fix(hooks): chain git-lfs pre-push after the ADR-0014 security scan

feat(upload): assemble raw counts/TPM/metadata into an h5ad inside the gate

feat(mouse-intake): read Carl's real Novogene metadata Excel directly

feat(mouse): thin mouse-intake path — staging script, ENSMUSG→MGI map, nested-batch guard

feat(metrics): instrument n_post_analysis_reads to test the 808b91d claim

chore(scripts): rename the limma probe so pytest stops collecting it

chore(security): make SBOM generation deterministic

merge: gse205154 sears vst + filtered_tmm assemble scripts

chore(deps-dev): update xlrd requirement from >=2.0 to >=2.0.2 (#6)

refactor: tighten invariant-length zips to strict=True (B905)

style: apply ruff lint --fix + ruff format across the tree

feat(sears): assemble scripts for gse205154 vst + filtered_tmm siblings

feat(security): ADR-0014 CI security scanning + shared scan definition

feat(logging): add verify_s3_sink.py live-verify script (ADR-0009 Phase 2 prep)

scripts: add WIP cptac_pda_counts (raw-counts/Path A) assembly script

fix: resolve CollecTRI TF symbols + restore igraph network plot

scripts: pin BIODATA_REGISTRY_COMMIT to 533906d for GSE205154 provenance

scripts: add GSE205154 (Sears) h5ad assembly + fix anni-voigt->anne-voigt HF repo

Lint cleanup: remove unused imports, empty f-strings, split import lines

Remove dead assignments in gradio_ui/assemble script/test (F841)

Stage: pinned deps, API-key fallback, apt probe, security scan

Add scripts/requirements-dev.txt for curation-script deps

Bump biodata-registry pin to 3bf0eb9; add Nones symbol-fix script

Bump biodata-registry pin to dfbf8c4; add Collisson subtype script

Add probe-collapse precompute Phase 2 (collapsed_url support)

Switch GPL platform annotation to NCBI .annot.gz instead of _family.soft.gz

Add precompute-cache assemble scripts for 5 GEO datasets; bump registry pin

Add TCGA-PAAD scoping doc, dataset assembly scripts, ignore .claude/

Add PATH B-norm routing for normalized data; add GEO validation script

Add PDAC dataset adapter, workflow, semantic, and analysis layers