PubMatrixR NEWS

This file is ordered with the most recent release at the top.

Changes in version 1.0.0

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.