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Add conditional print method for objects that contain alternative experiments #89

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222aeea
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d1ce30f
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Remove MASS import requirement
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50 changes: 50 additions & 0 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -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
2 changes: 1 addition & 1 deletion .github/workflows/rworkflows.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -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
6 changes: 6 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -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<-")
Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand Down
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