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• add-load-all-evidence
• add-parquet-export-test
• add-refs-aggregator-20260420
• align-version-with-pypi
• allele-resolution
• attribution-per-donor-rows
• audit-pmid-overrides
• binding-index-split
• builder-memory-reduction
• bulk-proteomics-abundance-and-metadata
• bulk-proteomics-non-tryptic-bj
• category2-per-donor-curation
• cell-name-parser
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• ci/corpus-cache
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• codex/apc-lineage-curation
• codex/curate-pmid-24366607
• codex/curate-pmid-29093164
• codex/export-ms-peptide-summary
• codex/training-export-unified
• curate-batch-2
• curate-batch-3
• curate-top-studies
• expand-proteome-registry-bacteria
• faridi-per-transfectant
• feat/261-cell-type-column
• feat/allele-bag-expansion-137
• feat/apm-perturbation-columns
• feat/assay-iri-evidence-row-id
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• feat/class-label-severity-tiers
• feat/condition-categories
• feat/curate-shapiro-2025
• feat/discrepancies-per-sample
• feat/engineered-mhc-flag
• feat/exclude-class-label-suspect
• feat/export-cleanup
• feat/export-provenance
• feat/gomez-raji-plasma
• feat/instrument-category-and-gomez-zepeda
• feat/line-expression-anchors
• feat/line-expression-cache
• feat/list-args-space-separated
• feat/maptac-dp-dq-match
• feat/normalize-and-class-suspect
• feat/observations-export
• feat/pmhc-binder-classification
• feat/pmhc-flat-and-optional
• feat/pmhc-query-and-toplevel-reshuffle
• feat/pmhc-sample-paired
• feat/pmhc-serotype-expansion
• feat/ptm-aware-peptides
• feat/qc-plan-roadmap
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• feat/severity-tiers-in-qc-and-cli
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Build # 26994604019

Build Type

push

github

Committed by web-flow

Commit Message

v1.30.63: cap integration-test workers in CI to avoid OOM (#272 follow-up) (#274)

Seeding the ci-corpus-v1 release exposed a bug in the corpus mechanism:
once the corpus is present, the 3.11 job ran the integration suite under
'pytest -n auto' (4 workers on a 16 GB runner) and got OOM-killed
('The operation was canceled' mid-run, ~48%). Each integration test
materializes the full ~4.4M-row observations table, and the #262 Arrow
xdist fixture only shares numeric/categorical columns zero-copy — string
columns materialize per worker, so 4 workers exceed RAM.

Fix: split the 3.11 test step — non-integration with -n auto (full
parallelism), integration capped at -n 2 (still exercises the cross-worker
mmap fixture, but the build peak + 2 workers fit in 16 GB). Coverage
accumulates via --cov-append. Add timeout-minutes: 25 so a future
hang/OOM fails fast instead of burning the 360-min default.

Verified: pytest -m integration -n 2 -> 20 passed, 1 skipped locally.

Coverage Stats

4843 of 6290 relevant lines covered (77.0%)

0.77 hits per line