Issue 115

.github/workflows/check-bioc.yml

@@ -22,7 +22,6 @@
 
 on:
   push:
-  pull_request:
 
 name: R-CMD-check-bioc
 
@@ -52,9 +51,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.5', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-#          - { os: macOS-latest, r: '4.5', bioc: 'devel'}
-#          - { os: windows-latest, r: '4.5', bioc: 'devel'}
+          #- { os: ubuntu-latest, r: '4.5', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://p3m.dev/cran/__linux__/noble/latest" }
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://p3m.dev/cran/__linux__/noble/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: 'devel'}
+          #- { os: windows-latest, r: 'devel', bioc: 'devel'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -116,24 +116,13 @@ jobs:
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-
 
-      # - name: Install Linux system dependencies
-      #   if: runner.os == 'Linux'
-      #   run: |
-      #     sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
-      #     echo $sysreqs
-      #     sudo -s eval "$sysreqs"
-
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
           ## Enable installing XML from source if needed
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
 
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
           ## For textshaping, required by ragg, and required by pkgdown
           brew install harfbuzz fribidi
 
@@ -171,7 +160,11 @@ jobs:
 
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
+          install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories())
+
+          ## TEMP REMOVE LATER:
+          ## For now install Rarr from github since ZarrArray needs >= 1.11.33
+          remotes::install_github("Huber-group-EMBL/Rarr")
 
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
@@ -183,7 +176,7 @@ jobs:
         run: |
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics

.gitignore

@@ -10,3 +10,4 @@ inst/extdata/xenium1.zarr
 inst/extdata/visiumhd.zarr
 *.Rproj
 *.html
+R/_*

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
-Depends: R (>= 4.4)
-Version: 0.99.23
+Depends: R (>= 4.6)
+Version: 0.99.29
 Description: Interface to Python's 'SpatialData', currently including:
-    reticulate-based use of 'spatialdata-io' for reading of manufracturer
+    reticulate-based use of 'spatialdata-io' for reading of manufacturer
     data and writing to .zarr, on-disk representation of images/labels as
     'ZarrArray's ('Rarr') and shapes/points as 'arrow' objects, and method 
     drafts for visualization and coordinate system handling.
@@ -38,27 +38,28 @@ Imports:
     BiocGenerics,
     DelayedArray,
     dplyr,
+    EBImage,
     geoarrow,
     graph,
-    jsonlite,
     Matrix,
     methods,
+    ZarrArray,
     Rarr,
     RBGL,
     reticulate,
+    anndataR,
     sf,
     S4Arrays,
     S4Vectors,
     SingleCellExperiment,
     SummarizedExperiment,
-    zellkonverter,
     EBImage,
-    stringr
+    stringr,
+    jsonlite
 Suggests:
     BiocStyle,
     ggnewscale,
     knitr,
-    magick,
     patchwork,
     paws,
     Rgraphviz,
@@ -71,7 +72,6 @@ Enhances:
     anndataR,
     pizzarr
 Remotes:
-    keller-mark/pizzarr,
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,
     HelenaLC/SpatialData.plot

NAMESPACE

@@ -7,6 +7,7 @@ S3method(.DollarNames,Zattrs)
 S3method(filter,PointFrame)
 S3method(select,PointFrame)
 export(.SpatialData)
+export(CTplot)
 export(ImageArray)
 export(LabelArray)
 export(PointFrame)
@@ -17,20 +18,17 @@ export(create_zarr)
 export(create_zarr_group)
 export(do_tx_to_ext)
 export(mask)
-export(plotCoordGraph)
 export(readImage)
 export(readLabel)
 export(readPoint)
 export(readShape)
 export(readSpatialData)
 export(readTable)
-export(read_zattrs)
 export(writeImage)
 export(writeLabel)
 export(writePoint)
 export(writeShape)
 export(writeSpatialData)
-export(write_zattrs)
 exportClasses(SpatialData)
 exportMethods("$")
 exportMethods("[")
@@ -48,34 +46,46 @@ exportMethods("table<-")
 exportMethods("tables<-")
 exportMethods(CTdata)
 exportMethods(CTgraph)
+exportMethods(CTlist)
 exportMethods(CTname)
 exportMethods(CTpath)
 exportMethods(CTtype)
 exportMethods(addCT)
 exportMethods(as.data.frame)
 exportMethods(axes)
+exportMethods(centroids)
 exportMethods(channels)
 exportMethods(colnames)
 exportMethods(data)
+exportMethods(data_type)
 exportMethods(dim)
 exportMethods(element)
+exportMethods(extent)
+exportMethods(feature_key)
+exportMethods(flip)
+exportMethods(flop)
+exportMethods(geom_type)
 exportMethods(getTable)
 exportMethods(hasTable)
 exportMethods(image)
 exportMethods(imageNames)
 exportMethods(images)
+exportMethods(instance_key)
 exportMethods(label)
 exportMethods(labelNames)
 exportMethods(labels)
 exportMethods(layer)
 exportMethods(length)
 exportMethods(mask)
 exportMethods(meta)
+exportMethods(mirror)
 exportMethods(names)
 exportMethods(point)
 exportMethods(pointNames)
 exportMethods(points)
 exportMethods(query)
+exportMethods(region)
+exportMethods(region_key)
 exportMethods(rmvCT)
 exportMethods(rotate)
 exportMethods(rownames)
@@ -89,6 +99,7 @@ exportMethods(tableNames)
 exportMethods(tables)
 exportMethods(translation)
 exportMethods(valTable)
+import(anndataR)
 import(geoarrow)
 importClassesFrom(S4Arrays,Array)
 importClassesFrom(S4Vectors,DFrame)
@@ -98,12 +109,16 @@ importFrom(BiocGenerics,rownames)
 importFrom(DelayedArray,DelayedArray)
 importFrom(DelayedArray,realize)
 importFrom(EBImage,resize)
+importFrom(EBImage,rotate)
+importFrom(EBImage,translate)
 importFrom(Matrix,rowSums)
+importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,sparseVector)
+importFrom(Matrix,summary)
 importFrom(Matrix,t)
 importFrom(RBGL,sp.between)
-importFrom(Rarr,ZarrArray)
-importFrom(S4Arrays,as.array.Array)
+importFrom(Rarr,read_zarr_attributes)
+importFrom(Rarr,zarr_overview)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isSequence)
@@ -115,9 +130,14 @@ importFrom(SingleCellExperiment,"int_metadata<-")
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,int_colData)
 importFrom(SingleCellExperiment,int_metadata)
+importFrom(SummarizedExperiment,"assay<-")
+importFrom(SummarizedExperiment,"assayNames<-")
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
+importFrom(ZarrArray,ZarrArray)
+importFrom(ZarrArray,path)
+importFrom(ZarrArray,type)
 importFrom(arrow,open_dataset)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)
@@ -142,7 +162,6 @@ importFrom(graph,graphAM)
 importFrom(graph,nodeData)
 importFrom(graph,nodes)
 importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,read_json)
 importFrom(jsonlite,toJSON)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
@@ -153,16 +172,15 @@ importFrom(methods,setReplaceMethod)
 importFrom(reticulate,import)
 importFrom(sf,"st_geometry<-")
 importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
 importFrom(sf,st_coordinates)
+importFrom(sf,st_crop)
 importFrom(sf,st_distance)
 importFrom(sf,st_geometry)
 importFrom(sf,st_geometry_type)
-importFrom(sf,st_point)
-importFrom(sf,st_sfc)
+importFrom(sf,st_intersects)
+importFrom(sf,st_polygon)
 importFrom(stats,setNames)
-importFrom(stringr,str_extract)
-importFrom(stringr,str_remove)
 importFrom(utils,.DollarNames)
 importFrom(utils,head)
 importFrom(utils,tail)
-importFrom(zellkonverter,AnnData2SCE)

