Merge branch 'dev' into eliminate-tidy-method

Author: stemangiola

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,21 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Thanks for submitting an issue.
+
+Please add the following information to the issue
+
+1. Describe the issue/bug
+2. Print out the input dataset immediately before the bug occurs
+3. Paste the code immediately leading to the bug
+4. Print out of the output, if any
+5. Print out of the complete error/warning message, if any
+6. sessionInfo()
+
+Thanks!

.github/workflows/check-bioc.yml

@@ -39,6 +39,7 @@ env:
   run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
+  run_docker: 'false'
 
 jobs:
   build-check:
@@ -51,9 +52,11 @@ 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: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.17'}
+          - { os: windows-latest, r: '4.3', bioc: '3.17'}
+          ## Check https://github.com/r-lib/actions/tree/master/examples
+          ## for examples using the http-user-agent
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -76,48 +79,49 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         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_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         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_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
 
-      - name: Install Linux system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
-          echo $sysreqs
-          sudo -s eval "$sysreqs"
+      # - name: Install Linux system dependencies
+      #   if: runner.os == 'Linux'
+      #   run: |
+      #     sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+      #     echo $sysreqs
+      #     sudo -s eval "$sysreqs"
 
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
@@ -136,9 +140,8 @@ 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
+          ## Required for tcltk
+          brew install xquartz --cask
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -154,7 +157,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -166,22 +169,21 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
+
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## 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")
-          BiocManager::install("BiocCheck")
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -192,13 +194,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("pkgdown")
         shell: Rscript {0}
@@ -213,10 +215,12 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
         run: |
+          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
-              args = c("--no-build-vignettes", "--no-manual", "--timings"),
-              build_args = c("--no-manual", "--no-resave-data"),
+              args = c("--no-manual", "--no-vignettes", "--timings"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
           )
@@ -234,6 +238,8 @@ jobs:
         shell: Rscript {0}
 
       - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
@@ -244,30 +250,89 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - name: Deploy package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
-        shell: bash {0}
+      - name: Build pkgdown site
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
         ## at least one locally before this will work. This creates the gh-pages
         ## branch (erasing anything you haven't version controlled!) and
         ## makes the git history recognizable by pkgdown.
 
+      - name: Install deploy dependencies
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy pkgdown site to GitHub pages 🚀
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
           path: check
+
+
+  ## Code adapted from
+  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
+  docker-build-and-push:
+    runs-on: ubuntu-latest
+    needs: build-check
+    steps:
+      - name: Checkout Repository
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: actions/checkout@v3
+
+      - name: Register repo name
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        id: reg_repo_name
+        run: |
+          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Docker Hub
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
+      ## account, not your actual dockerhub account password. You can get it
+      ## from https://hub.docker.com/settings/security.
+      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
+      ## for more details.
+      ## Alternatively, try checking
+      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
+
+      - name: Build and Push Docker
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: >
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

DESCRIPTION

@@ -1,61 +1,70 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.3.0
-Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
-                  role = c("aut", "cre")) )
-Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse' 
+Version: 1.11.4
+Authors@R: c(person("Stefano", "Mangiola", 
+    email="[email protected]",
+    role=c("aut", "cre")))
+Description: 'tidySingleCellExperiment' is an adapter that abstracts
+    the 'SingleCellExperiment' container in the form of a 'tibble'.
+    This allows *tidy* data manipulation, nesting, and plotting.
+    For example, a 'tidySingleCellExperiment' is directly compatible
+    with functions from 'tidyverse' packages `dplyr` and `tidyr`,
+    as well as plotting with `ggplot2` and `plotly`.
+    In addition, the package provides various utility
+    functions specific to single-cell omics data analysis
+    (e.g., aggregation of cell-level data to pseudobulks).
 License: GPL-3
 Depends:
-    R (>= 4.0.0),
+    R (>= 4.3.0),
     SingleCellExperiment
 Imports:
+    dplyr, tidyr, ttservice,
     SummarizedExperiment,
-    dplyr,
     tibble,
-    tidyr,
     ggplot2,
     plotly,
     magrittr,
     rlang,
     purrr,
+    pkgconfig,
     lifecycle,
     methods,
     utils,
     S4Vectors,
     tidyselect,
     ellipsis,
+    vctrs,
     pillar,
     stringr,
     cli,
-    fansi
+    fansi,
+    Matrix,
+    stats
 Suggests:
     BiocStyle,
     testthat,
     knitr,
-    markdown,
+    rmarkdown,
     SingleCellSignalR,
     SingleR,
     scater,
     scran,
     tidyHeatmap,
     igraph,
     GGally,
-    Matrix,
     uwot,
     celldex,
-    dittoSeq,
-    EnsDb.Hsapiens.v86
+    dittoSeq
 VignetteBuilder: 
     knitr
 RdMacros:
     lifecycle
 Biarch: true
-biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, featureion, featureomics
+biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, 
+    GeneExpression, Normalization, Clustering, QualityControl, Sequencing
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
-Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
 URL: https://github.com/stemangiola/tidySingleCellExperiment
 BugReports: https://github.com/stemangiola/tidySingleCellExperiment/issues