Changes in version 1.0.0 (2026-03-12)                  

Core functionality

  - Refactored PubMatrix() to use XML parsing via xml2::read_xml() with
    internal helpers for count extraction, retry handling, and
    date-range validation.
  - Added stricter input validation and clearer error messages for
    missing terms, malformed input files, invalid database values,
    invalid date ranges, and export arguments.
  - Standardized result assembly as a matrix-like data frame with rows
    from B and columns from A, with safer URL encoding for API queries
    and exported hyperlinks.

Heatmap helpers

  - Updated heatmap documentation and behavior to display overlap
    percentages and use Euclidean clustering terminology consistently.
  - Improved heatmap robustness for character inputs, NA handling, and
    automatic font scaling when saving plots.

Tests and vignettes

  - Replaced network-dependent tests with deterministic mocked tests for
    PubMatrix() and offline fixture-based XML parser tests.
  - Expanded heatmap tests to cover file output and avoid creating
    Rplots.pdf during checks.
  - Simplified the main vignette to an offline, CRAN-safe workflow with
    non-evaluated live-query examples.
  - Removed legacy vignette/test files that depended on live web access
    or large examples.

Packaging and documentation

  - Updated package metadata for a CRAN-oriented release
    (Version: 1.0.0, removed biocViews, cleaned imports/suggests, and
    refreshed LICENSE).
  - Added package-level documentation and updated README.md, Rd files,
    and inst/CITATION to match current behavior and examples.
  - Expanded .Rbuildignore to exclude local development and check
    artifacts.

Repository cleanup

  - Removed pkgdown configuration/generated doc/ artifacts and the
    bundled pubmatrix-app Shiny subproject files from the package source
    tree.

                        Changes in version 0.9.0                        

  - Finalized the pre-CRAN/Bioconductor-oriented package line after
    iterative "BioC optimization" updates and namespace fixes.
  - Added/updated the main PubMatrix.R implementation and related
    packaging files during refactoring.
  - Added a bundled Shiny app subproject (pubmatrix-app) and deployment
    metadata.
  - Added OpenDocument Spreadsheet (.ods) export support for result
    output.

Relevant commits include 5618668, 3c10f5d, fbc4846, 1c52679, 26e6597,
591d458, and 80699aa.