[r] Fixes for dense+2.27 #5913
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| 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 |