cellxgene_census package full unit tests #118
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| name: cellxgene_census package full unit tests | |
| # Run all unit tests, including those that are too expensive to run frequently. | |
| # This workflow requires a very large capacity runner, e.g., 1+TiB RAM, which is | |
| # currently available through self-hosted runners. These runners have no swap, | |
| # so an OOM will cause the workflow to fail with OOMKilled (exit code 137). | |
| # | |
| # By default, will install from `main` and run the latest acceptance tests in `main`. | |
| # | |
| # gh workflow run full-unittests.yml | |
| # | |
| # You can run it against a branch with: | |
| # | |
| # gh workflow run full-unittests.yml --ref _branch_name_ | |
| # | |
| # The python (not R) job supports installing a specific `tiledbsoma` version, allowing | |
| # the test to run with any tiledbsoma version, including branches from the TileDB-SOMA | |
| # repo. For example, to test against the head of main, do: | |
| # | |
| # gh workflow run full-unittests.yml \ | |
| # -f 'tiledbsoma_python_dependency=git+https://github.com/single-cell-data/TileDB-SOMA.git#egg=tiledbsoma&subdirectory=apis/python/' | |
| on: | |
| schedule: | |
| - cron: "0 1 * * 6" # every Saturday night, 1AM UTC | |
| workflow_dispatch: # used for debugging or manual validation of a branch | |
| inputs: | |
| tiledbsoma_python_dependency: | |
| # Accepts any package spec that pip understand, e.g., | |
| # tiledbsoma==1.0 | |
| # git+https://github.com/single-cell-data/TileDB-SOMA.git#egg=tiledbsoma&subdirectory=apis/python/ | |
| # git+https://github.com/single-cell-data/[email protected]#egg=tiledbsoma&subdirectory=apis/python/ | |
| # or whatever... | |
| description: "tiledbsoma package specified as pip requirement" | |
| required: false | |
| default: "" | |
| type: string | |
| env: | |
| CELLXGENE_CENSUS_USERAGENT: "CZI-test" | |
| jobs: | |
| py_unit_tests: | |
| runs-on: single-cell-1tb-runner | |
| timeout-minutes: 1440 # 24 hour timeout | |
| strategy: | |
| fail-fast: false # prevent this job from killing other jobs | |
| steps: | |
| - name: log system state | |
| run: | | |
| free | |
| echo --------- | |
| df -kh | |
| echo --------- | |
| lscpu | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| cache: "pip" | |
| cache-dependency-path: | | |
| api/**/pyproject.toml | |
| api/**/requirements*.txt | |
| - name: install python dependencies (including experimental) | |
| run: | | |
| python -m pip install -U pip setuptools setuptools_scm wheel | |
| pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython | |
| pip install -r ./api/python/cellxgene_census/scripts/requirements-dev.txt | |
| pip install './api/python/cellxgene_census/[experimental]' | |
| - name: install tiledbsoma version override | |
| if: github.event_name == 'workflow_dispatch' && github.event.inputs.tiledbsoma_python_dependency != '' | |
| run: | | |
| pip uninstall tiledbsoma -y | |
| pip install '${{ github.event.inputs.tiledbsoma_python_dependency }}' | |
| - name: pytest (--expensive --experimental) | |
| run: | | |
| echo '--------- tiledbsoma.show_package_version():' | |
| python -c 'import tiledbsoma; tiledbsoma.show_package_versions()' | |
| echo '--------- PIP package versions:' | |
| pip freeze | |
| PYTHONPATH=. pytest -v --durations=0 -rP --experimental --expensive ./api/python/cellxgene_census/tests/ | |
| r_unit_tests: | |
| runs-on: single-cell-1tb-runner | |
| timeout-minutes: 1440 # 24 hour timeout | |
| strategy: | |
| fail-fast: false # prevent this job from killing other jobs | |
| steps: | |
| - name: log system state | |
| run: | | |
| free | |
| echo --------- | |
| df -kh | |
| echo --------- | |
| lscpu | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| extra-repositories: https://tiledb-inc.r-universe.dev, https://cloud.r-project.org, https://chanzuckerberg.r-universe.dev | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: ./api/r/cellxgene.census | |
| extra-packages: any::rcmdcheck, any::remotes | |
| cache: true | |
| - name: testthat | |
| run: | | |
| Rscript -e 'remotes::install_local("./api/r/cellxgene.census")' | |
| Rscript -e 'library("tiledbsoma"); tiledbsoma::show_package_versions()' | |
| Rscript -e 'library("testthat"); library("cellxgene.census"); test_dir("./api/r/cellxgene.census/tests/")' | |
| cd ./api/r/cellxgene.census/tests/testthat/; Rscript ./acceptance-tests-run-script.R |