[Cvicnaire]

Closes #282

What changed

mergeDifexp() returns list(matrix, metadata) instead of a bare matrix. metadata is a data frame with one row per matrix column (same order, row names = column names) holding signature_name, the database signature_id (NA for supplied objects), every scalar metadata field of the signatures (vector fields such as keywords collapsed with "; ", nested lists such as others left out) and n_features. It plays the role of a SummarizedExperiment's colData without the Bioconductor dependency, so the pair stays usable outside R. Callers that used the result as a matrix need $matrix; nothing outside the function's own tests did yet.

To carry the database ids, fetchCompareSignatures() also returns ids and resolveCompareSignatureList() gains with_ids = TRUE. compareSignatures() is unchanged.

How it was verified

Rscript -e 'testthat::test_local(filter = "mergeDifexp|compareSignature", reporter = "summary", load_package = "source")'
# ══ DONE ══  (one skip: compareSignatures DB test, SIGREPO_TEST_DB_USER not set)

Rscript -e 'testthat::test_local(reporter = "summary", load_package = "source")'
# 0 failures; 20 skips, all database/live-service tests without credentials

tools::checkRd("man/mergeDifexp.Rd")   # clean

The roxygen example on the bundled signatures prints:

[1] 826   3
                 signature_name     organism  phenotype n_features
v1 Myc_reduce_mice_liver_24m_v1 Mus musculus Myc_reduce        826
v2 Myc_reduce_mice_liver_24m_v2 Mus musculus Myc_reduce        826
v3 Myc_reduce_mice_liver_24m_v3 Mus musculus Myc_reduce        826

New tests cover: list shape, one metadata row per column in column order with matching row names, scalar fields and types, vector collapse, nested-list drop, NA for a field missing from one signature, n_features under union and intersect, dropped signatures absent from the table, and signature_id filled for fetched vs NA for supplied signatures.

Checklist

• Closes #NNN is filled in above
• NEWS.md has a bullet for this change, or the PR is labelled no-changelog
• Branch is short-lived and will be merged on GitHub, then deleted

🤖 Generated with Claude Code