main_check.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.


name: R-CMD-check

on:
  pull_request:
    types: opened
    branches: [ "main" ]

permissions:
  contents: read


jobs:
  R-CMD-check:
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config: # matrix of system runners to run workflow on
          - {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'}

    steps:

      - name: Checkout repo for workflow access
        uses: actions/checkout@v4

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Set up R environment
        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

      - name: Set up dependencies (general)
        uses: r-lib/actions/setup-r-dependencies@v2
        env:
          _R_CHECK_FORCE_SUGGESTS: false
          _R_CHECK_RD_XREFS: false
        with:
          dependencies: '"hard"' # do not use suggested dependencies
          install-pandoc: false
          extra-packages: |
            any::rcmdcheck
            any::testthat
            any::rlang
            any::R.utils
            any::knitr
            any::rmarkdown
            any::qs
            any::sp
            any::stars
            any::raster
            any::sf
            any::scattermore
            any::exactextractr
            any::RTriangle
            any::geometry
            any::qs
            any::future.apply
            any::Biobase
            any::chihaya
            any::DelayedArray
            any::DelayedMatrixStats
            any::HDF5Array
            any::plotly
            any::rgl
            any::rhdf5
            any::S4Vectors
            any::ScaledMatrix
            any::XML
            any::Seurat
            any::SeuratObject
            any::SingleCellExperiment
            any::SpatialExperiment
            any::STexampleData
            any::SummarizedExperiment
            github::drieslab/GiottoData

      - uses: actions/setup-python@v5
        with:
          python-version: "3.10"

      - name: setup giotto_env
        shell: Rscript {0}
        run: |
          if (!GiottoClass::checkGiottoEnvironment()) {
            GiottoClass::installGiottoEnvironment()
          }
          
          reticulate::conda_install(
            envname = 'giotto_env',
            packages = 'scanpy',
            pip = TRUE
          )
          
          path_to_python <- GiottoClass::set_giotto_python_path()
          
          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
                     Sys.getenv("GITHUB_ENV"))

      - name: Run R CMD check
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          error-on: '"error"' # workflow errors on error only, can change to include warnings

      # show testthat output for ease of access
      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash