napistu 0.3.5__tar.gz → 0.3.6__tar.gz

{napistu-0.3.5 → napistu-0.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.5
+Version: 0.3.6
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -43,7 +43,7 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: testcontainers; extra == "dev"
 Provides-Extra: mcp
-Requires-Dist: fastmcp<3.0.0,>=2.0.0; extra == "mcp"
+Requires-Dist: fastmcp<2.9.0,>=2.0.0; extra == "mcp"
 Requires-Dist: mcp<2.0.0,>=1.0.0; extra == "mcp"
 Requires-Dist: httpx>=0.24.0; extra == "mcp"
 Requires-Dist: beautifulsoup4<5.0.0,>=4.11.0; extra == "mcp"

{napistu-0.3.5 → napistu-0.3.6}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napistu
-version = 0.3.5
+version = 0.3.6
 description = Connecting high-dimensional data to curated pathways
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -61,7 +61,7 @@ dev =
 	ruff
 	testcontainers
 mcp = 
-	fastmcp>=2.0.0,<3.0.0
+	fastmcp>=2.0.0,<2.9.0
 	mcp>=1.0.0,<2.0.0
 	httpx>=0.24.0
 	beautifulsoup4>=4.11.0,<5.0.0

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/__main__.py

@@ -54,12 +54,12 @@ def cli():
 
 
 @click.group()
-def load():
+def ingestion():
     """Command line tools to retrieve raw data."""
     pass
 
 
-@load.command(name="reactome")
+@ingestion.command(name="reactome")
 @click.argument("base_folder", type=str)
 @click.option(
     "--overwrite", "-o", is_flag=True, default=False, help="Overwrite existing files?"
@@ -70,7 +70,7 @@ def load_reactome(base_folder: str, overwrite=True):
     reactome.reactome_sbml_download(f"{base_folder}/sbml", overwrite=overwrite)
 
 
-@load.command(name="bigg")
+@ingestion.command(name="bigg")
 @click.argument("base_folder", type=str)
 @click.option(
     "--overwrite", "-o", is_flag=True, default=False, help="Overwrite existing files?"
@@ -81,7 +81,7 @@ def load_bigg(base_folder: str, overwrite: bool):
     bigg.bigg_sbml_download(base_folder, overwrite)
 
 
-@load.command(name="trrust")
+@ingestion.command(name="trrust")
 @click.argument("target_uri", type=str)
 @click_logging.simple_verbosity_option(logger)
 def load_ttrust(target_uri: str):
@@ -89,7 +89,7 @@ def load_ttrust(target_uri: str):
     trrust.download_trrust(target_uri)
 
 
-@load.command(name="proteinatlas-subcell")
+@ingestion.command(name="proteinatlas-subcell")
 @click.argument("target_uri", type=str)
 @click.option(
     "--url",
@@ -102,7 +102,7 @@ def load_proteinatlas_subcell(target_uri: str, url: str):
     hpa.download_hpa_data(target_uri, url)
 
 
-@load.command(name="gtex-rnaseq-expression")
+@ingestion.command(name="gtex-rnaseq-expression")
 @click.argument("target_uri", type=str)
 @click.option(
     "--url",
@@ -115,7 +115,7 @@ def load_gtex_rnaseq(target_uri: str, url: str):
     gtex.download_gtex_rnaseq(target_uri, url)
 
 
-@load.command(name="string-db")
+@ingestion.command(name="string-db")
 @click.argument("target_uri", type=str)
 @click.option(
     "--species",
@@ -128,7 +128,7 @@ def load_string_db(target_uri: str, species: str):
     string.download_string(target_uri, species)
 
