@@ -1,7 +1,7 @@

 Package: spatialDE

 Title: R wrapper for SpatialDE

-Date: 2023-01-23

-Version: 1.5.1

+Date: 2023-01-25

+Version: 1.5.2

 Authors@R: c(

     person("Davide", "Corso", role = "aut",

            email = "[email protected]",

@@ -21,7 +21,7 @@ License: MIT + file LICENSE

 Encoding: UTF-8

 LazyData: FALSE

 Roxygen: list(markdown = TRUE)

-RoxygenNote: 7.2.1

+RoxygenNote: 7.2.3

 URL: https://github.com/sales-lab/spatialDE, https://bioconductor.org/packages/spatialDE/

 BugReports: https://github.com/sales-lab/spatialDE/issues

 Depends: R (>= 4.1)

@@ -111,7 +111,7 @@ NULL

     coordinates <- sample_info[, c("x", "y")]

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_spatial_patterns(

         proc = proc, 

         x = regressed, coordinates = coordinates,

@@ -59,7 +59,7 @@ model_search <- function(x,

     }

     proc <- basiliskStart(spatialDE_env, testload="scipy.optimize")

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_model_search(proc, x, coordinates, de_results)

@@ -157,7 +157,7 @@ spatial_patterns <- function(x, coordinates, de_results,

     }

     proc <- basiliskStart(spatialDE_env, testload="scipy.optimize")

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_spatial_patterns(proc, x, coordinates, de_results, n_patterns, 

                                 length)

@@ -20,21 +20,20 @@ SpatialDE.base.tqdm = tqdm.autonotebook.tqdm

 #'

 #' @param proc A process object generated by [`basilisk::basiliskStart()`]

 #' @param patch_tqdm If `TRUE` patch calls to tqdm.

-#' @param set_fake_tqdm

-#' @param set_real_tqdm

 #' @return An R wrapper for the SpatialDE Python module.

 #'

 #' @importFrom reticulate import py_run_string

 #' @importFrom basilisk basiliskRun

 #'

 #' @keywords internal

-.importPyModule <- function(proc, patch_tqdm, set_fake_tqdm, set_real_tqdm) {

-  basiliskRun(proc, function(patch_tqdm, set_fake_tqdm, set_real_tqdm, store) {

+.importPyModule <- function(proc, patch_tqdm) {

+  imp <- function(patch_tqdm, store) {

     mod <- import("SpatialDE")

-    py_run_string(ifelse(patch_tqdm, set_fake_tqdm, set_real_tqdm))

+    py_run_string(ifelse(patch_tqdm, .set_fake_tqdm, .set_real_tqdm))

     store$spatialDE <- mod

     invisible(NULL)

-  }, patch_tqdm=patch_tqdm, set_fake_tqdm=set_fake_tqdm,

-  set_real_tqdm=set_fake_tqdm, persist=TRUE)

+  }

+

+  basiliskRun(proc, imp, patch_tqdm, persist=TRUE)

 }

@@ -93,7 +93,7 @@ NULL

     }, persist=TRUE)

     coordinates <- sample_info[, c("x", "y")]

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_model_search(proc, regressed, coordinates, de_results)

     out <- basiliskRun(proc, function(store) {

@@ -49,7 +49,7 @@ run <- function(x, coordinates, verbose = FALSE) {

     proc <- basiliskStart(spatialDE_env, testload="scipy.optimize")

-    .importPyModule(proc, !verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, !verbose)

     .spatialDE_run(proc, x, coordinates)

     out <- basiliskRun(proc, function(store) {

@@ -92,7 +92,7 @@ NULL

     assert_names(colnames(coords), identical.to = c("x", "y"))

     assert_matrix(regressed, any.missing = FALSE)

     assert_flag(verbose)

-    .importPyModule(proc, verbose, .set_fake_tqdm, .set_real_tqdm)

+    .importPyModule(proc, verbose)

     .spatialDE_run(proc, regressed, coords)

     # results

@@ -4,7 +4,7 @@

 \alias{.importPyModule}

 \title{Import SpatialDE}

 \usage{

-.importPyModule(proc, patch_tqdm, set_fake_tqdm, set_real_tqdm)

+.importPyModule(proc, patch_tqdm)

 }

 \arguments{

 \item{proc}{A process object generated by \code{\link[basilisk:basiliskStart]{basilisk::basiliskStart()}}}