[r] Add SOMA Experiment Query -> SingleCellExperiment outgestor #916
Workflow file for this run
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name: TileDB-SOMA R-Python interop testing | |
on: | |
pull_request: | |
paths: | |
- "apis/python/**" | |
- "apis/r/**" | |
- "apis/system/**" | |
push: | |
branches: [main] | |
jobs: | |
ci: | |
strategy: | |
matrix: | |
include: | |
- { os: ubuntu-latest } | |
runs-on: ${{ matrix.os }} | |
steps: | |
- name: Checkout TileDB-SOMA | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 # ensure we get all tags to inform package version determination | |
- name: Bootstrap | |
run: cd apis/r && tools/r-ci.sh bootstrap | |
- name: Dependencies | |
run: cd apis/r && tools/r-ci.sh install_all | |
- name: CMake | |
uses: lukka/get-cmake@latest | |
- name: MkVars | |
run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars | |
- name: Build and install libtiledbsoma | |
run: sudo scripts/bld --prefix=/usr/local && sudo ldconfig | |
- name: Install R-tiledbsoma | |
run: | | |
cd apis/r | |
R CMD build --no-build-vignettes --no-manual . | |
FILE=$(ls -1t *.tar.gz | head -n 1) | |
R CMD INSTALL $FILE | |
- name: 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 package versions | |
run: python scripts/show-versions.py | |
- name: Interop Tests | |
run: python -m pytest apis/system/tests/ |