remove seedform, code-generate codes and bump BPCells version to 0.2.0

.github/workflows/R-CMD-check.yaml

@@ -1,6 +1,7 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
+  workflow_dispatch:
   push:
     branches: [main, master]
   pull_request:

.github/workflows/pr-commands.yaml

@@ -1,6 +1,7 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
+  workflow_dispatch:
   issue_comment:
     types: [created]
 

DESCRIPTION

@@ -11,7 +11,7 @@ BugReports: https://github.com/Yunuuuu/BPCellsArray
 License: MIT + file LICENSE
 Imports: 
     methods,
-    BPCells (>= 0.1.0),
+    BPCells (>= 0.2.0),
     DelayedArray (>= 0.28.0),
     SparseArray,
     Matrix,
@@ -22,7 +22,7 @@ Imports:
     S4Vectors,
     BiocSingular
 Remotes: 
-    bnprks/BPCells
+    bnprks/BPCells/r
 Suggests: 
     SingleCellExperiment,
     BiocNeighbors,
@@ -39,13 +39,11 @@ Suggests:
 Encoding: UTF-8
 biocViews: Software, DataImport, DataRepresentation, Infrastructure
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 Collate: 
     'BPCellsSeed.R'
-    'utils.R'
-    'utils-BPCells.R'
     'Class-Delayed.R'
-    'Seed-management.R'
+    'utils-BPCells.R'
     'Class-BPCellsMatrix.R'
     'Class-BPCellsSeed.R'
     'Class-Transformed.R'
@@ -77,6 +75,7 @@ Collate:
     'showtree.R'
     'utils-Rd.R'
     'utils-check.R'
+    'utils.R'
     'zzz.R'
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -5,7 +5,6 @@ S3method(base::as.array,BPCellsMatrix)
 S3method(base::as.array,IterableMatrix)
 S3method(base::as.matrix,BPCellsDelayedOp)
 S3method(base::as.matrix,BPCellsMatrix)
-export("seedform<-")
 export(BPCellsArray)
 export(BPCellsMatrix)
 export(BPCellsSeed)
@@ -19,13 +18,11 @@ export(matrix_stats)
 export(pmin_by_col)
 export(pmin_by_row)
 export(pmin_scalar)
-export(pow_slow)
 export(rank_transform)
 export(readBPCells10xHDF5Matrix)
 export(readBPCellsDirMatrix)
 export(readBPCellsHDF5Matrix)
 export(seedApply)
-export(seedform)
 export(set_threads)
 export(showtree)
 export(storage_axis)
@@ -51,7 +48,6 @@ exportMethods("[<-")
 exportMethods("colnames<-")
 exportMethods("dimnames<-")
 exportMethods("rownames<-")
-exportMethods("seedform<-")
 exportMethods("type<-")
 exportMethods(Arith)
 exportMethods(BPCellsSeed)
@@ -100,7 +96,6 @@ exportMethods(pmin2)
 exportMethods(pmin_by_col)
 exportMethods(pmin_by_row)
 exportMethods(pmin_scalar)
-exportMethods(pow_slow)
 exportMethods(rank_transform)
 exportMethods(rbind)
 exportMethods(rbind2)
@@ -111,7 +106,6 @@ exportMethods(rowSds)
 exportMethods(rowSums)
 exportMethods(rowVars)
 exportMethods(runSVD)
-exportMethods(seedform)
 exportMethods(set_threads)
 exportMethods(show)
 exportMethods(storage_axis)

R/BPCellsSeed.R

@@ -89,3 +89,16 @@ coerce_into_dgCMatrix <- function(x) {
         }
     )
 }
+
+# helper function used to extract the `IterableMatrix` from the user input,
+# although user shouldn't provide `BPCellsDelayedOp` directly, but we also deal
+# with it
+extract_IterableMatrix <- function(x, seedform) {
+    if (is_BPCellsArray(x)) {
+        to_BPCells(x@seed)
+    } else if (methods::is(x, "BPCellsDelayedOp")) {
+        to_BPCells(x)
+    } else {
+        BPCellsSeed(x)
+    }
+}