use MultiAssayExperiment instead of SummarizedExperiment

insightsengineering · Oct 14, 2024 · fc3de91 · fc3de91
1 parent 95b92a8
commit fc3de91
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Showing 2 changed files with 29 additions and 11 deletions.
diff --git a/tests/testthat/test-deps_installation_proposal.R b/tests/testthat/test-deps_installation_proposal.R
@@ -288,20 +288,26 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles Bioc pack
   skip_if_offline()
   skip_if_empty_gh_token()
 
-  d_std_path <- local_description(list(SummarizedExperiment = "Import"))
+  d_std_path <- local_description(
+    list(MultiAssayExperiment = "Import"),
+    need_verdepcheck = c("bioc::MultiAssayExperiment")
+  )
 
   x <- new_min_cohort_deps_installation_proposal(d_std_path)
 
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common_bioc(x, "SummarizedExperiment")
+  test_proposal_common_bioc(x, "MultiAssayExperiment")
 })
 
 test_that("new_min_isolated_deps_installation_proposal correctly handles Bioc package", {
   skip_if_offline()
   skip_if_empty_gh_token()
 
-  d_std_path <- local_description(list(SummarizedExperiment = "Import"))
+  d_std_path <- local_description(
+    list(MultiAssayExperiment = "Import"),
+    need_verdepcheck = c("bioc::MultiAssayExperiment")
+  )
 
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
 
@@ -310,42 +316,51 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles Bioc pa
   # https://github.com/r-lib/pkgdepends/issues/365
   withr::with_options(
     opts_partial_match_old,
-    test_proposal_common_bioc(x, "SummarizedExperiment")
+    test_proposal_common_bioc(x, "MultiAssayExperiment")
   )
 })
 
 test_that("new_release_deps_installation_proposal correctly handles Bioc package", {
   skip_if_offline()
   skip_if_empty_gh_token()
 
-  d_std_path <- local_description(list(SummarizedExperiment = "Import"))
+  d_std_path <- local_description(
+    list(MultiAssayExperiment = "Import"),
+    need_verdepcheck = c("bioc::MultiAssayExperiment")
+  )
 
   x <- new_release_deps_installation_proposal(d_std_path)
 
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common_bioc(x, "SummarizedExperiment")
+  test_proposal_common_bioc(x, "MultiAssayExperiment")
 })
 
 test_that("new_max_deps_installation_proposal correctly handles Bioc package", {
   skip_if_offline()
   skip_if_empty_gh_token()
 
-  d_std_path <- local_description(list(SummarizedExperiment = "Import"))
+  d_std_path <- local_description(
+    list(MultiAssayExperiment = "Import"),
+    need_verdepcheck = c("bioc::MultiAssayExperiment")
+  )
 
   x <- new_max_deps_installation_proposal(d_std_path)
 
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common_bioc(x, "SummarizedExperiment")
+  test_proposal_common_bioc(x, "MultiAssayExperiment")
 })
 
 # ################################################################
 
 test_that("indirect dependencies in the config field - ignore on default", {
   skip_if_offline()
 
-  d_std_path <- local_description(list(dplyr = "Import"), need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang"))
+  d_std_path <- local_description(
+    list(dplyr = "Import"),
+    need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang")
+  )
 
   x <- new_max_deps_installation_proposal(d_std_path)
 
@@ -358,7 +373,10 @@ test_that("indirect dependencies in the config field - ignore on default", {
 test_that("indirect dependencies in the config field - include on match with `extra_deps`", {
   skip_if_offline()
 
-  d_std_path <- local_description(list(dplyr = "Import"), need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang"))
+  d_std_path <- local_description(
+    list(dplyr = "Import"),
+    need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang")
+  )
 
   x <- new_max_deps_installation_proposal(d_std_path, extra_deps = "rlang")
 

diff --git a/tests/testthat/test-get_ref.R b/tests/testthat/test-get_ref.R
@@ -68,7 +68,7 @@ test_that("get_release_date with any class other than remote_ref.{github,cran,st
 test_that("get_release_data returns date for Bioconductor", {
   skip_if_offline()
 
-  expect_false(any(is.na(get_release_data("SummarizedExperiment")$mtime)))
+  expect_false(any(is.na(get_release_data("MultiAssayExperiment")$mtime)))
 })
 
 test_that("get_ref_release returns a CRAN remote_reference if package exists", {