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• fix/python-310-314-support
• add-load-all-evidence
• add-parquet-export-test
• add-peptide-summary-export
• add-refs-aggregator-20260420
• adopt-mhcgnomes-species-api
• align-version-with-pypi
• allele-resolution
• apm-featurization-coverage
• attribution-per-donor-rows
• audit-fix-batch9-10-cellines
• audit-pmid-overrides
• binding-index-split
• bound-prefetch-phase
• builder-memory-reduction
• bulk-proteomics-abundance-and-metadata
• bulk-proteomics-non-tryptic-bj
• by-tissue-anatomical-rollup
• category2-per-donor-curation
• cell-name-parser
• centralize-repeated-logic
• chore/audit-cleanup-stale-docs
• chore/batch-todo-and-lessons
• chore/memory-and-allele-lessons
• chore/test-speed
• ci/build-smoke-test
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• codex/apc-lineage-curation
• codex/binding-assay-context-20261023
• codex/binding-context-availability-20261024
• codex/curate-pmid-24366607
• codex/curate-pmid-29093164
• codex/digestion-kinetic-recipe-20261023
• codex/digestion-processing-package-20261024
• codex/digestion-timecourse-source-20261023
• codex/export-ms-peptide-summary
• codex/goldberg-canonical-mapp-20261025
• codex/goldberg-composition-20261024
• codex/goldberg-mapp-source-825-20261024
• codex/goldberg-material-mapping-20261025
• codex/gomez-arm-projection-20261023
• codex/gomez-prediction-panel-20261024
• codex/gomez-source-20261023
• codex/hap1-quantitative-726-20261024
• codex/hap1-response-726-20261024
• codex/intact-degradomics-20261024
• codex/intact-kinetics-20261025
• codex/intact-organ-transfer-20261025
• codex/lymph-composition-recipe-20261024
• codex/mapp-canonical-api-20261024
• codex/mapp-condition-recipe-20261022
• codex/mapp-controls-source-20261023
• codex/mapp-pxd009438-admission-20261024
• codex/mapp-source-generation-20261022
• codex/mapp-source-mappings-20261024
• codex/mhc-ligand-ms-core-contract-20261025
• codex/ms-calibration-source-20261023
• codex/nanaware-lymph-quantities-20261024
• codex/native-contrast-recipe-20261025
• codex/native-psmd2-source-20261025
• codex/pbmc-composition-20261024
• codex/precursor-quantities-20261024
• codex/precursor-recipe-pairing-20261024
• codex/precursor-source-contract-20261024
• codex/proteometools-ms1-source-20261024
• codex/pxd024809-observation-20261025
• codex/pxd024917-calibration-20261025
• codex/record-precursor-release-20261024
• codex/release-2-0-39-20261025
• codex/supplement-peptidoform-recovery-20261029
• codex/tcell-processing-package-20261024
• codex/tmab-native-measurements-20261024
• codex/tmab-provenance-corrections-20261024
• codex/tmab-semantics-791-20261024
• codex/training-export-unified
• codex/wolf-levy-material-crosswalk-20261025
• correctness-fixes
• cta-from-cancerdata
• cta-hpa-vetting-and-fixes
• curate-36-batch10
• curate-36-batch11
• curate-36-batch9
• curate-36-cellline-batch12
• curate-36-cellline-batch13
• curate-36-cellline-batch14
• curate-36-hct116
• curate-36-mixed-cohorts
• curate-actb-31887370-source-organism
• curate-batch-2
• curate-batch-3
• curate-bola-36423003
• curate-other-cell-lines-by-tissue
• curate-top-studies
• curate/33b-batch2
• curate/33b-batch3
• curate/33b-batch4
• curate/33b-monoallelic-batch1
• curate/36-batch6
• curate/36-batch7
• curate/36-batch8
• curate/36-singleallele-batch5
• curate/human-specimen-lineage
• curation-sanity-conditions-sources-20260924
• curation/literature-species-context
• docs-curation-rewrite
• docs/performance-skip-wording-20261029
• download-progress-cache-status
• expand-proteome-registry-bacteria
• faridi-per-transfectant
• 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/615-training-binding-filters
• feat/622-616-training-provenance
• feat/668-canine-peptide-evidence
• feat/allele-bag-expansion-137
• feat/apm-perturbation-columns
• feat/assay-iri-evidence-row-id
• feat/atlas-lineage-crosswalk
• feat/atomic-dataset-generations
• feat/binding-response-measured-stacked
• feat/build-top-level
• feat/bulk-proteomics-n-replicates-possible
• feat/canine-bulk-evidence
• feat/canine-ligand-curation
