Changes in version 0.5.0                        

  - 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.

                        Changes in version 0.4.0                        

  - 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    object’s DuckDB connection is no longer valid.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.

                        Changes in version 0.3.0                        

  - 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).

                        Changes in version 0.2.0                        

  - 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.

                        Changes in version 0.1.0                        

  - Initial release with IO/convert functionality migrated from phiper.