[python] Using optimized reindexer in blockwise iterators #2495
Workflow file for this run
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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@v3 | |
| 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: Dependencies | |
| run: cd apis/r && tools/r-ci.sh install_all | |
| - name: CMake | |
| uses: lukka/get-cmake@latest | |
| - name: MkVars | |
| run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars | |
| - 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: ${{ matrix.os != 'macOS-latest' }} | |
| run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" | |
| - name: Build and install libtiledbsoma | |
| run: sudo scripts/bld --prefix=/usr/local && sudo ldconfig | |
| - name: Install R-tiledbsoma | |
| run: | | |
| cd apis/r | |
| R CMD build --no-build-vignettes --no-manual . | |
| FILE=$(ls -1t *.tar.gz | head -n 1) | |
| R CMD INSTALL $FILE | |
| - name: Show R package versions | |
| run: Rscript -e 'tiledbsoma::show_package_versions()' | |
| - name: Install testing prereqs | |
| run: python -m pip -v install -U pip pytest-cov 'typeguard<3.0' types-setuptools | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: ./apis/python/setup.py | |
| - name: Install tiledbsoma | |
| run: python -m pip -v install -e apis/python | |
| - 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 | |
| run: python -m pytest apis/system/tests/ |