LICENSE
README.md
pyproject.toml
src/mmcontext/__init__.py
src/mmcontext/callback.py
src/mmcontext/file_utils.py
src/mmcontext/hub_utils.py
src/mmcontext/sanity_helpers.py
src/mmcontext/simulator.py
src/mmcontext/training.py
src/mmcontext/utils.py
src/mmcontext.egg-info/PKG-INFO
src/mmcontext.egg-info/SOURCES.txt
src/mmcontext.egg-info/dependency_links.txt
src/mmcontext.egg-info/requires.txt
src/mmcontext.egg-info/top_level.txt
src/mmcontext/_legacy/__init__.py
src/mmcontext/_legacy/adapters.py
src/mmcontext/_legacy/cell_sentence_transformer.py
src/mmcontext/_legacy/mmcontextencoder.py
src/mmcontext/_legacy/omicsencoder.py
src/mmcontext/_legacy/onehot.py
src/mmcontext/embed/__init__.py
src/mmcontext/embed/dataset_prep.py
src/mmcontext/embed/dataset_utils.py
src/mmcontext/embed/encode.py
src/mmcontext/embed/mining.py
src/mmcontext/embed/model_utils.py
src/mmcontext/embed/pipeline.py
src/mmcontext/eval/__init__.py
src/mmcontext/eval/ari.py
src/mmcontext/eval/base.py
src/mmcontext/eval/evaluate_scib.py
src/mmcontext/eval/label_similarity.py
src/mmcontext/eval/query_annotate.py
src/mmcontext/eval/registry.py
src/mmcontext/eval/scib_wrapper.py
src/mmcontext/eval/utils.py
src/mmcontext/io/__init__.py
src/mmcontext/io/_adata_subset.py
src/mmcontext/io/_zarr_read.py
src/mmcontext/io/prepare_store.py
src/mmcontext/io/vector_store.py
src/mmcontext/modules/__init__.py
src/mmcontext/modules/adapter_module.py
src/mmcontext/modules/mmcontext_module.py
src/mmcontext/modules/omics_attention_module.py
src/mmcontext/pl/__init__.py
src/mmcontext/pl/metric_plots.py
src/mmcontext/pl/plotting.py
tests/test_adapter_callback.py
tests/test_adapter_module.py
tests/test_data_properties.py
tests/test_dataset_prep.py
tests/test_gradients.py
tests/test_miniOmicsEncoder.py
tests/test_mmcontext_encoder.py
tests/test_mmcontext_module.py
tests/test_mmcontext_tokenizer.py
tests/test_omics_attention_module.py
tests/test_prepare_store.py
tests/test_query_annotate.py
tests/test_register_initial_embeddings.py
tests/test_sentence_transformer_integration.py
tests/test_st_integration.py
tests/test_training.py