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openvax / topiary
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Repo Added 05 Jan 2018 08:34PM UTC
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  • absent-vs-empty-audit
  • add-agents-md
  • add-cache-sharding
  • add-cached-predictor
  • add-model-colon-kind-syntax
  • add-netmhc-cache-loaders
  • add-protected-tissues-scope
  • add-self-proteome-nearest
  • align-custom-dsl-nodes-with-normalized-keys
  • allele-class-mhcgnomes
  • allele-free-rows
  • allele-set
  • antigen-fragment
  • autowrap-allele-free
  • bare-ident-brackets
  • best-allele-aggregation
  • cache-allele-nulls
  • cache-duplicate-keys
  • cache-key-allele-set
  • cached-predictor-cli
  • cached-predictor-vaxrank-polish
  • canonical-methods
  • centralize-amino-acid-data
  • chore/295-335-ci-reliability
  • chore/316-release-tooling
  • chore/osteosarc-0.11
  • chore/osteosarc-0.12
  • chore/osteosarc-0.13
  • chore/osteosarc-0.14
  • chore/osteosarc-0.7
  • chore/osteosarc-0.9
  • chore/release-chain-cleanup
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  • cleanup-dsl-version-syntax
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  • codex/mhctools-3-7-compat
  • codex/predict-wt-peptides
  • combine-predictor-results
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  • correct-preference-claim
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  • csv-fasta-inputs
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  • deps/gtfparse3-pandas3
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  • expression-data
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  • feat/124-oncoref-cta
  • feat/contextual-cache-468
  • feat/contextual-peptide-rescoring
  • feat/historical-table-prediction-source
  • feat/native-exacto-ingestion
  • feat/occurrence-policy-audit
  • feat/orf-evidence-reconciliation
  • feat/osteosarc-rna-overlay
  • feat/osteosarc-sid-fixtures
  • feat/policy-coverage
  • feat/self-match-evidence
  • feat/versioned-ranking-profiles
  • feature/571-shared-data
  • feature/peptide-aware-isovar-context
  • feature/peptide-property-dsl
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  • feature/table-combination-rescoring
  • feature/weirdo-foreignness
  • filter-auto-aggregate
  • fix-127-autowrap-test
  • fix-165-backfill-value-from-score
  • fix-biopython-dependency
  • fix-cache-mode-ignores-requested-alleles
  • fix-cached-protein-scan-occurrence-context
  • fix-cli-coverage-gap-error-handling
  • fix-cli-oserror-message-regression
  • fix-coverage-allele-set-and-half-life-dsl
  • fix-coverage-error-str-and-cli-handling
  • fix-cross-sample-evidence-review
  • fix-declared-deps-and-dead-surface
  • fix-deploy-python-selection
  • fix-flank-mismatch-kind-coverage
  • fix-lazy-model-discovery
  • fix-peptiverse-fixture-mhctools-3446
  • fix-pirlygenes-tissue-columns
  • fix-pvacseq-presentation
  • fix-review-followups-coverage-error-and-diagnostics
  • fix-sort-ordering
  • fix-wide-list-valued-annotations
  • fix/304-374-cache-batches
  • fix/307-protein-context-fallback
  • fix/322-cli-help-flags
  • fix/324-310-cli-errors
  • fix/326-output-files
  • fix/364-imported-mutation-geometry
  • fix/388-preserve-terminal-flanks
  • fix/390-isovar-hypothesis-comparisons
  • fix/390-review-preserve-hypothesis-identities
  • fix/397-repeated-isovar-translations
  • fix/398-isovar-export-versions
  • fix/409-reference-version-identity
  • fix/410-measurement-context-roundtrip
  • fix/414-reject-non-node-dsl-args
  • fix/472-categorical-roundtrip
  • fix/486-short-expression-tables
  • fix/496-pandas3-baseline
  • fix/507-pandas31-json-cells
  • fix/517-protein-boundary-context
  • fix/audit-continuity-shared-osteosarc
  • fix/cache-loading-323
  • fix/cache-scan-lengths-329
  • fix/canonical-ensembl-ci-reference
  • fix/ci-retries-and-test-collection
  • fix/cli-results-325
  • fix/consistent-numeric-columns
  • fix/cufflinks-hidata-476
  • fix/dsl-expression-roundtrip-448
  • fix/dsl-literal-compatibility
  • fix/dsl-transform-arguments-471
  • fix/ensembl-ci-artifact-handoff
  • fix/fragment-identity-and-typed-audit-inputs
  • fix/human-audit-genetic-code
  • fix/isovar-read-identity-contract
  • fix/metadata-extra-collisions
  • fix/metadata-extra-text-encoding
  • fix/mixed-annotation-codec
  • fix/osteosarc-all-variant-outcomes
  • fix/pandas-warning-cleanup
  • fix/raise-min-python-311
  • fix/readme-release-validation
  • fix/reject-conflicting-measurements
  • fix/release-preflight
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  • fix/require-osteosarc
  • fix/sample-identity-and-review-findings
  • fix/shared-fixture-mechanics
  • fragment-counts-to-frame
  • fragment-read-evidence
  • from-predictions
  • from-predictions-columns
  • group-keys-everywhere
  • guide-corrections
  • haplotype-autoproject
  • honest-dna-subject
  • improve-cli-errors
  • inline-blosum62
  • io-wide-v4.11
  • isovar-fragments
  • isovar-run
  • kind-mhc-dependence
  • lazy-varcode-imports
  • lens-loader
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  • lens-multi-version
  • lens-version-agnostic
  • master
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  • openvax_switch
  • optional-dependency-extras
  • peptide-level-named-allele
  • peptide-provenance
  • peptide-view
  • peptide-view-followups
  • per-peptide-alleles
  • pirlygenes-5.1-expression-accessors
  • plumb-kind-support
  • pr-b-fragment-refactor
  • promote-kind-aliases-public
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  • pvacseq-branch-vocabulary
  • pvacseq-loader
  • read-evidence
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  • refactor-for-protein-sequences
  • regression-all-blank-allele
  • release-4.8.0
  • remove-model-lookup-global
  • restore-varcode-cli-parser-delegation
  • rna-evidence-accessors
  • scoped-fields-in-filters
  • self-nearest-population
  • shrink-cached-predictor-index
  • simplify-eval-context-frame-names
  • symmetric-ambiguous-amino-acid-distance
  • symmetric-evidence-columns
  • test-audit-v4.10
  • test/osteosarc-additional-indels
  • test/osteosarc-pvacseq-corpus
  • tests/369-363-hygiene
  • tests/openvax-v1
  • topiary-result
  • unify-release-python
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  • verify-isovar-integration
  • verify-pirlygenes-integration