 
-@load.command(name="string-aliases")
+@ingestion.command(name="string-aliases")
 @click.argument("target_uri", type=str)
 @click.option(
     "--species",
@@ -343,9 +343,9 @@ def infer_uncompartmentalized_species_location(model_uri: str, output_model_uri:
     If the compartment of a subset of compartmentalized species was
     not specified, infer an appropriate compartment from other members of reactions they particpate in
     """
-    model = utils.load_pickle(model_uri)
-    model = sbml_dfs_core.infer_uncompartmentalized_species_location(model)
-    utils.save_pickle(output_model_uri, model)
+    sbml_dfs = utils.load_pickle(model_uri)
+    sbml_dfs.infer_uncompartmentalized_species_location()
+    utils.save_pickle(output_model_uri, sbml_dfs)
 
 
 @refine.command(name="name_compartmentalized_species")
@@ -357,9 +357,9 @@ def name_compartmentalized_species(model_uri: str, output_model_uri: str):
 
     Rename compartmentalized species if they have the same name as their species
     """
-    model = utils.load_pickle(model_uri)
-    model = sbml_dfs_core.name_compartmentalized_species(model)
-    utils.save_pickle(output_model_uri, model)
+    sbml_dfs = utils.load_pickle(model_uri)
+    sbml_dfs.name_compartmentalized_species()
+    utils.save_pickle(output_model_uri, sbml_dfs)
 
 
 @refine.command(name="merge_model_compartments")
@@ -786,9 +786,9 @@ def export_sbml_dfs_tables(
     logger.debug(f"nondogmatic = {nondogmatic}; dogmatic = {dogmatic}")
     logger.info(f"Exporting tables with dogmatic = {dogmatic}")
 
-    model = utils.load_pickle(model_uri)
-    sbml_dfs_core.export_sbml_dfs(
-        model_prefix, model, output_uri, overwrite=overwrite, dogmatic=dogmatic
+    sbml_dfs = utils.load_pickle(model_uri)
+    sbml_dfs.export_sbml_dfs(
+        model_prefix, output_uri, overwrite=overwrite, dogmatic=dogmatic
     )
 
 
@@ -884,7 +884,7 @@ def calculate_igraph_stats(input_uri, output_uri):
     utils.save_json(output_uri, stats)
 
 
-cli.add_command(load)
+cli.add_command(ingestion)
 cli.add_command(integrate)
 cli.add_command(consensus)
 cli.add_command(refine)

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/consensus.py

@@ -843,9 +843,10 @@ def report_consensus_merges(
         indexed_models = merges_lookup.set_index("model").sort_index()
         merges_dict = dict()
         for mod in indexed_models.index.unique():
-            merges_dict[mod] = sbml_dfs_core.reaction_summaries(
-                sbml_dfs_dict[mod], indexed_models.loc[mod]["r_id"]
+            merges_dict[mod] = sbml_dfs_dict[mod].reaction_formulas(
+                indexed_models.loc[mod]["r_id"]
             )
+
         merge_labels = pd.concat(merges_dict, names=["model", "r_id"]).rename("label")
 
         # add labels to models + r_id

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/constants.py

@@ -135,7 +135,7 @@ REQUIRED_REACTION_FROMEDGELIST_COLUMNS = [
     "r_isreversible",
 ]
 
-CPR_STANDARD_OUTPUTS = SimpleNamespace(
+NAPISTU_STANDARD_OUTPUTS = SimpleNamespace(
     SPECIES_IDENTIFIERS="species_identifiers.tsv",
     SPECIES="species.json",
     REACTIONS="reactions.json",

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/context/filtering.py

@@ -5,6 +5,7 @@ from typing import Union, List, Optional
 import pandas as pd
 
 from napistu import sbml_dfs_core
+from napistu import sbml_dfs_utils
 from napistu import utils
 from napistu.constants import SBML_DFS
 
@@ -236,7 +237,7 @@ def _find_reactions_with_disconnected_cspecies(
     sbml_dfs._validate_table(SBML_DFS.REACTION_SPECIES)
     sbml_dfs._validate_table(SBML_DFS.COMPARTMENTALIZED_SPECIES)
 
-    reaction_species = sbml_dfs_core.add_sbo_role(sbml_dfs.reaction_species)
+    reaction_species = sbml_dfs_utils.add_sbo_role(sbml_dfs.reaction_species)
 
     logger.info(
         "Finding disconnected pairs of cspecies based on the zero values in the coccurrence_edgelist"

