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pirl-unc / hitlist
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DEFAULT BRANCH: main
Repo Added 30 Mar 2026 02:32PM UTC
Token 2BMOPfDLihNAYkvRMkn4Pz38iRgZjmtXf regen
Build 516 Last
Files 30
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  • 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
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  • curate-actb-31887370-source-organism
  • curate-batch-2
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  • curate-top-studies
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  • docs-curation-rewrite
  • 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/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
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  • 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

19 Jun 2026 06:27PM UTC coverage: 80.498% (+0.06%) from 80.435%
27842275440

push

github

web-flow
Subtle ANSI coloring for --help (cli_help.SubtleHelpFormatter) (#346)

Adds hitlist.cli_help with a SubtleHelpFormatter (subcommand names in cyan,
section headings in bold) and a ColorArgumentParser that defaults to it. Because
add_subparsers uses type(self) as its parser class, making the root a
ColorArgumentParser colors the whole command tree from one declaration.

- Gated on a TTY; honors NO_COLOR (off) and FORCE_COLOR (on), so piped output
  and `--help | cat` stay plain.
- Alignment-safe: coloring is applied in _format_action AFTER argparse measures
  the plain text, only wrapping the already-positioned token in escapes. The
  round-trip test asserts stripping the ANSI reproduces the plain help exactly.
- Exposed for reuse: tsarina imports the same formatter so both CLIs match.

Bumps 1.44.0 -> 1.45.0 (new public hitlist.cli_help).

5911 of 7343 relevant lines covered (80.5%)

0.8 hits per line

Relevant lines Covered
Build:
Build:
7343 RELEVANT LINES 5911 COVERED LINES
0.8 HITS PER LINE
Source Files on main
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  • Changed 2
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  • Coverage Changed 2
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
27842275440 main Subtle ANSI coloring for --help (cli_help.SubtleHelpFormatter) (#346) Adds hitlist.cli_help with a SubtleHelpFormatter (subcommand names in cyan, section headings in bold) and a ColorArgumentParser that defaults to it. Because add_subparsers uses... push 19 Jun 2026 06:32PM UTC web-flow github
80.5
27839676262 cli-help-color Merge 1eca6430b into 81eef49f6 Pull #346 19 Jun 2026 05:28PM UTC web-flow github
80.53
27800559606 main Friendlier CLI + accurate docs + curated top-level API (#345) Friendliness: - Stale deprecation targets: every "Run: hitlist data build" / "data fetch-proteomes" error + help string (qc, observations, mappings, builder, cli, bulk_proteomics) ... push 19 Jun 2026 01:58AM UTC web-flow github
80.44
27800398117 friendliness-and-docs Merge b1ebb5194 into 1b695987c Pull #345 19 Jun 2026 01:52AM UTC web-flow github
80.44
27799766194 main Fix silent-wrong-result bugs in the data/observations layer (#344) Six correctness fixes surfaced by a holistic review (all reproduced, regression tests added): - observations: mhc_allele_in_set was silently skipped when the caller's columns= ... push 19 Jun 2026 01:32AM UTC web-flow github
80.37
27799593533 correctness-fixes Merge 105205e24 into f2859918f Pull #344 19 Jun 2026 01:27AM UTC web-flow github
80.37
27790016011 main Auto-fetch IEDB/CEDAR; add reusable VersionedDatasetRegistry (#343) IEDB/CEDAR: - Move iedb/cedar from MANUAL_DATASETS to FETCHABLE_DATASETS. The downloader.php endpoints serve the zip directly (no enforced login), so there's no technical rea... push 18 Jun 2026 09:24PM UTC web-flow github
80.32
27789391371 versioned-datasets-iedb-autofetch Merge 94633aafe into a953ad42a Pull #343 18 Jun 2026 09:12PM UTC web-flow github
80.32
27783875082 main Add progress bar + cache status to downloads; expose reusable download_to_file (closes #341) (#342) The core streaming download (_download_to_file) showed no progress despite tqdm already being a dependency, and cache-hit messaging was ad-hoc acr... push 18 Jun 2026 07:28PM UTC web-flow github
80.04
27777451563 download-progress-cache-status Merge a125ccb4a into 6aef86416 Pull #342 18 Jun 2026 05:33PM UTC web-flow github
80.04
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