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LAST BUILD ON BRANCH correctness-fixes

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• correctness-fixes
• add-load-all-evidence
• add-parquet-export-test
• add-peptide-summary-export
• add-refs-aggregator-20260420
• align-version-with-pypi
• allele-resolution
• attribution-per-donor-rows
• audit-fix-batch9-10-cellines
• audit-pmid-overrides
• binding-index-split
• builder-memory-reduction
• bulk-proteomics-abundance-and-metadata
• bulk-proteomics-non-tryptic-bj
• by-tissue-anatomical-rollup
• category2-per-donor-curation
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• chore/audit-cleanup-stale-docs
• chore/test-speed
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• cli-help-color
• codex/apc-lineage-curation
• codex/curate-pmid-24366607
• codex/curate-pmid-29093164
• codex/export-ms-peptide-summary
• codex/training-export-unified
• cta-from-cancerdata
• cta-hpa-vetting-and-fixes
• curate-36-batch10
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• curate-36-hct116
• curate-36-mixed-cohorts
• curate-actb-31887370-source-organism
• curate-batch-2
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• curate-other-cell-lines-by-tissue
• curate-top-studies
• curate/33b-batch2
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• curate/33b-batch4
• curate/33b-monoallelic-batch1
• curate/36-batch6
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• docs-curation-rewrite
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• expand-proteome-registry-bacteria
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• feat-46-multiaxis-species
• feat-by-tissue-cancer-healthy-split
• feat-by-tissue-cell-type-grouping
• feat-by-tissue-formatting
• feat-by-tissue-observation-breakdown
• feat-by-tissue-sections
• feat-externalize-bundled-data
• feat-noncancer-line-ecn90
• feat-pmhc-by-tissue
• feat-pmhc-species-source-context
• feat/261-cell-type-column
• feat/261-stage3-cell-type-filter
• feat/allele-bag-expansion-137
• feat/apm-perturbation-columns
• feat/assay-iri-evidence-row-id
• feat/binding-response-measured-stacked
• feat/build-top-level
• feat/bulk-proteomics-n-replicates-possible
• 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
• feat/qc-proteome-coverage
• feat/qc-top-level
• feat/quantitative-binding-fields
• feat/register-aav-proteomes
• feat/register-mtb-plasmodium-proteomes
• feat/rename-map-source-proteins
• feat/report-from-index
• feat/severity-tiers-in-curation-plan
• feat/severity-tiers-in-qc-and-cli
• feat/training-export-136
• feat/transcript-aware-mappings
• feat/vectorize-and-version
• fix-306-coalesce-source-species
• fix-306-deprecate-species-name
• fix-307-per-pmid-source-organism
• fix-314-per-pmid-provenance
• fix-allele-resolution-categorical-fillna
• fix-alpizar-2017-split-b-alleles
• fix-build-smoke-myeloblast
• fix-chen-2020-hela-abc-ko
• fix-classify-allele-pair-gene-gene
• fix-ebv-lcl-direct-ex-vivo
• fix-hla-only-filter
• fix-illing-2018-split-b57-transfectants
• fix-pandas-categorical-warnings
• fix-pmid-arrow-conversion
• fix-sarango-2022-precision
• fix-supplementary-species-curation
• fix-trolle-2016-split-721-221-transfectants
• fix-weingarten-gabbay-2021-no-hbec
• fix/255-download-timeout
• fix/audit-19-remaining
• fix/c1r-allele-curation
• fix/class-ii-implausible-45
• fix/class-ii-implausible-threshold
• fix/cross-reference-class-only-pmids
• fix/derived-column-passthrough
• fix/ebv-lcl-classification
• fix/multi-allele-genotype-tokenization
• fix/per-sample-mhc-curation
• fix/pmhc-progress-wording
• fix/pmid-curation-audits-128-132
• fix/proteome-cache-bounded
• fix/report-keyerror-and-cli-help
• fix/run-all-include-proteome-coverage
• fix/sample-resolver-tiebreak
• fix/scanner-close-csv-files
• fix/severity-tier-ptm-aware
• friendliness-and-docs
• gene-rollup-and-gene-sets
• ingest-abelin-2019-maptac
• ingest-bekker-jensen-peptides
• ingest-ccle-bulk-proteomics
• ingest-strazar-2023-hla2
• is-non-peptide-ligand-228
• issue-104-108-digest-and-bounds
• issue-105-atomic-rebuild
• issue-106-export-bulk-cli
• issue-110-proteome-index-memory
• issue-117-summary-from-indices
• issue-119-export-progress
• issue-12-human-51-100
• issue-121-118-normalize-and-lengths
• issue-122-short-mhc2-filter
• issue-8-nonclassical-hla
• issue-85-scanner-perf
• issue-86-proteome-index-cache
• issue-93-remove-hla-filter
• issue-98-fractionation-ph
• issue-99-proteome-kmer-set
• main
• map-remaining-gene-ids
• mono-allelic-detection
• mono-allelic-method
• obliterate-legacy-index-cache
• parallelize-mappings
• per-transfectant-splits
• perf/250-vectorized-kmer-index
• perf/262-arrow-xdist-cache
• perf/263-tighten-dtypes
• perf/batch-drops-and-fillna
• perf/memory-aware-test-workers
• perf/merge-and-copy
• perf/proteome-build-inline
• perf/proteome-cache-build-order
• perf/test-speed
• perf/test-suite-integration-marker
• perf/unique-map-string-ops
• pin-mhcgnomes
• pmhc-by-tissue-totals-and-gene-check
• pmhc-filter-flags
• pmhc-group-by-species
• predictor-multi-allele-narrowing
• profile-build-pipeline
• proteome-cache-followups
• prune-low-value-tests
• qc/discrepancies-report
• readme-curation-table
• refactor/258-rename-pmhc-helpers
• register-saos2-skmel37-lineage
• rename-proteome-label
• retire-human-only
• retro-allele-predictor
• sarkizova-monoallelic-recovery-45
• scanner-v2
• serotype-mapping
• sex-stratified-reproductive-286
• split-gene-mapping-from-observations
• test/supplementary-build-e2e
• unified-observations
• update-readme-1.10
• upgrade-mhc-unknown
• vectorize-export-discriminator-loop
• versioned-datasets-iedb-autofetch

Build # 27799593533

Build Type

Pull #344

github

Committed by web-flow

Commit Message

Merge 105205e24 into f2859918f

Pull Request Pull Request #344: Fix silent-wrong-result bugs (filters, downloads, manifest, species)

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5863 of 7295 relevant lines covered (80.37%)

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