r-python-interop-testing.yml

name: TileDB-SOMA R-Python interop testing

on:
  pull_request:
    # TODO: leave this enabled for pre-merge signal for now. At some point we may want to go back to
    # only having this signal post-merge.
    #paths:
    #  - "apis/python/**"
    #  - "apis/r/**"
    #  - "apis/system/**"
  push:
    branches:
      - main
      - 'release-*'
  workflow_dispatch:

jobs:
  ci:
    strategy:
      matrix:
        include:
          - { os: ubuntu-latest }

    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout TileDB-SOMA
        uses: actions/checkout@v4
        with:
          fetch-depth: 0  # ensure we get all tags to inform package version determination

      - name: Bootstrap
        run: cd apis/r && tools/r-ci.sh bootstrap

      - name: Set additional repositories (Linux)
        if: ${{ matrix.os == 'ubuntu-latest' }}
        run: |
          rversion <- paste(strsplit(as.character(getRversion()), split = '\\.')[[1L]][1:2], collapse = '.')
          codename <-  system('. /etc/os-release; echo ${VERSION_CODENAME}', intern = TRUE)
          repo <- "https://tiledb-inc.r-universe.dev"
          (opt <- sprintf('options(repos = c("%s/bin/linux/%s/%s", "%s", getOption("repos")))', repo, codename, rversion, repo))
          cat(opt, "\n", file = "~/.Rprofile", append = TRUE)
        shell: Rscript {0}

      - name: Install tiledb-r
        run: cd apis/r && Rscript tools/install-tiledb-r.R

      - name: Dependencies
        run: cd apis/r && Rscript -e "remotes::install_deps(dependencies = TRUE, upgrade = FALSE)"

      - name: CMake
        uses: lukka/get-cmake@latest

      - name: MkVars
        run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars

      # Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for
      # which source is available but CRAN releases (and hence update r2u binaries) are not yet:
      #
      # IMPORTANT: these two stanzas should remain uncommented _only_ during the propagation time
      # between (a) publication of source for a new TileDB-R _upon which_ TileDB-SOMA depends in its
      # apis/R/DESCRIPTION file and (b) appearance of binaries.
      #
      # Please see https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases which
      # is crucial for anyone doing releases of TileDB-SOMA.
      #
      # Please edit both files in the same way:
      # * r-ci.yml
      # * r-python-interop-testing.yml
      #
      # Do not remove these comments until such time as we have eliminated our dependency on
      # the TileDB-R package.

      #- name: Install r-universe build of tiledb-r (macOS)
      #  if: ${{ matrix.os == 'macOS-latest' }}
      #  run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"

      #- name: Install r-universe build of tiledb-r (linux)
      #  if: ${{ matrix.os != 'macOS-latest' }}
      #  run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"

      - name: Build and install libtiledbsoma
        run: sudo scripts/bld --prefix=/usr/local --no-tiledb-deprecated=true --werror=true && sudo ldconfig

      - name: Install R-tiledbsoma
        run: |
          cd apis/r
          R CMD build --no-build-vignettes --no-manual .
          FILE=$(ls -1t *.tar.gz | head -n 1)
          R CMD INSTALL $FILE

      - name: Show R package versions
        run: Rscript -e 'tiledbsoma::show_package_versions()'

      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
          cache: pip
          cache-dependency-path: ./apis/python/setup.py

      - name: Install tiledbsoma
        run: pip -v install -e apis/python[dev] -C "--build-option=--no-tiledb-deprecated "

      - name: Show Python package versions
        run: |
          python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
          python scripts/show-versions.py

      - name: Update Packages
        run: Rscript -e 'update.packages(ask=FALSE)'

      - name: Interop tests with new-shape feature flag off
        run: python -m pytest apis/system/tests/
        env:
          TILEDB_SOMA_INIT_BUFFER_BYTES: 33554432 # accommodate tiny runners

      - name: Interop tests with new-shape feature flag on
        run: python -m pytest apis/system/tests/
        env:
          TILEDB_SOMA_INIT_BUFFER_BYTES: 33554432 # accommodate tiny runners
          SOMA_PY_NEW_SHAPE: true
          SOMA_R_NEW_SHAPE: true