Add conditional print method for objects that contain alternative experiments

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

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    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
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: error

.github/workflows/rworkflows.yml

@@ -54,4 +54,4 @@ jobs:
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
-        docker_registry: ghcr.io
+        docker_registry: ghcr.io

DESCRIPTION

@@ -68,6 +68,6 @@ biocViews:
     AssayDomain, Infrastructure, RNASeq, DifferentialExpression, SingleCell,
     GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues

NAMESPACE

@@ -49,11 +49,13 @@ export(tidy)
 export(unnest_single_cell_experiment)
 exportMethods(aggregate_cells)
 exportMethods(join_features)
+importFrom(MASS,rnegbin)
 importFrom(Matrix,rowSums)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,split)
+importFrom(SingleCellExperiment,altExpNames)
 importFrom(SingleCellExperiment,cbind)
 importFrom(SingleCellExperiment,reducedDims)
 importFrom(SummarizedExperiment,"assays<-")
@@ -74,11 +76,13 @@ importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_drop_default)
+importFrom(dplyr,group_keys)
 importFrom(dplyr,group_rows)
 importFrom(dplyr,group_split)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,pick)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,right_join)
@@ -113,10 +117,12 @@ importFrom(pillar,tbl_format_header)
 importFrom(pkgconfig,get_config)
 importFrom(purrr,as_mapper)
 importFrom(purrr,imap)
+importFrom(purrr,list_transpose)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_chr)
 importFrom(purrr,reduce)
+importFrom(purrr,set_names)
 importFrom(purrr,when)
 importFrom(rlang,":=")
 importFrom(rlang,dots_values)