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r-ci.yml
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name: TileDB-SOMA R CI
on:
pull_request:
paths-ignore:
- "apis/python/**"
- ".pre-commit-config.yaml"
push:
branches: [main]
env:
COVERAGE_FLAGS: "r"
COVERAGE_TOKEN: ${{ secrets.CODECOV_TOKEN }}
jobs:
ci:
strategy:
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@v3
- 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
#- name: Call ldconfig
# if: ${{ matrix.os == 'ubuntu-latest' }}
# run: sudo ldconfig
- name: Test
if: ${{ matrix.covr == 'no' }}
run: cd apis/r && tools/r-ci.sh run_tests
- name: View Install Output
run: cat $HOME/work/TileDB-SOMA/TileDB-SOMA/apis/r/tiledbsoma.Rcheck/00install.out
if: failure()
- name: Coverage
if: ${{ matrix.os == 'ubuntu-latest' && matrix.covr == 'yes' }}
run: cd apis/r && tools/r-ci.sh coverage