Use tempfile instead of re-creating the same directory in tempdir

pachterlab · May 16, 2024 · 94f4741 · 94f4741
1 parent 295a8af
commit 94f4741
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Showing 22 changed files with 161 additions and 162 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -12,7 +12,19 @@ permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          #- {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'oldrel-1'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -269,3 +269,7 @@ if (!isGeneric("unwrap")) {setGeneric("unwrap", function(x, ...) standardGeneric
 
 #' @export
 setGeneric("Img<-", function(x, sample_id = 1L, image_id, scale_fct = 1, value) standardGeneric("Img<-"))
+
+if (!isGeneric("aggregate")) {setGeneric("aggregate", function(x, ...) standardGeneric("aggregate"))}
+
+if (!isGeneric("split")) {setGeneric("split", function(x, f, drop = FALSE, ...) standardGeneric("split"))}
diff --git a/R/dimGeometries.R b/R/dimGeometries.R
@@ -398,8 +398,8 @@ nucSeg <- function(x, sample_id = 1L, withDimnames = TRUE) {
 #' @examples
 #' library(SFEData)
 #' library(RBioFormats)
-#' fp <- tempdir()
-#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fp <- tempfile()
+#' dir_use <- XeniumOutput("v2", file_path = fp)
 #' # RBioFormats issue
 #' try(sfe <- readXenium(dir_use, add_molecules = TRUE))
 #' sfe <- readXenium(dir_use, add_molecules = TRUE)

diff --git a/R/formatTxSpots.R b/R/formatTxSpots.R
@@ -122,13 +122,14 @@
 #' @examples
 #' library(SFEData)
 #' if (gdalParquetAvailable()) {
-#'     fp <- tempdir()
-#'     dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#'     fp <- tempfile()
+#'     dir_use <- XeniumOutput("v2", file_path = fp)
 #'     fn_tx <- formatTxTech(dir_use, tech = "Xenium", flip = TRUE, return = FALSE,
 #'                           file_out = file.path(dir_use, "tx_spots.parquet"))
 #'     gene_select <- c("ACE2", "BMX")
 #'     df <- readSelectTx(fn_tx, gene_select)
-#'
+#'     # RBioFormats null pointer error the first time
+#'     try(sfe <- readXenium(dir_use))
 #'     sfe <- readXenium(dir_use)
 #'     sfe <- addSelectTx(sfe, fn_tx, head(rownames(sfe), 5), swap_rownames = "Symbol")
 #'     unlink(dir_use, recursive = TRUE)
@@ -292,14 +293,14 @@ addSelectTx <- function(sfe, file, gene_select, sample_id = 1L,
 #' @rdname formatTxSpots
 #' @examples
 #' # Default arguments are for MERFISH
-#' fp <- tempdir()
-#' dir_use <- SFEData::VizgenOutput(file_path = file.path(fp, "vizgen_test"))
+#' fp <- tempfile()
+#' dir_use <- SFEData::VizgenOutput(file_path = fp)
 #' g <- formatTxSpots(file.path(dir_use, "detected_transcripts.csv"))
 #' unlink(dir_use, recursive = TRUE)
 #'
 #' # For CosMX, note the colnames, also dest = "colGeometry"
 #' # Results are written to the tx_spots directory
-#' dir_use <- SFEData::CosMXOutput(file_path = file.path(fp, "cosmx_test"))
+#' dir_use <- SFEData::CosMXOutput(file_path = fp)
 #' cg <- formatTxSpots(file.path(dir_use, "Run5642_S3_Quarter_tx_file.csv"),
 #' dest = "colGeometry", z = "all",
 #' cell_col = c("cell_ID", "fov"),
@@ -523,8 +524,8 @@ addTxSpots <- function(sfe, file, sample_id = 1L,
 #' @export
 #' @examples
 #' library(SFEData)
-#' fp <- tempdir()
-#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fp <- tempfile()
+#' dir_use <- XeniumOutput("v2", file_path = fp)
 #' fn_tx <- formatTxTech(dir_use, tech = "Xenium", flip = TRUE, return = FALSE,
 #'                       file_out = file.path(dir_use, "tx_spots.parquet"))
 #'

