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.