Changelog • phiperio

phiperio 0.5.2 (2026-07-08)

Fixed get_peptide_library() silently coercing alphanumeric ID-like columns (e.g. protein_id values such as "agilent_1") to all-NA. The character-to-numeric sanitizer previously matched any string containing a digit; it now requires the value to fully parse as numeric.
Added a regression test for the fix and a live test that flags checksum drift against the published library and any column collapsing to all-NA during sanitization.

Updated the peptide metadata library used by get_peptide_library() to combined_library_06.07.26.rds (with matching SHA-256 checksum) from the Polymerase3/phiper repository.

Added sample_id_from_filenames to convert_standard() to derive sample IDs from file stems when ingesting a directory of CSV/Parquet files; added tests.
New vignettes: “Importing multiple files with phiperio” (batch ingest + filename-derived sample IDs), and “Importing legacy PhIP-Seq data (convert_legacy)” for compact cross-sectional/longitudinal examples; updated “Importing long tidy data” with clearer workflows.
README/pkgdown refreshed: links to all vignettes, navigation updated, minimal section removed.
Robustified example handling and filename conflicts for vignette builds.
Version bumped to 0.5.0.

Make examples self-contained and reliable: fix convert_standard() example to use a temp CSV, switch expand_data() example to load_example_data(), and remove examples for internal helpers.
Remove all \donttest{} / \dontrun{} wrappers from examples in R and Rd files so they run during checks.
Harden load_example_data() caching by rebuilding when a cached object’s DuckDB connection is no longer valid.
Significantly improved coverage.

Rename exported API to verb_noun naming (e.g., create_data, convert_standard, convert_legacy, load_example_data, get_example_path, expand_data) and align docs/tests.
Rename internal helpers to .ph_ prefix and add internal roxygen docs.
Reorganize R/utils.R into themed sections with clearer helper descriptions.
Centralize connection teardown via close.phip_data() with GC finalizer and connection sync helpers.
Persist peptide metadata cache in user cache dir and reuse cached downloads with SHA-256 validation.
Improve peptide library preview columns in print.phip_data().
Update file naming under R/ to a consistent convention.
Adjust validation flow to reduce duplication around full-grid checks.
Update DESCRIPTION metadata (title, authors, description, dependencies).

Remove all comparisons/contrasts mechanics, validation, tests, and mock files.
Add centralized connection teardown via close.phip_data() and internal helpers; attach an auto-finalizer for GC cleanup.
Reduce duplicate validation by consolidating full-grid checks in validate_phip_data() and adding optional validation toggles for expansion.
Clean unused globals in R/zzz.R and remove unused utils helpers.
Update tests and docs to reflect the new API and validation flow.