├── .dockerignore ├── .github └── workflows │ ├── checks.yml │ ├── conventional-commits.yml │ ├── docs-publish.yml │ ├── publish-pypi.yml │ ├── release-please.yaml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── LICENSE.md ├── Makefile ├── README-pypi.md ├── README.md ├── SECURITY.md ├── docs ├── .nojekyll ├── Makefile ├── README.md ├── make.bat └── source │ ├── _static │ └── custom.css │ ├── api_reference.rst │ ├── assets.md │ ├── changelog_release_notes.rst │ ├── conf.py │ ├── developer_guides │ ├── datasets.md │ ├── debugging.md │ ├── design_overview.rst │ ├── index.rst │ ├── metrics.md │ ├── release_process.md │ ├── release_workflow.png │ └── tasks.md │ ├── examples │ ├── how_to_guides │ ├── add_custom_dataset.md │ ├── add_new_metric.md │ ├── add_new_task.md │ ├── guide_to_perturbation_expression_prediction_benchmark.md │ ├── index.rst │ ├── setup_guides.md │ └── visualize_results.md │ ├── index.rst │ ├── legal.rst │ ├── notebook_examples.rst │ ├── policy │ ├── code_of_conduct.rst │ ├── definitions.md │ └── index.rst │ ├── principles.md │ ├── quick_start.md │ └── roadmap.md ├── examples ├── README.md ├── end-to-end-tutorial.py ├── example.py ├── example_perturbation_expression_prediction.py ├── scvi_all_tasks_benchmark.ipynb ├── scvi_model_dev_workflow.ipynb └── using_czbenchmarks.ipynb ├── patch-cross-species.txt ├── patch.txt ├── pyproject.toml ├── src └── czbenchmarks │ ├── __init__.py │ ├── cli │ ├── __init__.py │ ├── cli.py │ ├── cli_list.py │ └── utils.py │ ├── conf │ ├── datasets.yaml │ └── datasets_deprecated.yaml │ ├── constants.py │ ├── datasets │ ├── README.md │ ├── __init__.py │ ├── dataset.py │ ├── single_cell.py │ ├── single_cell_labeled.py │ ├── single_cell_perturbation.py │ ├── types.py │ ├── utils.py │ ├── utils_single_cell.py │ └── validators │ │ ├── __init__.py │ │ ├── dataset_validator.py │ │ └── single_cell_validator.py │ ├── exceptions.py │ ├── file_cache.py │ ├── file_utils.py │ ├── metrics │ ├── README.md │ ├── __init__.py │ ├── implementations.py │ ├── types.py │ └── utils.py │ ├── tasks │ ├── README.md │ ├── __init__.py │ ├── clustering.py │ ├── constants.py │ ├── embedding.py │ ├── integration.py │ ├── label_prediction.py │ ├── sequential.py │ ├── single_cell │ │ ├── __init__.py │ │ ├── cross_species_integration.py │ │ ├── cross_species_label_prediction.py │ │ └── perturbation_expression_prediction.py │ ├── task.py │ ├── types.py │ └── utils.py │ ├── types.py │ └── utils.py ├── tests ├── README.md ├── __init__.py ├── cli │ ├── __init__.py │ ├── test_cli.py │ ├── test_cli_e2e_workflow.py │ └── test_cli_utils.py ├── conftest.py ├── datasets │ ├── __init__.py │ ├── test_dataset.py │ ├── test_single_cell_dataset.py │ ├── test_single_cell_labeled_dataset.py │ ├── test_single_cell_perturbation_dataset.py │ ├── test_types.py │ ├── test_utils.py │ ├── test_utils_single_cell.py │ └── validators │ │ ├── test_dataset_validator.py │ │ └── 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