CHANGES IN VERSION 0.99.2

NEW FEATURES

    o Added optional mart, gene_map, and enhancer-coordinate arguments so
      users can select an Ensembl mirror or provide local mapping resources.

    o Added small, package-installed PEREGRINE example files for deterministic
      offline execution of build_gp_links().

IMPROVEMENTS

    o Updated the minimum R version requirement to R 4.6.0.

    o Replaced the hard-coded chromosome list with
      GenomeInfoDb::standardChromosomes() for human sequence validation.

    o Added an explicit GenomicRanges import, declared IRanges as a runtime
      dependency, and refactored repeated input, cache, rowData, and
      peak-validation code into shared internal helpers.

    o Split long enhancer-building routines into focused internal helpers and
      normalized R source indentation to four-space multiples.

    o Avoided external chromosome-style lookups when aligning human sequence
      levels from EnsDb.Hsapiens.v86 with UCSC-style peak coordinates.

DOCUMENTATION

    o Added a package-level help page.

    o Added BiocManager installation instructions and executable, offline
      build_gp_links() examples to the vignette and function help page.

    o Documented the KPMP-derived example inputs and the source of the bundled
      PEREGRINE example records.

TESTS

    o Added regression tests for standard chromosomes, local BioMart mapping,
      local enhancer coordinates, shared helpers, sequence-level handling,
      and packaged example consistency.


CHANGES IN VERSION 0.99.0

NEW FEATURES

    o Added build_gp_links_wrapper() to support MultiAssayExperiment,
      SingleCellExperiment, and SummarizedExperiment inputs.

    o Added packaged example data via gp_example_inputs.

    o Added a Bioconductor-style vignette demonstrating direct and
      container-based workflows.

FIXES

    o Improved build_gp_links() handling of empty overlap cases so
      sparse inputs return empty results instead of errors.

    o Updated the closest-gene mapping to use gene TSS positions.
