pull master

Merge branch 'master' of github.com:stemangiola/tidySingleCellExperiment

Conflicts:
	DESCRIPTION

Author: stemangiola

.github/workflows/check-bioc.yml

@@ -51,9 +51,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.0', bioc: '3.12'}
-          - { os: windows-latest, r: '4.0', bioc: '3.12'}
+          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.1', bioc: '3.14'}
+          - { os: windows-latest, r: '4.1', bioc: '3.14'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -101,16 +101,16 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v2
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -135,10 +135,10 @@ jobs:
 
           ## For installing usethis's dependency gert
           brew install libgit2
-
+          
           ## To fix x11/cairo error with tidyHeatmap/Complexheatmap here https://github.com/stemangiola/tidybulk/runs/1388237421?check_suite_focus=true#step:14:2134
           ## Suggested here https://stackoverflow.com/questions/63648591/how-to-install-x11-before-testing-with-github-actions-for-macos
-          brew install --cask xquartz
+          brew install --cask xquartz 
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -177,7 +177,7 @@ jobs:
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
-
+          
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           remotes::install_cran("rcmdcheck")
@@ -269,5 +269,6 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results
           path: check
+          

DESCRIPTION

@@ -9,6 +9,7 @@ Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCe
 License: GPL-3
 Depends:
     R (>= 4.0.0),
+    ttservice,
     SingleCellExperiment
 Imports:
     SummarizedExperiment,

NAMESPACE

@@ -18,8 +18,6 @@ S3method(ggplot,SingleCellExperiment)
 S3method(glimpse,tidySingleCellExperiment)
 S3method(group_by,SingleCellExperiment)
 S3method(inner_join,SingleCellExperiment)
-S3method(join_features,SingleCellExperiment)
-S3method(join_features,default)
 S3method(join_transcripts,Seurat)
 S3method(join_transcripts,default)
 S3method(left_join,SingleCellExperiment)
@@ -78,7 +76,9 @@ export(tidy)
 export(unite)
 export(unnest)
 export(unnest_single_cell_experiment)
+importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,cbind)
 importFrom(SingleCellExperiment,counts)
 importFrom(SummarizedExperiment,"colData<-")
@@ -135,6 +135,8 @@ importFrom(rlang,is_spliced)
 importFrom(rlang,names2)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(stringr,regex)
+importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
@@ -147,7 +149,6 @@ importFrom(tidyr,separate)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
-importFrom(tidyselect,contains)
 importFrom(tidyselect,eval_select)
-importFrom(tidyselect,everything)
+importFrom(ttservice,join_features)
 importFrom(utils,tail)