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/identifiers.py

@@ -12,7 +12,6 @@ import pandas as pd
 from pydantic import BaseModel
 
 from napistu import sbml_dfs_core
-from napistu import sbml_dfs_utils
 from napistu import utils
 
 from napistu.constants import IDENTIFIERS
@@ -883,9 +882,7 @@ def _prepare_species_identifiers(
     """Accepts and validates species_identifiers, or extracts a fresh table if None."""
 
     if species_identifiers is None:
-        species_identifiers = sbml_dfs_utils.get_characteristic_species_ids(
-            sbml_dfs, dogmatic=dogmatic
-        )
+        species_identifiers = sbml_dfs.get_characteristic_species_ids(dogmatic=dogmatic)
     else:
         # check for compatibility
         try:
@@ -898,8 +895,8 @@ def _prepare_species_identifiers(
             logger.warning(
                 f"The provided identifiers are not compatible with your `sbml_dfs` object. Extracting a fresh species identifier table. {e}"
             )
-            species_identifiers = sbml_dfs_utils.get_characteristic_species_ids(
-                sbml_dfs, dogmatic=dogmatic
+            species_identifiers = sbml_dfs.get_characteristic_species_ids(
+                dogmatic=dogmatic
             )
 
     return species_identifiers

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/ingestion/bigg.py

@@ -122,10 +122,10 @@ def construct_bigg_consensus(
         raise NotImplementedError("Merging of models not implemented yet for BiGG")
 
     # In Bigg there should be only one model
-    model = list(sbml_dfs_dict.values())[0]
+    sbml_dfs = list(sbml_dfs_dict.values())[0]
     # fix missing compartimentalization
-    model = sbml_dfs_core.infer_uncompartmentalized_species_location(model)
-    model = sbml_dfs_core.name_compartmentalized_species(model)
-    rename_species_ontologies(model)
-    model.validate()
-    return model
+    sbml_dfs.infer_uncompartmentalized_species_location()
+    sbml_dfs.name_compartmentalized_species()
+    rename_species_ontologies(sbml_dfs)
+    sbml_dfs.validate()
+    return sbml_dfs

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/ingestion/string.py

@@ -5,6 +5,7 @@ import logging
 import pandas as pd
 from napistu import identifiers
 from napistu import sbml_dfs_core
+from napistu import sbml_dfs_utils
 from napistu import source
 from napistu import utils
 from napistu.constants import BQB
@@ -158,7 +159,7 @@ def convert_string_to_sbml_dfs(
     # Define compartments
     # Currently we are mapping everything to the `CELLULAR_COMPONENT`
     # which is a catch-all go: for unknown localisation
-    compartments_df = sbml_dfs_core._stub_compartments()
+    compartments_df = sbml_dfs_utils.stub_compartments()
 
     # define interactions
     interaction_edgelist = _build_interactor_edgelist(uq_string_edgelist)

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/ingestion/yeast.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 import pandas as pd
 from napistu import identifiers
 from napistu import sbml_dfs_core
+from napistu import sbml_dfs_utils
 from napistu import source
 from napistu import utils
 from napistu.constants import BQB
@@ -105,7 +106,7 @@ def convert_idea_kinetics_to_sbml_dfs(
     # Constant fields (for this data source)
 
     # setup compartments (just treat this as uncompartmentalized for now)
-    compartments_df = sbml_dfs_core._stub_compartments()
+    compartments_df = sbml_dfs_utils.stub_compartments()
 
