Bioc review

.Rbuildignore

@@ -5,3 +5,4 @@
 ^inst/scripts/HCATonsilDataRNA$
 ^inst/scripts/rna_raw_data$
 ^inst/scripts/cite_raw_data$
+^\.github$

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

@@ -0,0 +1,126 @@
+on:
+  push:
+  pull_request:
+    branches:
+      - devel
+  schedule:
+    - cron: '0 8 * * 5'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    container: ${{ matrix.config.image }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - { os: windows-latest, bioc: 'devel'}
+        - { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'}
+        - { os: ubuntu-latest, bioc: 'devel'}
+        - { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v2
+
+      - name: Set up R and install BiocManager
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        if: matrix.config.image == null
+        with:
+          bioc-version: ${{ matrix.config.bioc }}
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+        if: matrix.config.image == null
+
+      - name: Install remotes
+        run: |
+          install.packages('remotes')
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        run: |
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows' && matrix.config.image == null
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+          sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev libglpk-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install cairo
+          brew install --cask xquartz
+          brew install harfbuzz
+          brew install fribidi
+          brew install fftw
+
+      - name: Install dependencies
+        run: |
+          local_deps <- remotes::local_package_deps(dependencies = TRUE)
+          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L)
+          remotes::install_cran('rcmdcheck', Ncpu = 2L)
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Build, Install, Check
+        uses: grimbough/bioc-actions/build-install-check@v1
+
+      - name: Run BiocCheck
+        uses: grimbough/bioc-actions/run-BiocCheck@v1
+        with:
+          arguments: '--no-check-bioc-views --no-check-bioc-help'
+          error-on: 'error'
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results
+          path: check
+
+      - name: Test coverage
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          install.packages("covr")
+          covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+        shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: HCATonsilData
 Title: Provide programmatic access to the tonsil cell atlas datasets 
-Version: 0.99.3
+Version: 0.99.4
 Authors@R: c(person("Ramon", "Massoni-Badosa", role = c("aut", "cre"),
                     email ="[email protected]",
                     comment = c(ORCID = "0000-0001-7115-8145")),
@@ -39,6 +39,9 @@ Suggests:
     ggplot2,
     testthat (>= 3.0.0),
     scater,
+    Seurat,
+    Signac,
+    iSEE,
     ggspavis,
     kableExtra,
     BiocStyle

README.md

@@ -1,5 +1,9 @@
 # HCATonsilData
 
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/massonix/HCATonsilData/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/massonix/HCATonsilData/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 HCATonsilData is an R/ExperimentHub package that provides easy access to
 single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq (scATAC-seq), 10X Multiome,
 CITE-seq and spatial transcriptomics data (Visium) derived from the tonsil cell