NEWS

PubMatrixR 1.0.0 (2026-03-12)

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.

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.

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.

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.

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

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.