Changes in version 0.99.7                        

  - Optional annotation columns: batch, donor_id, and replicate are no
    longer required in the standard annotation TSV. The pipeline runs
    with only file, sample, sample_name, and condition. Missing optional
    columns are handled gracefully throughout the workflow.
  - Configurable block variable: test_limma_customized() and
    run_proteomics_pipeline() now accept a block_var parameter (default:
    "donor_id") specifying which colData column to use as the blocking
    variable for limma::duplicateCorrelation() when block_effect = TRUE.
    Previously the code hardcoded a block column that did not exist in
    the annotation schema.
  - Bug fix: readQuantTable() now dispatches to the mzTab reader
    (.pp_read_mztab_pg_matrix()) when the input file is in mzTab format,
    instead of always treating it as a DIA pg_matrix TSV.
  - Bug fix: Contrast column names in .tl_run_contrasts() were not
    preserved by limma::makeContrasts(contrasts = ...), causing
    topTable() to fail with a subscript-out-of-bounds error. Contrast
    names are now set explicitly after makeContrasts().
  - Removed unused dependencies: readxl (Imports) and htmltools
    (Suggests) to resolve DESCRIPTION/NAMESPACE mismatches reported by R
    CMD check.

                       Changes in version 0.99.0                        

  - Initial Bioconductor submission.