Changes in version 0.99.41 o fix vignette to call 'spatialdataR::transform()' explicitly o address R CMD check warnings re: undocumented arguments, undefined functions Changes in version 0.99.40 o validty & setters now assure that each layer is a completely named list o 'SpatialDataImage/Label()' now accept single array (previously required list) o simplified various code bits (e.g., using 'lengths()', 'seq_along()', etc.) Changes in version 0.99.39 o class revision: SpatialData slots were base::list, now prototyped S4Vectors::SimpleList with layer-specific properties & validation o added 'path()' to retrieve on-disk paths of spatial data elements Changes in version 0.99.38 o make use of new BiocGenerics: data,rotate,scale,sequence,table,transform Changes in version 0.99.37 o fix note regarding internal '.mask' generic o fix conclits with 'base::labels' and 'S4Vectors::transform' o in mask(), return 'j' instances that mapped to each 'i' Changes in version 0.99.36 o fix conflicts with 'base::table' and 'utils::data' Changes in version 0.99.35 o bug fix: 'centroids,shape' was previously returning vertex coordinates for polygons o class renaming: sdArray/Frame > SpatialDataArray/Frame, Image/LabelArray > SpatialDataImage/Label, Shape/PointFrame > SpatialDataShape/Point Changes in version 0.99.34 o omit SpatialData.data everywhere o improved Point/ShapeFrame constructor o consolidated sdFrame code, docs, methods Changes in version 0.99.33 o added validity checks and tests for Zattrs o improved handling of 'spatialdata_attrs' o synchronize tables when subsetting/renaming o more memory efficient mask(), keeping an observation of unmapped instances o revised package 'Description:' field to align with current capabilities Changes in version 0.99.32 o added unit tests for query() o improved 'table' element validation o split centroids/extent() code & docs o revised 'coordTrans' show method of Zattrs (refactored code, fixed 'sequence' display) o implemented internal data/meta() get & set to avoid @-accessiong throughout code base Changes in version 0.99.31 o refactored point/shape transformations o rebrand spatial queries as crop(); keeping table queries as query() o added object-wide spatial crop() o added .zattrs contructor o revised vignette Changes in version 0.99.30 o query() by table method draft o added xNames<-() methods (x = image, label, ...) o added combine() to make one SpatialData object from two o 'duckspatial' for handling of points and shapes o add ShapeFrame construction from matrix & 'sf' o bug fix in coord trans. graph representation for when element and space names collide Changes in version 0.99.29 o revision of Zarr version-specific .zattrs handling o added Zarr v3 example dataset 'inst/extdata/blobs_v3' o reorganization of unit tests to facilitate v3-specific testing Changes in version 0.99.28 o validity checks for 'table' elements o fixed and reenable broken/skipped tests o spatialdata_attrs utilities (instance_key(), region_key(), region()) Changes in version 0.99.27 o spatial queries (aka subsetting) by bounding box (all element types) or polygons (points and shapes), including unit tests, documentation, visual examples o masking draft to aggregate information across layers (image by label, point by shape, shape by shape; the latter aggregates values in an associated table) Changes in version 0.99.26 o added unit tests for existing transformations o implemented minimal layer-wise validity checks (Image/LabelArray and Shape/PointFrame elements) Changes in version 0.99.25 o improved Zattrs show method (cf., PR #117) o replace jsonlite::fromJSON() with Rarr::read_zarr_attributes() for reading .zattrs & rewrite code-/test-base accordingly Changes in version 0.99.24 o ZarrArray imported by Bioconductor/ZarrArray o Rarr replaces pizzarr for importing tables via anndataR o anndataR replaces zellkonverter o update basilisk env to spatialdata==0.7.0 o replace spatialdata.read with anndata.read_zarr to read tables Changes in version 0.99.22 o split off 'SpatialData.data' Changes in version 0.99.21 o use Python's 'spatialdata::read_zarr' for reading tables Changes in version 0.99.20 o 'ImageArray' subsetting with multiscales support o for 'tables', moved 'instance/region_key' to 'int_colData' Changes in version 0.99.19 o adding code to improve visualization of transformation network (PR #98) Changes in version 0.99.18 o split off 'SpatialData.plot' Changes in version 0.99.17 o rewrite of points and labels plotting, including documented examples and support for tables o setup 'basilisk' environment to use 'pip' for 'spatialdata' and 'spatialdata-io' Changes in version 0.99.16 o added draft for transformations (tbc) o added methods for table handling following draft from PR #74 o 'get/setTable' for adding/getting tables o 'valTable' to retrieve data from an existing table Changes in version 0.99.15 o added methods for coordinate transormation handling, namely: 'rmvCT()' for removal and 'addCT()' for adding/appending o major rewrite of 'ImageArray' plotting & bounding box 'query' o added vignettes demos of bounding box queries & multiscale plotting Changes in version 0.99.14 o added unit tests for image plotting, element & object handling o element-wise and object-wide subsetting à la `[` o fixed multiscales plotting Changes in version 0.99.13 o added 'do_tx_to_ext()' to align spatial elements within Py o fixed problem with 'basilisk' environment o added more validity checks Changes in version 0.99.12 o complete authors list in DESCRIPTION and vignette o include more information on elements in show method o basic vignette sections on data representation, handling etc. o added 'ggforce' dependency for visualizing circular shapes Changes in version 0.99.11 o in 'readSpatialData()', provide option to specify TRUE/FALSE/index/character to control reading Changes in version 0.99.10 o add support for multiscales in 'ImageArray's including show method to display available scales Changes in version 0.99.9 o add 'basilisk'-based interface to Python's 'spatialdata-io' to support readers across platforms & writing to .zarr Changes in version 0.99.8 o updated show method to include information on coordinate systems Changes in version 0.99.7 o added utility '.coord2graph()' in coord.R to represent element-coordinate system relationships as graph Changes in version 0.99.6 o option to read 'table' using 'anndataR' instead of 'anndata+zellkonverter' through 'basilisk'