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Changelog

Source: NEWS.md

GiottoDB 0.99.0 (2026-07-09)

Bug fixes

  • Update tessellate() generic/method to preserve GiottoClass extent behavior and error handling.

  • Improve reconnection after loading or moving GiottoDB projects, including top-level database connections, cached connections, and database lock-file handling.

  • Fix Giotto-backed PCA and HVF edge cases, including argument forwarding in runPCA(), k = 1 PCA scaling, and unsupported scaled-matrix selection.

  • Improve in-memory coercion through as_giotto() and safer placeholder handling in saveGiotto().

  • Fix dbSpatial overlap outputs, including row and column names, scalar matrix outputs, geometry validation, and dynamic argument filtering in calculateOverlap().

  • Resolve package installation errors caused by regex escaping.

Features

  • Public release of package!

  • Add dbSpatial-backed methods for spatial IDs, feature IDs, and subsetting.

  • Add findMarkers_one_vs_all() support for GiottoDB objects.

  • Support weighted overlapToMatrix() outputs for dbSpatial objects.

  • Support conversion of giottoPoints spatial vectors to dbSpatial objects in as_giottodb().

Chore

  • Remove stale generated vignette sources.

  • Update pkgdown configuration and site URL.

  • Update package collate metadata and imports.

Documentation

  • Refresh pkgdown vignettes, benchmark figures, README, and package capability overview.

  • Add concept tags and improve reference organization.

  • Clarify scale suppression and unsupported normalization methods.

  • Document as_giotto() and clean up roxygen links.

Code style

  • Reformat package code with jarl and air.

Refactoring

  • Simplify geometry type retrieval in createGiottoPoints and createGiottoPolygon.

Performance

  • Materialize overlap views in overlapToMatrix() to improve performance and output handling.

Testing

  • Validate calculateHVF() residual variance behavior against upstream Giotto changes.

  • Add reconnection, conversion, overlap, PCA, HVF, and full-pipeline test coverage.

  • Update calculateOverlap() test expectations for current behavior.

GiottoDB 0.0.0.9001

Bug fixes

  • Remove missing GiottoData dep from vignettes.

  • Replace dbMatrix::to_view with dbProject::to_view and update reconnection test expectations.

  • OverlapToMatrix conversion to matrix.

  • Missing DuckDB expression and simplify test.

Features

  • Add pkgdown workflow for building and deploying documentation site.

  • addStatistics generic and S3 method for giottodb, giotto objects + add tests.

  • processData methods.

Chore

  • Add ‘site’ to .Rbuildignore and .gitignore.

  • Update gitignore to exclude VSCode workspace file.

  • Update imports.

  • Update .gitignore and .Rbuildignore.

  • Require duckdb >= 1.4.0.

  • Migrate to dbverse-org.

  • Add dbProject to imports.

  • Update tests.

  • Update pkg improts.

  • Update vignette with fn table and GiottoDB functionality section.

  • Add metadata.

Documentation

  • Update Rd files.

Code style

  • Apply air formatting to giottodb.

Refactoring

  • .onLoad in zzz.R.

Testing

  • Fix warning.

Uncategorized

  • Merge branch ‘svd’.