diff --git a/.github/workflows/R-CMD-check-current.yaml b/.github/workflows/R-CMD-check-current.yaml
index 688352a9..3e109c29 100644
--- a/.github/workflows/R-CMD-check-current.yaml
+++ b/.github/workflows/R-CMD-check-current.yaml
@@ -10,12 +10,12 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/R-CMD-check-renv.yaml b/.github/workflows/R-CMD-check-renv.yaml
index de0a55e3..6d84885e 100644
--- a/.github/workflows/R-CMD-check-renv.yaml
+++ b/.github/workflows/R-CMD-check-renv.yaml
@@ -10,12 +10,12 @@ name: R-CMD-check-renv
 
 jobs:
   R-CMD-check-renv:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -53,8 +53,8 @@ jobs:
 
       - name: Install additional dependencies for testing
         run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_github("AlexsLemonade/scpcaData")
+          install.packages(c("pak", "rcmdcheck"))
+          pak::pak("AlexsLemonade/scpcaData")
         shell: Rscript {0}
 
       - name: Check package
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
index 9cf4a498..ea49c3b0 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/pr-commands.yaml
@@ -10,11 +10,11 @@ jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -55,7 +55,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -97,8 +97,6 @@ jobs:
         run: styler::style_pkg()
         shell: Rscript --no-init-file {0}
 
-
-
       - name: commit
         run: |
           git config --local user.name "$GITHUB_ACTOR"
diff --git a/tests/testthat/.gitignore b/tests/testthat/.gitignore
deleted file mode 100644
index bcd16254..00000000
--- a/tests/testthat/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-_snaps/
-test_anndata.h5
diff --git a/tests/testthat/_snaps/sce_to_anndata/anndata.h5 b/tests/testthat/_snaps/sce_to_anndata/anndata.h5
new file mode 100644
index 00000000..bf34238d
Binary files /dev/null and b/tests/testthat/_snaps/sce_to_anndata/anndata.h5 differ
diff --git a/tests/testthat/_snaps/sce_to_anndata/new_anndata.h5 b/tests/testthat/_snaps/sce_to_anndata/new_anndata.h5
new file mode 100644
index 00000000..5d5a5e9b
Binary files /dev/null and b/tests/testthat/_snaps/sce_to_anndata/new_anndata.h5 differ
diff --git a/tests/testthat/_snaps/sce_to_anndata/no_verbose_anndata.h5 b/tests/testthat/_snaps/sce_to_anndata/no_verbose_anndata.h5
new file mode 100644
index 00000000..bf34238d
Binary files /dev/null and b/tests/testthat/_snaps/sce_to_anndata/no_verbose_anndata.h5 differ
diff --git a/tests/testthat/test-sce_to_anndata.R b/tests/testthat/test-sce_to_anndata.R
index 9092ad00..5ec7c99b 100644
--- a/tests/testthat/test-sce_to_anndata.R
+++ b/tests/testthat/test-sce_to_anndata.R
@@ -49,8 +49,7 @@ test_that("Conversion of SCE to AnnData works as expected", {
   expect_equal(colnames(colData(sce)), colnames(colData(converted_sce)))
   expect_equal(colnames(rowData(sce)), colnames(rowData(converted_sce)))
 
-
-  # expect that sample metadata has been removed from converted SCE
+  # expect that metadata_list has been removed from converted SCE
   expect_setequal(
     c("library_id", "sample_metadata", "metadata_dataframe", "metadata_S4_DataFrame"),
     names(metadata(converted_sce))
@@ -68,7 +67,6 @@ test_that("Conversion of SCE to AnnData works as expected", {
     "logical"
   )
 
-
   # test that H5 file is created with new assay name
   # add logcounts
   logcounts(sce) <- counts(sce)