• feat/class-label-severity-tiers
• feat/condition-categories
• feat/corpus-qualification
• feat/corrected-corpus-generation
• feat/curate-shapiro-2025
• feat/current-corpus-publication
• feat/discrepancies-per-sample
• feat/engineered-mhc-flag
• feat/evidence-store-v2
• feat/exclude-class-label-suspect
• feat/export-cleanup
• feat/export-provenance
• feat/expression-evidence-bundle
• feat/external-quant-v2
• feat/flat-condition-columns
• feat/functional-evidence-audit
• feat/gomez-raji-plasma
• feat/human-cohort-qualification
• feat/human-self-tcell-functional
• feat/human-tcell-multimer-training
• 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/material-protocol-v2
• feat/mhc-v2-evidence
• feat/ms-detectability
• feat/multimer-adjudication
• feat/normalize-and-class-suspect
• feat/observations-export
• feat/orfdata-canine-protein
• 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/pxd013455-publication
• 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/species-evidence-bundles
• feat/supporting-modalities-v2
• feat/supporting-numeric-v2
• feat/tcell-assay-metadata
• feat/tcell-training-evidence-contract
• feat/tcell-v2
• feat/training-export-136
• feat/training-input-preflight
• feat/transcript-aware-mappings
• feat/unified-evidence-catalog
• feat/vectorize-and-version
• feat/versioned-uniprot
• fix-306-coalesce-source-species
• fix-306-deprecate-species-name
• fix-307-per-pmid-source-organism
• fix-314-per-pmid-provenance
• fix-394-class-ii-mappings
• fix-allele-resolution-categorical-fillna
• fix-alpizar-2017-split-b-alleles
• fix-alpizar-test-fixture
• fix-apm-arm-attribution
• fix-apm-unknown-arm-v2
• fix-assay-routing-and-provenance-cli
• fix-bola-a19-414
• fix-build-smoke-myeloblast
• fix-cedar-url-and-dedup
• fix-chen-2020-hela-abc-ko
• fix-classify-allele-pair-gene-gene
• fix-concat-futurewarnings
• fix-develop-sh-venv
• fix-ebv-lcl-direct-ex-vivo
• fix-flank-default
• fix-hla-only-filter
• fix-ig-tr-protein-mapping
• fix-illing-2018-split-b57-transfectants
• fix-mapping-build-contract-and-timeouts
• fix-mhc-identity-contract
• fix-mhc-sample-attribution
• fix-pandas-categorical-warnings
• fix-pmid-arrow-conversion
• fix-prefetch-worker-test-isolation
• fix-primata-tree-pin
• fix-restriction-evidence-415
• fix-sample-metadata-consistency
• fix-sarango-2022-precision
• fix-serotype-locus-attribution
• fix-supplementary-species-curation
• fix-thp1-typing-416
• fix-trolle-2016-split-721-221-transfectants
• fix-weingarten-gabbay-2021-no-hbec
• fix/230-phosphoantigen-restrictions
• fix/255-download-timeout
• fix/289-tool-neutral-dataset-errors
• fix/291-datacache-data-dir
• fix/306-canonical-source-organism
• fix/357-depmap-expression-fetch
• fix/358-hap1-depmap-reference
• fix/359-sample-group
• fix/366-arm-resolution
• fix/373-sample-override-and-note
• fix/386-export-species-filters
• fix/409-spdx-license-metadata
• fix/424-curation-cache-inputs
• fix/425-gene-query-union
• fix/426-species-filter-projection
• fix/427-export-allele-filters
• fix/436-targeted-study-curation
• fix/438-sample-inventory-conservation
• fix/442-arm-attribution
• fix/444-honor-exclude-from-ms
• fix/448-cache-current-predicate
• fix/451-class-pool-consensus
• fix/452-erap2-clone-arms
• fix/454-unique-key-yaml
• fix/456-retired-allele-identities
• fix/457-study-identities
• fix/462-serotype-test-strictness
• fix/467-mhcgnomes-tripwire
• fix/468-warmup-deadline-excludes-spawn
• fix/470-cedar-column-resolution
• fix/471-fixture-cache-leak
• fix/471-review-followups
• fix/473-review-followups
• fix/478-arrow-dictionary-concat
• fix/483-deploy-test-retry-once
• fix/483-preflight-memory-guard
• fix/483-two-pass-integration-split
• fix/484-mhc-allowlist-stale
• fix/490-predictor-genotype-boundary
• fix/491-mhc-allele-split-and-alias
• fix/493-flag-shared-cta-peptides
• fix/496-authoritative-gene-count
• fix/496-other-genes-review-findings
• fix/501-serotype-test-skips
• fix/502-by-gene-n-samples
• fix/504-required-mhcgnomes
• fix/508-explicit-boolean-mapping
• fix/509-class-scoped-fixtures
• fix/511-numeric-group-identifiers