diff --git a/R/geometry_operation.R b/R/geometry_operation.R
@@ -732,3 +732,7 @@ removeEmptySpace <- function(sfe, sample_id = "all") {
     }
     sfe
 }
+
+#' Aggregate data in SFE using geometry
+#'
+#' Gene expression and
diff --git a/R/image.R b/R/image.R
@@ -708,8 +708,8 @@ setMethod("dim", "BioFormatsImage", function(x) {
 #' library(EBImage)
 #' library(SFEData)
 #' library(RBioFormats)
-#' fp <- tempdir()
-#' fn <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fp <- tempfile()
+#' fn <- XeniumOutput("v2", file_path = fp)
 #' # Weirdly the first time I get the null pointer error
 #' try(sfe <- readXenium(fn))
 #' sfe <- readXenium(fn)

diff --git a/R/read.R b/R/read.R
@@ -388,8 +388,8 @@ read10xVisiumSFE <- function(samples = "",
 #' @importFrom data.table fread merge.data.table rbindlist is.data.table
 #' @importFrom stats na.omit
 #' @examples
-#' fp <- tempdir()
-#' dir_use <- SFEData::VizgenOutput(file_path = file.path(fp, "vizgen_test"))
+#' fp <- tempfile()
+#' dir_use <- SFEData::VizgenOutput(file_path = fp)
 #' sfe <- readVizgen(dir_use, z = 3L, image = "PolyT",
 #' flip = "geometry")
 #'
@@ -677,8 +677,8 @@ readVizgen <- function(data_dir,
 #' @export
 #' @concept Read data into SFE
 #' @examples
-#' fp <- tempdir()
-#' dir_use <- SFEData::CosMXOutput(file_path = file.path(fp, "cosmx_test"))
+#' fp <- tempfile()
+#' dir_use <- SFEData::CosMXOutput(file_path = fp)
 #' sfe <- readCosMX(dir_use, z = "all", add_molecules = TRUE)
 #' # Clean up
 #' unlink(dir_use, recursive = TRUE)
@@ -835,8 +835,8 @@ readCosMX <- function(data_dir,
 #' @examples
 #' library(SFEData)
 #' library(RBioFormats)
-#' fp <- tempdir()
-#' dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+#' fp <- tempfile()
+#' dir_use <- XeniumOutput("v2", file_path = fp)
 #' # RBioFormats issue
 #' try(sfe <- readXenium(dir_use, add_molecules = TRUE))
 #' sfe <- readXenium(dir_use, add_molecules = TRUE)

diff --git a/R/utils.R b/R/utils.R
@@ -173,8 +173,8 @@ bbox_center <- function(bbox) {
 #' @concept Utilities
 #' @examples
 #' library(SFEData)
-#' fp <- tempdir()
-#' dir_use <- XeniumOutput("v1", file_path = file.path(fp, "xenium_test"))
+#' fp <- tempfile()
+#' dir_use <- XeniumOutput("v1", file_path = fp)
 #' # RBioFormats null pointer error
 #' try(getPixelSize(file.path(dir_use, "morphology_focus.ome.tif")))
 #' getPixelSize(file.path(dir_use, "morphology_focus.ome.tif"))

diff --git a/man/Img-set-SpatialExperiment-method.Rd b/man/Img-set-SpatialExperiment-method.Rd
diff --git a/man/formatTxSpots.Rd b/man/formatTxSpots.Rd
diff --git a/man/formatTxTech.Rd b/man/formatTxTech.Rd
diff --git a/man/getPixelSize.Rd b/man/getPixelSize.Rd
diff --git a/man/readCosMX.Rd b/man/readCosMX.Rd
diff --git a/man/readSelectTx.Rd b/man/readSelectTx.Rd
diff --git a/man/readVizgen.Rd b/man/readVizgen.Rd
diff --git a/man/readXenium.Rd b/man/readXenium.Rd
diff --git a/man/rowGeometries.Rd b/man/rowGeometries.Rd
diff --git a/tests/testthat/test-formatTxSpots.R b/tests/testthat/test-formatTxSpots.R
@@ -1,8 +1,8 @@
 library(SFEData)
 library(sf)
 test_that("Read MERFISH transcript spots into rowGeometries", {
-    fp <- tempdir()
-    dir_use <- VizgenOutput("hdf5", file_path = file.path(fp, "vizgen_test"))
+    fp <- tempfile()
+    dir_use <- VizgenOutput("hdf5", file_path = fp)
     sfe <- readVizgen(dir_use, z = 3L, image = "PolyT", add_molecules = TRUE)
     expect_equal(rowGeometryNames(sfe), "txSpots")
     rg <- txSpots(sfe)
@@ -15,8 +15,8 @@ test_that("Read MERFISH transcript spots into rowGeometries", {
 })
 
