[python] Geneformer updates for July 2024 LTS #1994
Workflow file for this run
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| name: R cellxgene.census package checks | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - "api/python/**" | |
| - "tools/cellxgene_census_builder/**" | |
| push: | |
| branches: [main] | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| tiledbsoma_version: [tiledbsoma_release, tiledbsoma_latest] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| extra-repositories: https://tiledb-inc.r-universe.dev | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: ./api/r/cellxgene.census | |
| extra-packages: any::rcmdcheck, any::styler, any::roxygen2, any::remotes | |
| cache: true | |
| - name: install tiledbsoma | |
| # install tiledbsoma either from r-universe (release) or git HEAD (latest), | |
| # overwriting any version cached by setup-r-dependencies. | |
| run: | | |
| if [[ '${{ matrix.tiledbsoma_version }}' == 'tiledbsoma_latest' ]]; then | |
| Rscript -e 'remotes::install_git("https://github.com/single-cell-data/TileDB-SOMA.git", subdir="apis/r")' | |
| else | |
| Rscript -e 'install.packages("tiledbsoma", repos = c("https://tiledb-inc.r-universe.dev", | |
| "https://cloud.r-project.org"))' | |
| fi | |
| - name: styler | |
| run: Rscript -e 'library("styler"); style_pkg("api/r/cellxgene.census", dry="fail")' | |
| - name: check session info | |
| run: Rscript -e 'sessionInfo()' | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| working-directory: ./api/r/cellxgene.census | |
| args: 'c("--no-manual", "--as-cran", "--no-build-vignettes")' | |
| build_args: 'c("--no-manual", "--no-build-vignettes")' | |
| error-on: '"error"' | |