26 Oct 2026 03:21AM UTC coverage: 93.467% (+0.02%) from 93.447%
40263696271-1

push

github

web-flow
Preserve protein scan context through caching and replay (#518)

* Preserve declared protein flank limits in cached scans

* Keep scan metadata with each model through wide replay

102 of 105 new or added lines in 6 files covered. (97.14%)

2 existing lines in 1 file now uncovered.

10888 of 11649 relevant lines covered (93.47%)

0.93 hits per line

Relevant lines Covered
Build:
Build:
11649 RELEVANT LINES 10888 COVERED LINES
0.93 HITS PER LINE
Source Files on master
  • Tree
  • List 62
  • Changed 7
  • Source Changed 7
  • Coverage Changed 6
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
40263696... master Preserve protein scan context through caching and replay (#518) * Preserve declared protein flank limits in cached scans * Keep scan metadata with each model through wide replay push 26 Oct 2026 03:38AM UTC web-flow github
93.47
40261849... fix/517-protein-boundary-context Merge 3390036fa into 71c09eda5 Pull #518 26 Oct 2026 03:16AM UTC web-flow github
93.47
40258057... fix/517-protein-boundary-context Merge 8c5fb8d0e into 71c09eda5 Pull #518 26 Oct 2026 02:29AM UTC web-flow github
93.45
40217843... master Resolve protein-context cache misses through validated scanner fallback (#516) * Fill protein-scan cache misses through context-preserving fallback * Reject incompatible protein context before peptide-only fallback push 25 Oct 2026 05:58PM UTC web-flow github
93.45
40215479... fix/307-protein-context-fallback Merge 1d71813bb into 2cda74347 Pull #516 25 Oct 2026 05:32PM UTC web-flow github
93.45
40201528... master Add sparse historical prediction sources with preserved provenance (#506) * Trying to resolve the issue * Preserve historical provenance through sparse occurrence rescoring * Retain scalar historical measurement contexts in feature provenance ... push 25 Oct 2026 02:31PM UTC web-flow github
93.47
40199969... feat/historical-table-prediction-source Merge 30a8e53ed into 9a276be9f Pull #506 25 Oct 2026 02:11PM UTC web-flow github
93.46
40198603... feat/historical-table-prediction-source Merge 645279bf8 into 9a276be9f Pull #506 25 Oct 2026 01:56PM UTC web-flow github
93.47
40156287... master Keep PirlyGenes CI inputs independent of cache eviction (#511) push 25 Oct 2026 03:22AM UTC web-flow github
93.65
40153959... fix/ensembl-ci-artifact-handoff Merge b0842ae73 into 6108cbb64 Pull #511 25 Oct 2026 02:50AM UTC web-flow github
93.65
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