Merge branch 'drieslab:dev' into dev

Author: iqraAmin

.github/workflows/staging_branch_workflow.yml

@@ -164,9 +164,9 @@ jobs:
             quiet = FALSE,
             clean = FALSE,
             branch = "staging",
-            type = c("tests"),
+            type = c("tests", "examples", "vignettes"),
             combine_types = TRUE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package", auth_token = Sys.getenv("GITHUB_PAT"))
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
           )
         shell: Rscript {0}
         env:

.gitignore

@@ -6,7 +6,7 @@ inst/doc
 .git_old
 .vscode/*
 .Rprofile
-docs
 codecov.yml
-pkgdown
 cell_rna*
+docs
+pkgdown

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoClass
 Title: Giotto Suite Object Definitions and Framework
-Version: 0.4.10
+Version: 0.5.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -42,7 +42,8 @@ Imports:
     reticulate (>= 1.25),
     stats,
     terra (>= 1.8-21)
-Suggests: 
+Suggests:
+    GiottoDB,
     Biobase,
     chihaya,
     DelayedArray,
@@ -80,13 +81,20 @@ Suggests:
 Remotes: drieslab/GiottoUtils
 Config/testthat/edition: 3
 Collate: 
+    'classes-virtuals.R'
+    'classes-utils.R'
+    'classes-images.R'
+    'classes-overlaps.R'
+    'classes-points.R'
+    'classes-polygons.R'
     'package_imports.R'
     'classes.R'
     'generics.R'
     'NN_network.R'
     'aggregate.R'
     'auxilliary.R'
     'buffer.R'
+    'classes-binpoints.R'
     'combine_metadata.R'
     'slot_accessors.R'
     'create.R'

NAMESPACE

@@ -8,7 +8,10 @@ S3method(.DollarNames,processParam)
 S3method(.DollarNames,spatEnrObj)
 S3method(.DollarNames,spatLocsObj)
 S3method(.DollarNames,terraVectData)
+S3method(as.data.frame,overlapIntensityDT)
+S3method(as.data.frame,overlapPointDT)
 S3method(as.data.table,SpatVector)
+S3method(as.data.table,giottoBinPoints)
 S3method(as.data.table,giottoPoints)
 S3method(as.data.table,giottoPolygon)
 S3method(print,ghistory)
@@ -28,6 +31,7 @@ export(addNetworkLayout)
 export(addSpatialCentroidLocations)
 export(addSpatialCentroidLocationsLayer)
 export(add_img_array_alpha)
+export(aggregateFeatures)
 export(aggregateStacks)
 export(aggregateStacksExpression)
 export(aggregateStacksLocations)
@@ -72,6 +76,7 @@ export(createCellMetaObj)
 export(createDimObj)
 export(createExprObj)
 export(createFeatMetaObj)
+export(createGiottoBinPoints)
 export(createGiottoImage)
 export(createGiottoInstructions)
 export(createGiottoLargeImage)
@@ -292,11 +297,13 @@ exportClasses(exprObj)
 exportClasses(featMetaObj)
 exportClasses(featureNetwork)
 exportClasses(giotto)
+exportClasses(giottoBinPoints)
 exportClasses(giottoImage)
 exportClasses(giottoLargeImage)
 exportClasses(giottoPoints)
 exportClasses(giottoPolygon)
 exportClasses(nnNetObj)
+exportClasses(overlapPointDT)
 exportClasses(processParam)
 exportClasses(spatEnrObj)
 exportClasses(spatLocsObj)
@@ -349,6 +356,7 @@ exportMethods(ext)
 exportMethods(featIDs)
 exportMethods(featType)
 exportMethods(flip)
+exportMethods(head)
 exportMethods(hist)
 exportMethods(hull)
 exportMethods(instructions)
@@ -377,6 +385,7 @@ exportMethods(splitGeom)
 exportMethods(subset)
 exportMethods(symdif)
 exportMethods(t)
+exportMethods(tail)
 exportMethods(union)
 exportMethods(vect)
 exportMethods(wrap)
@@ -402,7 +411,16 @@ importFrom(methods,show)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(methods,validObject)
-importFrom(utils,.DollarNames)
+importMethodsFrom(Matrix,"%*%")
+importMethodsFrom(Matrix,as.matrix)
+importMethodsFrom(Matrix,coerce)
+importMethodsFrom(Matrix,colMeans)
+importMethodsFrom(Matrix,colSums)
+importMethodsFrom(Matrix,diag)
+importMethodsFrom(Matrix,dim)
+importMethodsFrom(Matrix,rowMeans)
+importMethodsFrom(Matrix,rowSums)
+importMethodsFrom(Matrix,summary)
 importMethodsFrom(Matrix,t)
 importMethodsFrom(terra,"ext<-")
 importMethodsFrom(terra,as.data.frame)
@@ -415,6 +433,7 @@ importMethodsFrom(terra,density)
 importMethodsFrom(terra,erase)
 importMethodsFrom(terra,ext)
 importMethodsFrom(terra,flip)
+importMethodsFrom(terra,head)
 importMethodsFrom(terra,hist)
 importMethodsFrom(terra,hull)
 importMethodsFrom(terra,intersect)
@@ -427,6 +446,7 @@ importMethodsFrom(terra,snap)
 importMethodsFrom(terra,spin)
 importMethodsFrom(terra,symdif)
 importMethodsFrom(terra,t)
+importMethodsFrom(terra,tail)
 importMethodsFrom(terra,union)
 importMethodsFrom(terra,vect)
 importMethodsFrom(terra,wrap)

NEWS.md

@@ -1,3 +1,35 @@
+# GiottoClass 0.5.0
+
+## changes
+- added superseded note to `createGiottoImage()` documentation
+- `calculateOverlap()` and `overlapToMatrix()` param harmonization
+- refactor of `saveGiotto()` and `loadGiotto()`
+- code reorganization for `classes.R`
+
+## new
+- `aggregateFeatures()` giotto object wrapper function for running `calculateOverlap()` and `overlapToMatrix()`
+- `overlapPointDT()` and `overlapIntensityDT()` classes to store overlaps relationships efficiently and help with aggregation pipeline
+- `giottoBinPoints` class for efficient binned spatial points
+- `rbind` method for `giottoPoints`
+
+## bug fixes
+- `overlaps()` will now properly find image overlaps
+- fix a naming bug when exporting images during save
+
+
+
+# GiottoClass 0.4.12 (2025/12/12)
+
+## enhancements
+- automatic checking for `"count"` column in feature info
+
+
+## new
+- `misc` slot for storing unstructured data
+
+## enhancements
+- escape hatch for gobject initialize checking. Set option `"giotto.init_check_severity"` to `"stop"` (default), or `"warning"` depending on needs.
+
 # GiottoClass 0.4.10 (2025/09/30)
 
 ## bug fixes