NEWS

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spatialdataR 0.99.41

• fix vignette to call 'spatialdataR::transform()' explicitly
• address R CMD check warnings re: undocumented arguments, undefined functions

spatialdataR 0.99.40

• validty & setters now assure that each layer is a completely named list
• 'SpatialDataImage/Label()' now accept single array (previously required list)
• simplified various code bits (e.g., using 'lengths()', 'seq_along()', etc.)

spatialdataR 0.99.39

• class revision: SpatialData slots were base::list, now prototyped S4Vectors::SimpleList with layer-specific properties & validation
• added 'path()' to retrieve on-disk paths of spatial data elements

spatialdataR 0.99.38

• make use of new BiocGenerics: data,rotate,scale,sequence,table,transform

spatialdataR 0.99.37

• fix note regarding internal '.mask' generic
• fix conclits with 'base::labels' and 'S4Vectors::transform'
• in mask(), return 'j' instances that mapped to each 'i'

spatialdataR 0.99.36

• fix conflicts with 'base::table' and 'utils::data'

spatialdataR 0.99.35

• bug fix: 'centroids,shape' was previously returning vertex coordinates for polygons
• class renaming: sdArray/Frame > SpatialDataArray/Frame, Image/LabelArray > SpatialDataImage/Label, Shape/PointFrame > SpatialDataShape/Point

spatialdataR 0.99.34

• omit SpatialData.data everywhere
• improved Point/ShapeFrame constructor
• consolidated sdFrame code, docs, methods

spatialdataR 0.99.33

• added validity checks and tests for Zattrs
• improved handling of 'spatialdata_attrs'
• synchronize tables when subsetting/renaming
• more memory efficient mask(), keeping an observation of unmapped instances
• revised package 'Description:' field to align with current capabilities

spatialdataR 0.99.32

• added unit tests for query()
• improved 'table' element validation
• split centroids/extent() code & docs
• revised 'coordTrans' show method of Zattrs (refactored code, fixed 'sequence' display)
• implemented internal data/meta() get & set to avoid @-accessiong throughout code base

spatialdataR 0.99.31

• refactored point/shape transformations
• rebrand spatial queries as crop(); keeping table queries as query()
• added object-wide spatial crop()
• added .zattrs contructor
• revised vignette

spatialdataR 0.99.30

• query() by table method draft
• added xNames<-() methods (x = image, label, ...)
• added combine() to make one SpatialData object from two
• 'duckspatial' for handling of points and shapes
• add ShapeFrame construction from matrix & 'sf'
• bug fix in coord trans. graph representation for when element and space names collide

spatialdataR 0.99.29

• revision of Zarr version-specific .zattrs handling
• added Zarr v3 example dataset 'inst/extdata/blobs_v3'
• reorganization of unit tests to facilitate v3-specific testing

spatialdataR 0.99.28

• validity checks for 'table' elements
• fixed and reenable broken/skipped tests
• spatialdata_attrs utilities (instance_key(), region_key(), region())

spatialdataR 0.99.27

• spatial queries (aka subsetting) by bounding box (all element types) or polygons (points and shapes), including unit tests, documentation, visual examples
• masking draft to aggregate information across layers (image by label, point by shape, shape by shape; the latter aggregates values in an associated table)

spatialdataR 0.99.26

• added unit tests for existing transformations
• implemented minimal layer-wise validity checks (Image/LabelArray and Shape/PointFrame elements)

spatialdataR 0.99.25

• improved Zattrs show method (cf., PR #117)
• replace jsonlite::fromJSON() with Rarr::read_zarr_attributes() for reading .zattrs & rewrite code-/test-base accordingly

spatialdataR 0.99.24

• ZarrArray imported by Bioconductor/ZarrArray
• Rarr replaces pizzarr for importing tables via anndataR
• anndataR replaces zellkonverter
• update basilisk env to spatialdata==0.7.0
• replace spatialdata.read with anndata.read_zarr to read tables

spatialdataR 0.99.22

• split off 'SpatialData.data'

spatialdataR 0.99.21

• use Python's 'spatialdata::read_zarr' for reading tables

spatialdataR 0.99.20

• 'ImageArray' subsetting with multiscales support
• for 'tables', moved 'instance/region_key' to 'int_colData'

spatialdataR 0.99.19

• adding code to improve visualization of transformation network (PR #98)

spatialdataR 0.99.18

• split off 'SpatialData.plot'

spatialdataR 0.99.17

• rewrite of points and labels plotting, including documented examples and support for tables
• setup 'basilisk' environment to use 'pip' for 'spatialdata' and 'spatialdata-io'

spatialdataR 0.99.16

• added draft for transformations (tbc)
• added methods for table handling following draft from PR #74
• 'get/setTable' for adding/getting tables
• 'valTable' to retrieve data from an existing table

spatialdataR 0.99.15

• added methods for coordinate transormation handling, namely: 'rmvCT()' for removal and 'addCT()' for adding/appending
• major rewrite of 'ImageArray' plotting & bounding box 'query'
• added vignettes demos of bounding box queries & multiscale plotting

spatialdataR 0.99.14

• added unit tests for image plotting, element & object handling
• element-wise and object-wide subsetting à la '['
• fixed multiscales plotting

spatialdataR 0.99.13

• added 'do_tx_to_ext()' to align spatial elements within Py
• fixed problem with 'basilisk' environment
• added more validity checks

spatialdataR 0.99.12

• complete authors list in DESCRIPTION and vignette
• include more information on elements in show method
• basic vignette sections on data representation, handling etc.
• added 'ggforce' dependency for visualizing circular shapes

spatialdataR 0.99.11

• in 'readSpatialData()', provide option to specify TRUE/FALSE/index/character to control reading

spatialdataR 0.99.10

• add support for multiscales in 'ImageArray's including show method to display available scales

spatialdataR 0.99.9

• add 'basilisk'-based interface to Python's 'spatialdata-io' to support readers across platforms & writing to .zarr

spatialdataR 0.99.8

• updated show method to include information on coordinate systems

spatialdataR 0.99.7

• added utility '.coord2graph()' in coord.R to represent element-coordinate system relationships as graph

spatialdataR 0.99.6

• option to read 'table' using 'anndataR' instead of 'anndata+zellkonverter' through 'basilisk'