Allow connecting to private LaminDB instances #339
Workflow file for this run
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| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| name: R-CMD-check.yaml | |
| permissions: read-all | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # note: we use python 3.12 on mac os x so we can install scipy 1.13 from a wheel | |
| - { os: macos-latest, r: "release", python: "3.12" } | |
| - { os: windows-latest, r: "release", python: "3.x" } | |
| - { | |
| os: ubuntu-latest, | |
| r: "devel", | |
| http-user-agent: "release", | |
| python: "3.x", | |
| } | |
| - { os: ubuntu-latest, r: "release", python: "3.x" } | |
| - { os: ubuntu-latest, r: "oldrel-1", python: "3.9" } | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| # manually installing openblas as a workaround for issue | |
| # https://github.com/laminlabs/laminr/issues/57 | |
| - name: Install OpenBLAS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install openblas | |
| OPENBLAS=$(brew --prefix openblas) | |
| echo "LDFLAGS=-L$OPENBLAS/lib" >> $GITHUB_ENV | |
| echo "CPPFLAGS=-I$OPENBLAS/include" >> $GITHUB_ENV | |
| - name: Install lamindb | |
| run: | | |
| pip install lamindb[aws] | |
| - name: Log in to Lamin | |
| run: | | |
| lamin login | |
| - name: Set cellxgene as default instance | |
| run: | | |
| lamin connect laminlabs/cellxgene | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' |