[c++] Fix fast path for SparseNDArray nnz
#6691
Workflow file for this run
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| name: TileDB-SOMA R CI | |
| on: | |
| pull_request: | |
| paths: | |
| - '**' | |
| - '!**.md' | |
| - '!.github/**' | |
| - '.github/workflows/r-ci.yml' | |
| - '!.pre-commit-config.yaml' | |
| - '!apis/python/**' | |
| - '!docs/**' | |
| - '!LICENSE' | |
| push: | |
| branches: | |
| - main | |
| - 'release-*' | |
| workflow_dispatch: | |
| env: | |
| COVERAGE_FLAGS: "r" | |
| COVERAGE_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| CATCHSEGV: "TRUE" | |
| R_REMOTES_UPGRADE: "never" | |
| TILEDB_SOMA_INIT_BUFFER_BYTES: 33554432 # accommodate tiny runners | |
| jobs: | |
| ci: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: linux | |
| os: ubuntu-latest | |
| covr: 'no' | |
| - name: macos | |
| os: macOS-latest | |
| covr: 'no' | |
| - name: coverage | |
| os: ubuntu-latest | |
| covr: 'yes' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Show matrix OS | |
| run: echo "matrix.os:" ${{ matrix.os }} | |
| - name: Linux CPU info | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: cat /proc/cpuinfo | |
| - name: MacOS CPU info | |
| if: ${{ matrix.os == 'macOS-latest' }} | |
| run: sysctl -a | grep cpu | |
| - name: Bootstrap | |
| run: cd apis/r && tools/r-ci.sh bootstrap | |
| - name: Set additional repositories (macOS) | |
| if: ${{ matrix.os != 'ubuntu-latest' }} | |
| run: echo 'options(repos = c("https://tiledb-inc.r-universe.dev", getOption("repos")), timeout = 300L)' | tee -a ~/.Rprofile | |
| - 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")), timeout = 300L)', 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: Install BioConductor package SingleCellExperiment | |
| run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment | |
| # 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: Dependencies | |
| run: cd apis/r && Rscript -e "remotes::install_deps(dependencies = TRUE, upgrade = FALSE)" | |
| # - name: Install dataset packages from source (macOS) | |
| # if: ${{ matrix.os == 'macOS-latest' }} | |
| # run: cd apis/r && _CI_PKG_TYPE_=both _CI_USE_BIOC_=true Rscript tools/install_missing_deps.R | |
| # - name: CMake | |
| # uses: lukka/get-cmake@latest | |
| #- name: MkVars | |
| # run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars | |
| #- name: Build and install libtiledbsoma | |
| # run: sudo scripts/bld --prefix=/usr/local | |
| #- name: Call ldconfig | |
| # if: ${{ matrix.os == 'ubuntu-latest' }} | |
| # run: sudo ldconfig | |
| # | |
| # - name: Update Packages | |
| # run: Rscript -e 'update.packages(ask=FALSE)' | |
| - name: Build Package | |
| run: cd apis/r && R CMD build --no-build-vignettes --no-manual . | |
| - name: Install Package | |
| run: cd apis/r && R CMD INSTALL $(ls -1tr *.tar.gz | tail -1) | |
| # - name: Diagnostics | |
| # run: Rscript -e 'print(Sys.info())' | |
| # - name: Downgrade TileDB-R if needed | |
| # run: cd apis/r && Rscript tools/controlled_downgrade.R | |
| #- name: Test | |
| # if: ${{ matrix.covr == 'no' }} | |
| # run: | | |
| # cd apis/r | |
| # Rscript -e "install.packages('devtools')" \ | |
| # -e "devtools::install(upgrade = FALSE)" \ | |
| # -e "testthat::test_local('tests/testthat', load_package = 'installed')" | |
| - name: Test without new shape | |
| if: ${{ matrix.covr == 'no' }} | |
| run: cd apis/r/tests && Rscript testthat.R | |
| # https://github.com/single-cell-data/TileDB-SOMA/issues/2407 | |
| - name: Test with new shape | |
| if: ${{ matrix.covr == 'no' }} | |
| run: export SOMA_R_NEW_SHAPE=true && cd apis/r/tests && Rscript testthat.R | |
| - name: Coverage | |
| if: ${{ matrix.os == 'ubuntu-latest' && matrix.covr == 'yes' && github.event_name == 'workflow_dispatch' }} | |
| run: apis/r/tools/r-ci.sh coverage | |
| - name: View Logs | |
| run: apis/r/tools/r-ci.sh dump_logs | |
| if: failure() |