcf_rdfizer_vocab.py 87.59% 50 Missing ⚠️
vcf_rdfizer_link.py 72.54% 42 Missing ⚠️
vcf_rdfizer_linking/manifest.py 89.30% 23 Missing ⚠️
test/test_vcf_rdfizer_unit.py 93.35% 22 Missing ⚠️
vcf_rdfizer_linking/inputs.py 83.76% 19 Missing ⚠️
vcf_rdfizer_linking/reference.py 88.88% 14 Missing ⚠️
vcf_rdfizer_linking/runner.py 94.00% 13 Missing ⚠️
vcf_rdfizer_linking/session.py 93.33% 10 Missing ⚠️
test/test_linking_unit.py 99.74% 1 Missing ⚠️
... and 6 more

📢 Thoughts on this report? Let us know!

@ecrum19
ecrum19 merged commit f895371 into main Sep 11, 2026
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2 participants