 test_that("Format MERFISH transcript spots for colGeometries", {
-    fp <- tempdir()
-    dir_use <- VizgenOutput("hdf5", file_path = file.path(fp, "vizgen_test"))
+    fp <- tempfile()
+    dir_use <- VizgenOutput("hdf5", file_path = fp)
     expect_error(formatTxSpots(file.path(dir_use, "detected_transcripts.csv"),
                                dest = "colGeometry"),
                  "file_out must be specified")
@@ -63,8 +63,8 @@ test_that("Format MERFISH transcript spots for colGeometries", {
 })
 
 test_that("Error messages in formatTxSpots", {
-    fp <- tempdir()
-    dir_use <- VizgenOutput("hdf5", file_path = file.path(fp, "vizgen_test"))
+    fp <- tempfile()
+    dir_use <- VizgenOutput("hdf5", file_path = fp)
     file <- file.path(dir_use, "detected_transcripts.csv")
     expect_error(formatTxSpots(file, dest = "colGeometry", file_out = NULL),
                  "file_out must be specified")
@@ -84,8 +84,8 @@ test_that("Error messages in formatTxSpots", {
 })
 
 test_that("Format CosMX spots for colGeometry, multiple z-planes", {
-    fp <- tempdir()
-    dir_use <- CosMXOutput(file_path = file.path(fp, "cosmx_test"))
+    fp <- tempfile()
+    dir_use <- CosMXOutput(file_path = fp)
 
     cg <- formatTxSpots(file.path(dir_use, "Run5642_S3_Quarter_tx_file.csv"),
                         dest = "colGeometry", z = "all", z_option = "split",
@@ -111,8 +111,8 @@ test_that("Format CosMX spots for colGeometry, multiple z-planes", {
 
 test_that("Read transcript spots from a subset of genes", {
     skip_if_not(gdalParquetAvailable())
-    fp <- tempdir()
-    fn <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+    fp <- tempfile()
+    fn <- XeniumOutput("v2", file_path = fp)
     fn_tx <- formatTxTech(fn, tech = "Xenium", flip = TRUE, return = FALSE,
                           file_out = file.path(fn, "tx_spots.parquet"))
     gene_select <- c("ACE2", "BMX")
@@ -126,8 +126,8 @@ test_that("Read transcript spots from a subset of genes", {
 
 test_that("Error message when Parquet driver is unavailable", {
     skip_if(gdalParquetAvailable())
-    fp <- tempdir()
-    fn <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+    fp <- tempfile()
+    fn <- XeniumOutput("v2", file_path = fp)
     fn_tx <- formatTxTech(fn, tech = "Xenium", flip = TRUE, return = FALSE,
                           file_out = file.path(fn, "tx_spots.parquet"))
     gene_select <- c("ACE2", "BMX")
@@ -139,8 +139,8 @@ test_that("Error message when Parquet driver is unavailable", {
 test_that("Add a subset of spots", {
     skip_if_not(gdalParquetAvailable())
     library(RBioFormats)
-    fp <- tempdir()
-    fn <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
+    fp <- tempfile()
+    fn <- XeniumOutput("v2", file_path = fp)
     try(sfe <- readXenium(fn))
     sfe <- readXenium(fn)
     fn_tx <- formatTxTech(fn, tech = "Xenium", flip = TRUE, return = FALSE,
@@ -155,8 +155,8 @@ test_that("Add a subset of spots", {
 
 test_that("Add subset of spots, multiple files in tx spots output", {
     skip_if_not(gdalParquetAvailable())
-    fp <- tempdir()
-    dir_use <- CosMXOutput(file_path = file.path(fp, "cosmx_test"))
+    fp <- tempfile()
+    dir_use <- CosMXOutput(file_path = fp)
 
     sfe <- readCosMX(dir_use)
     fn_tx <- formatTxTech(dir_use, tech = "CosMX", z = "all", z_option = "split",
@@ -175,9 +175,3 @@ test_that("Add subset of spots, multiple files in tx spots output", {
     expect_true(all(is_empty1[-(1:5)]))
     unlink(dir_use, recursive = TRUE)
 })
-
-# Final cleanup in case failed test messed with cleanup
-fp <- tempdir()
-unlink(file.path(fp, "cosmx_test"), recursive = TRUE)
-unlink(file.path(fp, "vizgen_test"), recursive = TRUE)
-unlink(file.path(fp, "xenium_test"), recursive = TRUE)