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Moves R/pgx-read.R, R/pgx-check.R, read.gmt, h5.readMatrix, first_feature, example_file, PGX_CHECKS (data + builder), inst/extdata and the reader tests to bigomics/playbase.ingest. playbase declares it in Imports/Remotes and calls it through explicit playbase.ingest::, with no re-exports, matching the playbase.preprocess boundary. - pgx.createFromFiles, pgxinfo.*, mofa.exampledata, the GEOquery reader and pgx.getGeneFamilies now call playbase.ingest:: (the nested read.gmt copy in pgx.getGeneFamilies is dropped) - bit64 and OlinkAnalyze leave Imports - unittest image installs playbase.ingest before R CMD INSTALL - test-reexports.R asserts playbase neither exports nor defines any playbase.ingest export Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
…ngest R/pgx-getgeo.R, trimsame/trimsame.ends/trimsame0, seurat2pgx and pgx.read_singlecell_counts now live in playbase.ingest (nothing else in playbase called them). ArrayExpress, Biobase, biomaRt, GEOquery, msa, R.utils and recount leave Imports. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Clanker found few things:
playbase.ingest/data-raw/PGX_CHECKS.csv (moved here, byte-identical) and playbaseCore::PGX_CHECKS (pinned separately, consumed by r-service/.../svc_upload_validate.R:47). Whichever is canonical, nothing enforces it. Drift risk worth a bead. |
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Moves data ingestion to the new leaf package bigomics/playbase.ingest. playbase calls it via
playbase.ingest::, with no re-exports (same asplaybase.preprocess).Moved:
pgx-read.R,pgx-check.R,pgx-getgeo.R,read.gmt,h5.readMatrix,trimsame*,seurat2pgx,pgx.read_singlecell_counts,example_file,PGX_CHECKS, fixtures and tests.Not moved (on purpose, for now): epigenomics ingestion (IDAT readers in playbase.epigenetics).
test-reexports.Rnow checks that playbase doesn't redefine anything in playbase.ingest. Downstreamplaybase::read_*/ GEO calls must switch toplaybase.ingest::.🤖 Generated with Claude Code