R/AllGenerics.R

@@ -22,18 +22,6 @@ setGeneric("shapeNames", \(x, ...) standardGeneric("shapeNames"))
 setGeneric("pointNames", \(x, ...) standardGeneric("pointNames"))
 setGeneric("tableNames", \(x, ...) standardGeneric("tableNames"))
 
-setMethod("images", "SpatialData", \(x) x$images)
-setMethod("labels", "SpatialData", \(x) x$labels)
-setMethod("shapes", "SpatialData", \(x) x$shapes)
-setMethod("points", "SpatialData", \(x) x$points)
-setMethod("tables", "SpatialData", \(x) x$tables)
-
-setMethod("imageNames", "SpatialData", \(x) names(images(x)))
-setMethod("labelNames", "SpatialData", \(x) names(labels(x)))
-setMethod("shapeNames", "SpatialData", \(x) names(shapes(x)))
-setMethod("pointNames", "SpatialData", \(x) names(points(x)))
-setMethod("tableNames", "SpatialData", \(x) names(tables(x)))
-
 # set one -----
 
 setGeneric("image<-", \(x, i, ..., value) standardGeneric("image<-"))
@@ -52,7 +40,7 @@ setGeneric("tables<-", \(x, value) standardGeneric("tables<-"))
 
 # trs ----
 
-setGeneric("axes", \(x, ...) standardGeneric("axes"))
+setGeneric("CTlist", \(x, ...) standardGeneric("CTlist"))
 setGeneric("CTdata", \(x, ...) standardGeneric("CTdata"))
 setGeneric("CTname", \(x, ...) standardGeneric("CTname"))
 setGeneric("CTtype", \(x, ...) standardGeneric("CTtype"))
@@ -68,6 +56,17 @@ setGeneric("rotate", \(x, t, ...) standardGeneric("rotate"))
 setGeneric("transform", \(x, ...) standardGeneric("transform"))
 setGeneric("translation", \(x, t, ...) standardGeneric("translation"))
 
+setGeneric("flip", \(x, ...) standardGeneric("flip"))
+setGeneric("flop", \(x, ...) standardGeneric("flop"))
+setGeneric("mirror", \(x, ...) standardGeneric("mirror"))
+
+# sda ----
+
+setGeneric("region", \(x, ...) standardGeneric("region"))
+setGeneric("region_key", \(x, ...) standardGeneric("region_key"))
+setGeneric("feature_key", \(x, ...) standardGeneric("feature_key"))
+setGeneric("instance_key", \(x, ...) standardGeneric("instance_key"))
+
 # uts ----
 
 setGeneric("layer", \(x, i, ...) standardGeneric("layer"))
@@ -79,7 +78,13 @@ setGeneric("meta", \(x, ...) standardGeneric("meta"))
 setGeneric("query", \(x, ...) standardGeneric("query"))
 setGeneric("mask", \(x, i, j, ...) standardGeneric("mask"))
 
+setGeneric("axes", \(x, ...) standardGeneric("axes"))
+setGeneric("extent", \(x, ...) standardGeneric("extent"))
 setGeneric("channels", \(x, ...) standardGeneric("channels"))
+setGeneric("centroids", \(x, ...) standardGeneric("centroids"))
+setGeneric("data_type", \(x, ...) standardGeneric("data_type"))
+setGeneric("geom_type", \(x, ...) standardGeneric("geom_type"))
+setGeneric("multiscales", \(x, ...) standardGeneric("multiscales"))
 
 # tbl ----