Refactor from/to Seurat conversion (#183)

* wip new seurat conversion * fix var * fix test * style pkg * refactor seurat approach * add graph mappings * update to_Seurat function * update from_Seurat * add assay name to helper functions * improve to_seurat docs * improvements to seurat docs * update documentation * run styler * make sure that assay meta.data ends up in the output * fix unit test * fix to_seurat * add to_seurat test * update docs and styler * add seurat to suggests * remove biocstyle from vignette * fix variable * fix guess_varms * do not export to/from_Seurat helper functions * roxygen * remove accidental comment * fix links * undo changes not related to seurat * add more info to layer mapping * Update R/Seurat.R Co-authored-by: Luke Zappia <[email protected]> * Apply suggestions from code review Co-authored-by: Luke Zappia <[email protected]> * update descriptions * map all uns to misc my default * use `check_requires` to check required packages * roxygenise * simplify flow * improve readability * change warning into stop * remove do.call * clarify * address comments * fix imports * styler * fix check_requires if packages are on bioconductor * uniformise notation * apply suggestions from review * apply suggestions * Apply suggestions from code review Co-authored-by: Luke Zappia <[email protected]> * apply suggestions from review * trycatch generator * restyle * fix guess function * Update R/Seurat.R Co-authored-by: Luke Zappia <[email protected]> --------- Co-authored-by: Luke Zappia <[email protected]>
scverse · Nov 12, 2024 · 1d07188 · 1d07188
1 parent 60f7d7b
commit 1d07188
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Showing 11 changed files with 1,157 additions and 161 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -62,9 +62,12 @@ BugReports: https://github.com/scverse/anndataR/issues
 Depends: 
     R (>= 4.0.0)
 Imports:
+    cli,
     Matrix,
     methods,
-    R6
+    purrr,
+    R6,
+    rlang
 Suggests:
     anndata,
     BiocStyle,
@@ -73,6 +76,7 @@ Suggests:
     hdf5r (>= 1.3.11),
     rmarkdown,
     S4Vectors,
+    Seurat,
     SeuratObject,
     SingleCellExperiment,
     SummarizedExperiment,

diff --git a/NAMESPACE b/NAMESPACE
@@ -5,9 +5,16 @@ export(from_Seurat)
 export(from_SingleCellExperiment)
 export(generate_dataset)
 export(read_h5ad)
+export(to_Seurat)
 export(write_h5ad)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,t)
 importFrom(R6,R6Class)
+importFrom(cli,cli_abort)
+importFrom(cli,cli_inform)
+importFrom(cli,cli_warn)
 importFrom(methods,as)
+importFrom(methods,new)
+importFrom(purrr,map_lgl)
+importFrom(rlang,caller_env)
diff --git a/R/HDF5AnnData.R b/R/HDF5AnnData.R
@@ -255,9 +255,7 @@ HDF5AnnData <- R6::R6Class("HDF5AnnData", # nolint
                           shape = NULL,
                           mode = c("r", "r+", "a", "w", "w-", "x"),
                           compression = c("none", "gzip", "lzf")) {
-      if (!requireNamespace("hdf5r", quietly = TRUE)) {
-        stop("The HDF5 interface requires the 'hdf5r' package to be installed")
-      }
+      check_requires("HDF5AnnData", "hdf5r")
 
       # check arguments
       compression <- match.arg(compression)
@@ -446,3 +444,12 @@ to_HDF5AnnData <- function(
     mode = mode
   )
 }
+
+cleanup_HDF5AnnData <- function(...) { # nolint object_name_linter
+  args <- list(...)
+
+  if (!is.null(args$file) && is.character(args$file) && file.exists(args$file)) {
+    cli::cli_alert("Removing file: ", args$file)
+    unlink(args$file)
+  }
+}