• fix/512-deposited-dose-attribution
• fix/514-genotype-consistent-attribution
• fix/520-genotype-restriction
• fix/522-expression-source-provenance
• fix/526-phase-memory-retry
• fix/528-mutant-sample-genotypes
• fix/532-stable-attribution-context
• fix/534-cohort-scoped-attribution
• fix/538-ci-release-artifacts
• fix/540-ci-corpus-provenance
• fix/541-explicit-mapping-spawn
• fix/543-spawned-mapping-cache
• fix/547-sample-genotype-reassignment
• fix/549-current-actions-runtimes
• fix/551-isolated-predictor-invocations
• fix/553-develop-metadata-check
• fix/555-556-curation-attribution
• fix/558-559-567-source-verification
• fix/564-validator-and-docs
• fix/565-pan-class-ii-candidates
• fix/566-integration-memory
• fix/566-integration-memory-residency
• fix/566-release-join-buffers
• fix/566-split-integration-ci
• fix/574-563-predictor-eligibility
• fix/576-577-anchor-provenance
• fix/579-import-side-effects
• fix/586-sibling-mhc-context
• fix/590-fetch-file-timeout-and-sha
• fix/591-proteome-cache-resolution
• fix/611-curated-label-join-lifetime
• fix/613-retain-oversized-index
• fix/614-donor-observation-identity
• fix/665-positive-ms-outcomes
• fix/assay-modality
• fix/audit-19-remaining
• fix/bekker-jensen-ph-provenance
• fix/bulk-replicate-provenance
• fix/c1r-allele-curation
• fix/canine-instrument-provenance
• fix/canine-sample-curation
• fix/cell-line-registry-src-cancer-480
• fix/class-ii-implausible-45
• fix/class-ii-implausible-threshold
• fix/cli-error-handling-886
• fix/correctness-gates-and-exports
• fix/cross-reference-class-only-pmids
• fix/data-preflight-and-deprecation-884-893
• fix/derived-column-passthrough
• fix/download-integrity-882
• fix/ebv-lcl-classification
• fix/empty-export-fallback
• fix/engineering-control-claims
• fix/evidence-snapshot-inodes
• fix/expression-input-defaults
• fix/haplotype-roster-candidates
• fix/hgnc-failure-cache-885
• fix/index-row-selection
• fix/integration-ci-timeout
• fix/known-nonroster-alleles
• fix/legacy-cache-status-compatibility
• fix/manifest-transaction-883
• fix/mhcflurry-predict-alleles-arg
• fix/multi-allele-genotype-tokenization
• fix/per-sample-mhc-curation
• fix/pmhc-progress-wording
• fix/pmid-curation-audits-128-132
• fix/pr-validation-concurrency
• fix/proteome-cache-bounded
• fix/release-integration-memory
• fix/release-verifier-timeout
• fix/reliability-pandas3-20261028
• fix/report-keyerror-and-cli-help
• fix/restriction-compatible-allele-candidates
• fix/run-all-include-proteome-coverage
• fix/sample-resolver-tiebreak
• fix/scanner-close-csv-files
• fix/serotype-candidate-intersection
• fix/serotype-source-and-map-keys
• fix/severity-tier-ptm-aware
• fix/soluble-mhc-context
• fix/species-summary-peptide-pmid-invariant
• fix/thp1-control-knockout-absence
• fix/uniprot-2015-10
• fix/unmatched-allele-taxonomy
• friendliness-and-docs
• gene-rollup-and-gene-sets
• guard-pooled-allele-curation
• harden-public-peptide-allele-api
• 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
• mhcgnomes-class-parsing
• 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/bounded-provenance-build
• perf/contributor-storage-63-20261029
• perf/full-build-63-20261029
• perf/hermetic-tests-and-cta
• 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
• pin-ruff
• pmhc-by-tissue-totals-and-gene-check
• pmhc-filter-flags
• pmhc-group-by-species
• predictor-multi-allele-narrowing
• probe/566-read-dictionary
• profile-build-pipeline
• proteome-cache-followups
• prune-low-value-tests
• public-peptide-alleles-api
• qc/discrepancies-report
• readme-curation-table
• refactor/258-rename-pmhc-helpers
• refactor/589-datacache-downloads
• refactor/589-shared-registry
• refactor/cli-split-887
• 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
• ship-peptide-attributions
• single-seed-index
• 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 # 39314067183

Build Type

Pull #717

github

Committed by web-flow

Commit Message

Merge 24809acdf into 25044799c

Pull Request Pull Request #717: Align Python support with 3.10–3.14 (#684)

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