Publication readiness: primary-call matrix, EVE toolchain, vignette suite, hygiene - #7

Merged

mdmanurung merged 60 commits into

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claude/pub-readiness-hygiene

Jul 21, 2026

Commits on Jul 15, 2026

feat(detection): add EVE artifact flags to viral_summary.tsv (closes PLAN SH2.6)

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cff9895
fix(covid): commit evidence rerun script + RUNBOOK Stage 5 (closes T5)

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512d0d3
docs(findings): add T6 CellTypist enrichment result + resolve T5 reproducibility note

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98ef8a2
docs(living): session-end triage — T5/T6 decisions, plasma-cell EVE learning, last-session update

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1c9924f

Commits on Jul 17, 2026

docs(living): EVE analysis conclusion — all anellovirus confirmed artifact (job 25237061)

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4fcd748
build(deps): declare anndata and sync scikit-learn into conda env

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25139a8
build(docker): install package with --no-deps against complete env

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c1aaca0
fix(benchmark): resolve STAR from PATH/env, not a hardcoded abs path

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e4b8734
chore: gitignore untracked covid clinical outputs

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b8f8e74
docs: add 2026-07-17 publication-readiness delta assessment

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622f987
docs(living): record CI --no-deps undeclared-dependency blind spot

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d439386
chore(package): remove all institutional abs paths from shipped files

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c37492a
refactor(cli): rename check_output -> confirm_and_clear_output_dir

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7d4c288
refactor: remove dead conditional branches

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98d6d49
release: reconcile version to 2.6.0 and close CHANGELOG [Unreleased]

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12b3384
docs(manuscript): fix data-availability label, runtime claim, citations

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baf348e

Commits on Jul 20, 2026

feat(detection): route viral numerators through the primary-call matrix

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ce5f429
feat(covid): add EVE annotation toolchain and harden the SLURM pipeline

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2dd1d41
docs(vignettes): replace basic_usage with an 8-vignette suite

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567dcfc
chore(living): record sessions and register aifi convention pack

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66bef4b
chore(curation): add gitignored symlink curation view

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1fda25d
fix(covid): correct EVE annotation coordinate and chromosome-name bugs

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607a340
refactor(detection): dedupe primary-call matrix plumbing

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f143d94
chore(hygiene): scrub third-party path from docs, gitignore telemetry

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739c221
chore(living): record curation-view session and pattern

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3dd145d

Commits on Jul 21, 2026

perf(multimap): hoist per-record pd.isna out of the hot loop

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5e95077
chore(bloat): untrack redundant bundled viral GTFs

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6bb5c64
chore(living): record perf profiling + 29GB->8.9MB gc

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perf(multimap): collapse duplicate (cell,ec) records before the hot loop

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bbb05f3
chore(living): record multimap collapse rewrite + learning L-26

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refactor(multimap): leaner collapse intermediates

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4e32b43
chore(living): record max code review of session commits

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d0533f6
refactor: remove dead code and a dead special case (Linus review)

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chore(living): record Linus dead-code removal

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chore(living): record clean code review of dead-code removal

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chore(living): note uncommitted /tmp verification harnesses

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docs(living): record viral-read positional-profiling capability assessment

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docs(roadmap): add read-start feature plan and extensive roadmap

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c52e9fb
docs(plan): add sequenced back-to-back implementation plan for the roadmap

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27874b8
fix(robustness): P1 — var_names safety, EVE legacy sseqid, ambig clamp (D1-D3)

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afc2625
feat(evidence): A1 — read-start distribution + PCR-dup handling

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fix: address parallel-review findings on the A1/P1 increment

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docs(living): record roadmap-execution increment (P1+A1) and parallel review

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88cdf51
feat(evidence): A3 — cell-tagged viral BAM for per-cell IGV inspection

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feat(detection): G1 — write reference-annotation provenance per run

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fix(evidence): harden cell-tag SAM handling (A3 review)

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docs(living): record roadmap increment 2 (A3+G1) and parallel review

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test(hostresponse): C1 — unit tests for Ensembl->symbol annotation

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ci(F5)+test(G2): nbmake vignette gate; lock non-human host support

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docs(living): record roadmap increment 3 (C1/G2 tests, F5, E-defer)

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de9afba
docs(changelog): populate [Unreleased] with post-2.6.0 changes

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release: bump version to 2.7.0 and close CHANGELOG [Unreleased]

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d148983
docs(living): record 2.7.0 release prep + version-bump decision

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4320481
fix(ci): py3.9 union compat, un-bundled GTF test, ruff format

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e6e13b7
fix(ci): conda-env smoke-test uses `kb --help` not `kb --version`

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95dbed2
fix(ci): satisfy mypy strict lint on new evidence/multimap code

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a14eb86
docs(living): record PR #7 CI-green work

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b6fe99e
fix(ci): stop mypy choking on scverse PEP 695 syntax; fix figlet fallback

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7a5c726
fix(ci): conda-env smoke test checks kb on PATH, not `kb --help`

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ed7b788
docs(living): record CI round-2 fixes (mypy/anndata, kb smoke-test)

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