Add snapshot files

.github/workflows/R-CMD-check-current.yaml

@@ -10,33 +10,33 @@
 
 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
 
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - name: Remove renv
         run: rm -f renv.lock .Rprofile
 
       - name: Set up Pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
       - name: Set up dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
       - name: Check package
         uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual")'

.github/workflows/R-CMD-check-renv.yaml

@@ -10,54 +10,54 @@
 
 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
 
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: "renv"
           use-public-rspm: true
 
       - name: Set up Pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install additional system dependencies
         run: |
           sudo apt-get install -y libcurl4-openssl-dev libglpk40 jags
 
       # remove requirements file to prevent renv from worrying about python
       - name: Remove requirements.txt file
         run: |
           rm -f requirements.txt
 
       - name: Set up Renv & install packages
         uses: r-lib/actions/setup-renv@v2
 
       - name: Clean up temp files
         run: |
           rm -rf /tmp/downloaded_packages
           rm -rf /tmp/Rtmp*
 
       - name: Remove unneeded system files
         run: |
           sudo rm -rf /opt/hostedtoolcache/CodeQL
           sudo rm -rf /opt/hostedtoolcache/PyPy
           sudo rm -rf /opt/hostedtoolcache/Ruby
 
       - 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
         uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual")'

.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"

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)