LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
src/napistu/__init__.py
src/napistu/__main__.py
src/napistu/consensus.py
src/napistu/constants.py
src/napistu/identifiers.py
src/napistu/indices.py
src/napistu/sbml_dfs_core.py
src/napistu/sbml_dfs_utils.py
src/napistu/source.py
src/napistu/utils.py
src/napistu.egg-info/PKG-INFO
src/napistu.egg-info/SOURCES.txt
src/napistu.egg-info/dependency_links.txt
src/napistu.egg-info/entry_points.txt
src/napistu.egg-info/requires.txt
src/napistu.egg-info/top_level.txt
src/napistu/context/__init__.py
src/napistu/context/discretize.py
src/napistu/context/filtering.py
src/napistu/gcs/__init__.py
src/napistu/gcs/constants.py
src/napistu/gcs/downloads.py
src/napistu/gcs/utils.py
src/napistu/ingestion/__init__.py
src/napistu/ingestion/bigg.py
src/napistu/ingestion/constants.py
src/napistu/ingestion/gtex.py
src/napistu/ingestion/hpa.py
src/napistu/ingestion/identifiers_etl.py
src/napistu/ingestion/intact.py
src/napistu/ingestion/napistu_edgelist.py
src/napistu/ingestion/obo.py
src/napistu/ingestion/psi_mi.py
src/napistu/ingestion/reactome.py
src/napistu/ingestion/reactome_fi.py
src/napistu/ingestion/sbml.py
src/napistu/ingestion/string.py
src/napistu/ingestion/trrust.py
src/napistu/ingestion/yeast.py
src/napistu/matching/__init__.py
src/napistu/matching/constants.py
src/napistu/matching/interactions.py
src/napistu/matching/mount.py
src/napistu/matching/species.py
src/napistu/mcp/__init__.py
src/napistu/mcp/__main__.py
src/napistu/mcp/client.py
src/napistu/mcp/codebase.py
src/napistu/mcp/codebase_utils.py
src/napistu/mcp/component_base.py
src/napistu/mcp/config.py
src/napistu/mcp/constants.py
src/napistu/mcp/documentation.py
src/napistu/mcp/documentation_utils.py
src/napistu/mcp/execution.py
src/napistu/mcp/health.py
src/napistu/mcp/profiles.py
src/napistu/mcp/server.py
src/napistu/mcp/tutorials.py
src/napistu/mcp/tutorials_utils.py
src/napistu/mcp/utils.py
src/napistu/modify/__init__.py
src/napistu/modify/constants.py
src/napistu/modify/curation.py
src/napistu/modify/gaps.py
src/napistu/modify/pathwayannot.py
src/napistu/modify/uncompartmentalize.py
src/napistu/network/__init__.py
src/napistu/network/constants.py
src/napistu/network/data_handling.py
src/napistu/network/ig_utils.py
src/napistu/network/neighborhoods.py
src/napistu/network/net_create.py
src/napistu/network/net_create_utils.py
src/napistu/network/net_propagation.py
src/napistu/network/ng_core.py
src/napistu/network/ng_utils.py
src/napistu/network/paths.py
src/napistu/network/precompute.py
src/napistu/ontologies/__init__.py
src/napistu/ontologies/constants.py
src/napistu/ontologies/dogma.py
src/napistu/ontologies/genodexito.py
src/napistu/ontologies/id_tables.py
src/napistu/ontologies/mygene.py
src/napistu/ontologies/renaming.py
src/napistu/rpy2/__init__.py
src/napistu/rpy2/callr.py
src/napistu/rpy2/constants.py
src/napistu/rpy2/rids.py
src/napistu/scverse/__init__.py
src/napistu/scverse/constants.py
src/napistu/scverse/loading.py
src/napistu/statistics/__init__.py
src/napistu/statistics/constants.py
src/napistu/statistics/hypothesis_testing.py
src/napistu/statistics/quantiles.py
src/tests/__init__.py
src/tests/conftest.py
src/tests/test_consensus.py
src/tests/test_constants.py
src/tests/test_context_discretize.py
src/tests/test_context_filtering.py
src/tests/test_curation.py
src/tests/test_gaps.py
src/tests/test_gcs.py
src/tests/test_identifiers.py
src/tests/test_indices.py
src/tests/test_ingestion_napistu_edgelist.py
src/tests/test_ingestion_obo.py
src/tests/test_matching_interactions.py
src/tests/test_matching_mount.py
src/tests/test_matching_species.py
src/tests/test_mcp_config.py
src/tests/test_mcp_documentation_utils.py
src/tests/test_mcp_server.py
src/tests/test_network_data_handling.py
src/tests/test_network_ig_utils.py
src/tests/test_network_neighborhoods.py
src/tests/test_network_net_create.py
src/tests/test_network_net_create_utils.py
src/tests/test_network_net_propagation.py
src/tests/test_network_ng_core.py
src/tests/test_network_ng_utils.py
src/tests/test_network_paths.py
src/tests/test_network_precompute.py
src/tests/test_ontologies_genodexito.py
src/tests/test_ontologies_id_tables.py
src/tests/test_ontologies_mygene.py
src/tests/test_ontologies_renaming.py
src/tests/test_pathwayannot.py
src/tests/test_rpy2_callr.py
src/tests/test_rpy2_init.py
src/tests/test_sbml.py
src/tests/test_sbml_dfs_core.py
src/tests/test_sbml_dfs_utils.py
src/tests/test_sbo.py
src/tests/test_scverse_loading.py
src/tests/test_source.py
src/tests/test_statistics_hypothesis_testing.py
src/tests/test_statistics_quantiles.py
src/tests/test_uncompartmentalize.py
src/tests/test_utils.py
src/tests/utils.py
src/tests/test_data/__init__.py