     # Per convention unaggregated models receive an empty source
     interaction_source = source.Source(init=True)

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/matching/interactions.py

@@ -40,7 +40,7 @@ def edgelist_to_pathway_species(
         pd.Dataframe containing a "identifier_upstream" and "identifier_downstream" variables used to to match entries
     species_identifiers: pd.DataFrame
         A table of molecular species identifiers produced from sbml_dfs.get_identifiers("species") generally using
-        sbml_dfs_core.export_sbml_dfs()
+        sbml_dfs.export_sbml_dfs()
     ontologies: set
         A set of ontologies used to match features to pathway species
     feature_id_var: str, default=FEATURE_ID_VAR_DEFAULT
@@ -138,7 +138,7 @@ def edgelist_to_scids(
         A mechanistic model
     species_identifiers: pd.DataFrame
         A table of molecular species identifiers produced from
-        sbml_dfs.get_identifiers("species") generally using sbml_dfs_core.export_sbml_dfs()
+        sbml_dfs.get_identifiers("species") generally using sbml_dfs.export_sbml_dfs()
     ontologies: set
         A set of ontologies used to match features to pathway species
 
@@ -218,7 +218,7 @@ def filter_to_direct_mechanistic_interactions(
     species_identifiers: pd.DataFrame
         A table of molecular species identifiers
         produced from sbml_dfs.get_identifiers("species") generally
-        using sbml_dfs_core.export_sbml_dfs()
+        using sbml_dfs.export_sbml_dfs()
     ontologies: set
         A set of ontologies used to match features to pathway species
 
@@ -342,7 +342,7 @@ def filter_to_indirect_mechanistic_interactions(
         A mechanistic model
     species_identifiers: pandas.DataFrame
         A table of molecular species identifiers produced from
-        sbml_dfs.get_identifiers("species") generally using sbml_dfs_core.export_sbml_dfs()
+        sbml_dfs.get_identifiers("species") generally using sbml_dfs.export_sbml_dfs()
     napistu_graph: igraph.Graph
         A network representation of the sbml_dfs model
     ontologies: set

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/modify/uncompartmentalize.py

@@ -48,7 +48,7 @@ def uncompartmentalize_sbml_dfs(
         )
 
     # 1. update the compartments table to the stubbed default level: GO CELLULAR_COMPONENT
-    stubbed_compartment = sbml_dfs_core._stub_compartments().assign(
+    stubbed_compartment = sbml_dfs_utils.stub_compartments().assign(
         c_Source=_create_stubbed_source()
     )
 

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/network/net_create.py

@@ -1697,7 +1697,7 @@ def _create_topology_weights(
         base_score (float): offset which will be added to all weights.
         protein_multiplier (int): multiplier for non-metabolite species (lower weight paths will tend to be selected).
         metabolite_multiplier (int): multiplier for metabolites [defined a species with a ChEBI ID).
-        unknown_multiplier (int): multiplier for species without any identifier. See sbml_dfs_core.species_type_types.
+        unknown_multiplier (int): multiplier for species without any identifier. See sbml_dfs_utils.species_type_types.
         scale_multiplier_by_meandegree (bool): if True then multipliers will be rescaled by the average number of
             connections a node has (i.e., its degree) so that weights will be relatively similar regardless of network
             size and sparsity.

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/network/paths.py

@@ -489,7 +489,7 @@ def _label_path_reactions(sbml_dfs: sbml_dfs_core.SBML_dfs, paths_df: pd.DataFra
         reaction_info = (
             pd.concat(
                 [
-                    sbml_dfs_core.reaction_summaries(sbml_dfs, r_ids=x)
+                    sbml_dfs.reaction_formulas(r_ids=x)
                     for x in set(reaction_paths["node"])
                 ]
             )

{napistu-0.3.5 → napistu-0.3.6}/src/napistu/ontologies/dogma.py

@@ -4,6 +4,7 @@ import logging
 import pandas as pd
 
 from napistu import sbml_dfs_core
+from napistu import sbml_dfs_utils
 from napistu import source
 from napistu import identifiers
 from napistu import utils
@@ -59,7 +60,7 @@ def create_dogmatic_sbml_dfs(
     )
 
     # stub required but invariant variables
-    compartments_df = sbml_dfs_core._stub_compartments()
+    compartments_df = sbml_dfs_utils.stub_compartments()
     interaction_source = source.Source(init=True)
 
     # interactions table. This is required to create the sbml_dfs but we'll drop the info later