├── .github └── workflows │ ├── docker.yaml │ ├── pages.yaml │ ├── pypi-publish.yaml │ └── pypi-test.yaml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── NEWS.rst ├── README.rst ├── docker ├── Dockerfile └── start-notebook.sh ├── docs ├── Makefile ├── _static │ ├── advanced_thumbnail.png │ ├── annotation_model.png │ ├── annotation_thumbnail.png │ ├── custom.css │ ├── environment.yaml │ ├── model_training.png │ ├── query_model.png │ ├── search_engine.png │ ├── search_thumbnail_1.png │ ├── search_thumbnail_2.png │ ├── search_thumbnail_3.png │ └── training_thumbnail.png ├── about.rst ├── api.rst ├── conf.py ├── index.rst ├── install.rst ├── modules │ ├── anndata_data_models.rst │ ├── cell_annotation.rst │ ├── cell_embedding.rst │ ├── cell_query.rst │ ├── cell_search_knn.rst │ ├── interpreter.rst │ ├── nn_models.rst │ ├── ontologies.rst │ ├── tiledb_data_models.rst │ ├── training_models.rst │ ├── triplet_selector.rst │ ├── utils.rst │ ├── visualizations.rst │ ├── zarr_data_models.rst │ └── zarr_dataset.rst ├── news.rst ├── notebooks │ ├── advanced_tutorial.ipynb │ ├── cell_annotation_tutorial.ipynb │ ├── cell_search_tutorial_1.ipynb │ ├── cell_search_tutorial_2.ipynb │ ├── cell_search_tutorial_3.ipynb │ └── training_tutorial.ipynb ├── requirements.txt └── tutorials.rst ├── pyproject.toml ├── scripts ├── anndata │ ├── build_annotation_knn_anndata.py │ └── train_anndata.py ├── build_annotation_knn.py ├── build_cellsearch_knn.py ├── build_cellsearch_metadata.py ├── build_embeddings.py └── train.py ├── setup.cfg ├── setup.py ├── src └── scimilarity │ ├── __init__.py │ ├── anndata_data_models.py │ ├── cell_annotation.py │ ├── cell_embedding.py │ ├── cell_query.py │ ├── cell_search_knn.py │ ├── interpreter.py │ ├── nn_models.py │ ├── ontologies.py │ ├── tiledb_data_models.py │ ├── training_models.py │ ├── triplet_selector.py │ ├── utils.py │ ├── visualizations.py │ ├── zarr_data_models.py │ └── zarr_dataset.py └── tox.ini /.github/workflows/docker.yaml: 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