napistu 0.4.3__tar.gz → 0.4.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {napistu-0.4.3/src/napistu.egg-info → napistu-0.4.4}/PKG-INFO +1 -1
- {napistu-0.4.3 → napistu-0.4.4}/setup.cfg +1 -1
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/neighborhoods.py +28 -7
- {napistu-0.4.3 → napistu-0.4.4/src/napistu.egg-info}/PKG-INFO +1 -1
- {napistu-0.4.3 → napistu-0.4.4}/LICENSE +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/README.md +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/pyproject.toml +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/setup.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/__main__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/consensus.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/context/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/context/discretize.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/context/filtering.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/gcs/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/gcs/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/gcs/downloads.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/gcs/utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/identifiers.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/indices.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/bigg.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/gtex.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/hpa.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/identifiers_etl.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/napistu_edgelist.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/obo.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/psi_mi.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/reactom_fi.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/reactome.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/sbml.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/string.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/trrust.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ingestion/yeast.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/matching/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/matching/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/matching/interactions.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/matching/mount.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/matching/species.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/__main__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/client.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/codebase.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/codebase_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/component_base.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/config.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/documentation.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/documentation_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/execution.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/health.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/profiles.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/server.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/tutorials.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/tutorials_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/mcp/utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/curation.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/gaps.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/pathwayannot.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/modify/uncompartmentalize.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/data_handling.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/ig_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/net_create.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/net_create_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/net_propagation.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/ng_core.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/ng_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/paths.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/network/precompute.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/dogma.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/genodexito.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/id_tables.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/mygene.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/ontologies/renaming.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/rpy2/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/rpy2/callr.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/rpy2/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/rpy2/rids.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/sbml_dfs_core.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/sbml_dfs_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/scverse/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/scverse/constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/scverse/loading.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/source.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/statistics/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/statistics/hypothesis_testing.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/statistics/quantiles.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu/utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu.egg-info/SOURCES.txt +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu.egg-info/dependency_links.txt +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu.egg-info/entry_points.txt +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu.egg-info/requires.txt +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/napistu.egg-info/top_level.txt +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/conftest.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_consensus.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_constants.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_context_discretize.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_context_filtering.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_curation.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_data/__init__.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_gaps.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_gcs.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_identifiers.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_indices.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ingestion_napistu_edgelist.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ingestion_obo.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_matching_interactions.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_matching_mount.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_matching_species.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_mcp_config.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_mcp_documentation_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_mcp_server.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_data_handling.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_ig_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_neighborhoods.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_net_create.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_net_create_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_net_propagation.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_ng_core.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_ng_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_paths.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_network_precompute.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ontologies_genodexito.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ontologies_id_tables.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ontologies_mygene.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_ontologies_renaming.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_pathwayannot.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_rpy2_callr.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_rpy2_init.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_sbml.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_sbml_dfs_core.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_sbml_dfs_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_sbo.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_scverse_loading.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_source.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_statistics_hypothesis_testing.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_statistics_quantiles.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_uncompartmentalize.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/test_utils.py +0 -0
- {napistu-0.4.3 → napistu-0.4.4}/src/tests/utils.py +0 -0
@@ -34,6 +34,7 @@ def find_and_prune_neighborhoods(
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napistu_graph: ig.Graph,
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compartmentalized_species: str | list[str],
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precomputed_distances: pd.DataFrame | None = None,
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source_total_counts: pd.Series | None = None,
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network_type: str = NEIGHBORHOOD_NETWORK_TYPES.DOWNSTREAM,
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order: int = 3,
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verbose: bool = True,
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Wrapper which combines find_neighborhoods() and prune_neighborhoods()
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Parameters
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----------
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sbml_dfs: sbml_dfs_core.SBML_dfs
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A mechanistic molecular model
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Compartmentalized species IDs for neighborhood centers
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precomputed_distances : pd.DataFrame or None
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If provided, an edgelist of origin->destination path weights and lengths
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Optional, A series of the total counts of each source. As produced by
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network_type: str
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If the network is directed should neighbors be located "downstream",
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or "upstream" of each compartmentalized species. The "hourglass" option
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verbose=verbose,
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precomputed_neighbors=precomputed_neighbors,
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)
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pruned_neighborhoods = prune_neighborhoods(neighborhoods, top_n=top_n)
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(and overwrite = False) and otherwise construct
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neighborhoods using the provided settings
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----------
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) -> dict:
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"""
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Find Neighborhood
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Create a network composed of all species and reactions within N steps of
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which will be used to skip on-the-fly neighborhood generation.
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A dict containing the neighborhood of each compartmentalized species.
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Each entry in the dict is a dict of the subgraph, vertices, and edges.
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"""
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neighborhood_df=neighborhood_df,
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+
source_total_counts: pd.Series | None = None,
|
583
598
|
verbose: bool = False,
|
584
599
|
) -> dict[str, Any]:
|
585
600
|
"""
|
@@ -597,6 +612,9 @@ def create_neighborhood_dict_entry(
|
|
597
612
|
A mechanistic molecular model
|
598
613
|
napistu_graph: igraph.Graph
|
599
614
|
A network connecting molecular species and reactions
|
615
|
+
source_total_counts: pd.Series
|
616
|
+
Optional, A series of the total counts of each source. As produced by
|
617
|
+
source.get_source_total_counts()
|
600
618
|
verbose: bool
|
601
619
|
Extra reporting?
|
602
620
|
|
@@ -645,7 +663,10 @@ def create_neighborhood_dict_entry(
|
|
645
663
|
|
646
664
|
try:
|
647
665
|
edge_sources = ng_utils.get_minimal_sources_edges(
|
648
|
-
vertices.rename(columns={"name": "node"}),
|
666
|
+
vertices.rename(columns={"name": "node"}),
|
667
|
+
sbml_dfs,
|
668
|
+
# optional, counts of sources across the whole model
|
669
|
+
source_total_counts,
|
649
670
|
)
|
650
671
|
except Exception:
|
651
672
|
edge_sources = None
|
@@ -1441,7 +1462,7 @@ def _prune_vertex_set(one_neighborhood: dict, top_n: int) -> pd.DataFrame:
|
|
1441
1462
|
----------
|
1442
1463
|
one_neighborhood: dict
|
1443
1464
|
The neighborhood around a single compartmentalized species - one of the values
|
1444
|
-
|
1465
|
+
in dict created by find_neighborhoods().
|
1445
1466
|
top_n: int
|
1446
1467
|
How many neighboring molecular species should be retained?
|
1447
1468
|
If the neighborhood includes both upstream and downstream connections
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