Add X_ref parameter: accept reference panel genotype matrix instead of LD #202
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| name: Continuous Integration | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - .github/* | |
| - .gitignore | |
| - README.md | |
| concurrency: | |
| group: ci-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| ci: | |
| name: CI (${{ matrix.platform }} / ${{ matrix.environment }}) | |
| runs-on: ${{ matrix.runner }} | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| runner: [ubuntu-latest, macos-latest] | |
| environment: ["r44", "r45"] | |
| include: | |
| - runner: ubuntu-latest | |
| platform: linux-64 | |
| - runner: macos-latest | |
| platform: osx-arm64 | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create TOML from recipe | |
| run: | | |
| .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE} | |
| mkdir /tmp/pixi | |
| mv ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi | |
| - name: Setup pixi | |
| uses: prefix-dev/setup-pixi@v0.9.5 | |
| with: | |
| manifest-path: /tmp/pixi/pixi.toml | |
| - name: Run unit tests | |
| run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test | |
| - name: Run R CMD CHECK | |
| run: | | |
| pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build | |
| pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck | |
| - name: Check unit test code coverage | |
| if: matrix.runner == 'ubuntu-latest' && matrix.environment == 'r44' | |
| run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov |