napistu 0.3.2.dev1__py3-none-any.whl → 0.3.4__py3-none-any.whl

napistu/ingestion/string.py

@@ -8,7 +8,6 @@ from napistu import sbml_dfs_core
 from napistu import source
 from napistu import utils
 from napistu.constants import BQB
-from napistu.constants import COMPARTMENTS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.ingestion import napistu_edgelist
 from napistu.ingestion.constants import SBML_SPECIES_DICT_IDENTIFIERS
@@ -28,6 +27,7 @@ from napistu.ingestion.constants import STRING_UPSTREAM_COMPARTMENT
 from napistu.ingestion.constants import STRING_UPSTREAM_NAME
 from napistu.ingestion.constants import STRING_URL_EXPRESSIONS
 from napistu.ingestion.constants import STRING_VERSION
+from napistu.ingestion.constants import GENERIC_COMPARTMENT
 from fs import open_fs
 
 logger = logging.getLogger(__name__)
@@ -297,7 +297,7 @@ def _build_interactor_edgelist(
     downstream_col_name: str = STRING_TARGET,
     add_reverse_interactions: bool = False,
     sbo_term: str = "interactor",
-    compartment: str = COMPARTMENTS["CELLULAR_COMPONENT"],
+    compartment: str = GENERIC_COMPARTMENT,
 ) -> pd.DataFrame:
     """Format STRING interactions as reactions."""
 

napistu/modify/gaps.py

@@ -15,18 +15,18 @@ from napistu import utils
 from napistu.network import net_create
 
 from napistu.constants import SBML_DFS
-from napistu.constants import COMPARTMENTS
 from napistu.constants import IDENTIFIERS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.constants import SBOTERM_NAMES
 from napistu.constants import SOURCE_SPEC
+from napistu.ingestion.constants import EXCHANGE_COMPARTMENT
 
 logger = logging.getLogger(__name__)
 
 
 def add_transportation_reactions(
     sbml_dfs: sbml_dfs_core.SBML_dfs,
-    exchange_compartment: str = COMPARTMENTS["CYTOSOL"],
+    exchange_compartment: str = EXCHANGE_COMPARTMENT,
 ) -> sbml_dfs_core.SBML_dfs:
     """
     Add transportation reactions to connect all forms of a protein across compartments.
@@ -73,7 +73,7 @@ def add_transportation_reactions(
 def update_sbml_df_with_exchange(
     species_needing_transport_rxns: np.ndarray,
     sbml_dfs: sbml_dfs_core.SBML_dfs,
-    exchange_compartment: str = COMPARTMENTS["CYTOSOL"],
+    exchange_compartment: str = EXCHANGE_COMPARTMENT,
 ) -> sbml_dfs_core.SBML_dfs:
     """
     Add transportation reactions between all locations of a set of molecular species by

napistu/network/precompute.py

@@ -120,7 +120,7 @@ def save_precomputed_distances(
     OSError
         If the file cannot be written to (permission issues, etc.)
     """
-    save_json(str(uri), precomputed_distances.to_dict(orient="index"))
+    save_json(str(uri), precomputed_distances.to_json())
 
 
 def load_precomputed_distances(uri: Union[str, Path]) -> pd.DataFrame:
@@ -143,12 +143,18 @@ def load_precomputed_distances(uri: Union[str, Path]) -> pd.DataFrame:
         If the specified file does not exist
     """
     try:
-        data_dict = load_json(str(uri))
+        json_string = load_json(str(uri))
+        df = pd.read_json(json_string)
+
+        # Convert integer columns to float
+        for col in df.columns:
+            if df[col].dtype in ["int64", "int32", "int16", "int8"]:
+                df[col] = df[col].astype(float)
+
+        return df
     except ResourceNotFound as e:
         raise FileNotFoundError(f"File not found: {uri}") from e
 
-    return pd.DataFrame.from_dict(data_dict, orient="index").rename(index=int)
-
 
 def _calculate_distances_subset(
     napistu_graph: NapistuGraph,

napistu/sbml_dfs_core.py

@@ -13,6 +13,7 @@ from napistu import identifiers
 from napistu import sbml_dfs_utils
 from napistu import source
 from napistu import utils
+from napistu.ingestion import sbml
 from napistu.constants import SBML_DFS
 from napistu.constants import SBML_DFS_SCHEMA
 from napistu.constants import IDENTIFIERS
@@ -23,9 +24,6 @@ from napistu.constants import BQB_PRIORITIES
 from napistu.constants import ONTOLOGY_PRIORITIES
 from napistu.constants import BQB
 from napistu.constants import BQB_DEFINING_ATTRS
-from napistu.constants import COMPARTMENTS
-from napistu.constants import COMPARTMENT_ALIASES
-from napistu.constants import COMPARTMENTS_GO_TERMS
 from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.constants import MINI_SBO_TO_NAME
 from napistu.constants import ONTOLOGIES
@@ -34,8 +32,9 @@ from napistu.constants import SBOTERM_NAMES
 from napistu.constants import SBO_ROLES_DEFS
 from napistu.constants import ENTITIES_W_DATA
 from napistu.constants import ENTITIES_TO_ENTITY_DATA
-from napistu.constants import CHARACTERISTIC_COMPLEX_ONTOLOGIES
-from napistu.ingestion import sbml
+from napistu.ingestion.constants import GENERIC_COMPARTMENT
+from napistu.ingestion.constants import COMPARTMENT_ALIASES
+from napistu.ingestion.constants import COMPARTMENTS_GO_TERMS
 from fs import open_fs
 
 logger = logging.getLogger(__name__)
@@ -145,7 +144,7 @@ class SBML_dfs:
                 if ent in sbml_model:
                     setattr(self, ent, sbml_model[ent])
         else:
-            self = sbml.sbml_df_from_sbml(self, sbml_model)
+            self = sbml.sbml_dfs_from_sbml(self, sbml_model)
 
         for ent in SBML_DFS_SCHEMA.OPTIONAL_ENTITIES:
             # Initialize optional entities if not set
@@ -1421,8 +1420,8 @@ def filter_to_characteristic_species_ids(
     complexes and non-characteristic annotations such as pubmed references and
     homologues.
 
-    Parameters
-    ----------
+        Parameters
+        ----------
     species_ids: pd.DataFrame
         A table of identifiers produced by sdbml_dfs.get_identifiers("species")
     max_complex_size: int
@@ -1471,12 +1470,6 @@ def filter_to_characteristic_species_ids(
     # add components within modestly sized protein complexes
     # look at HAS_PART IDs
     bqb_has_parts_species = species_ids[species_ids[IDENTIFIERS.BQB] == BQB.HAS_PART]
-    # filter to genes
-    bqb_has_parts_species = bqb_has_parts_species[
-        bqb_has_parts_species[IDENTIFIERS.ONTOLOGY].isin(
-            CHARACTERISTIC_COMPLEX_ONTOLOGIES
-        )
-    ]
 
     # number of species in a complex
     n_species_components = bqb_has_parts_species.value_counts(
@@ -1488,38 +1481,10 @@ def filter_to_characteristic_species_ids(
         ].index.get_level_values(SBML_DFS.S_ID)
     )
 
-    # number of complexes a species is part of
-    n_complexes_involvedin = bqb_has_parts_species.value_counts(
-        [IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]
-    )
-    promiscuous_component_identifiers_index = n_complexes_involvedin[
-        n_complexes_involvedin > max_promiscuity
-    ].index
-    promiscuous_component_identifiers = pd.Series(
-        data=[True] * len(promiscuous_component_identifiers_index),
-        index=promiscuous_component_identifiers_index,
-        name="is_shared_component",
-        dtype=bool,
+    filtered_bqb_has_parts = _filter_promiscuous_components(
+        bqb_has_parts_species, max_promiscuity
     )
 
-    if len(promiscuous_component_identifiers) == 0:
-        # no complexes to filter
-        return species_ids
-
-    filtered_bqb_has_parts = bqb_has_parts_species.merge(
-        promiscuous_component_identifiers,
-        left_on=[IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER],
-        right_index=True,
-        how="left",
-    )
-
-    filtered_bqb_has_parts["is_shared_component"] = filtered_bqb_has_parts[
-        "is_shared_component"
-    ].fillna(False)
-    # drop identifiers shared as components across many species
-    filtered_bqb_has_parts = filtered_bqb_has_parts[
-        ~filtered_bqb_has_parts["is_shared_component"]
-    ].drop(["is_shared_component"], axis=1)
     # drop species parts if there are many components
     filtered_bqb_has_parts = filtered_bqb_has_parts[
         ~filtered_bqb_has_parts[SBML_DFS.S_ID].isin(big_complex_sids)
@@ -1812,8 +1777,8 @@ def export_sbml_dfs(
         If True then treat genes, transcript, and proteins as separate species. If False
         then treat them interchangeably.
 
-    Returns
-    -------
+        Returns
+        -------
     None
 
     """
@@ -2257,7 +2222,7 @@ def _sbml_dfs_from_edgelist_check_cspecies_merge(
 
 
 def _stub_compartments(
-    stubbed_compartment: str = "CELLULAR_COMPONENT",
+    stubbed_compartment: str = GENERIC_COMPARTMENT,
 ) -> pd.DataFrame:
     """Stub Compartments
 
@@ -2281,7 +2246,6 @@ def _stub_compartments(
             f"{stubbed_compartment} is not defined in constants.COMPARTMENTS_GO_TERMS"
         )
 
-    stubbed_compartment_name = COMPARTMENTS[stubbed_compartment]
     stubbed_compartment_id = COMPARTMENTS_GO_TERMS[stubbed_compartment]
 
     formatted_uri = identifiers.format_uri(
@@ -2294,7 +2258,7 @@ def _stub_compartments(
 
     compartments_df = pd.DataFrame(
         {
-            SBML_DFS.C_NAME: [stubbed_compartment_name],
+            SBML_DFS.C_NAME: [stubbed_compartment],
             SBML_DFS.C_IDENTIFIERS: [identifiers.Identifiers([formatted_uri])],
         }
     )
@@ -2507,9 +2471,9 @@ def validate_sbml_dfs_table(table_data: pd.DataFrame, table_name: str) -> None:
     table_name : str
         Name of the table in the SBML_dfs schema
 
-    Raises
-    ------
-    ValueError
+        Raises
+        ------
+        ValueError
         If table_name is not in schema or validation fails
     """
     if table_name not in SBML_DFS_SCHEMA.SCHEMA:
@@ -2533,8 +2497,8 @@ def _perform_sbml_dfs_table_validation(
     This function performs the actual validation checks for any table against its schema,
     regardless of whether it's part of an SBML_dfs object or standalone.
 
-    Parameters
-    ----------
+        Parameters
+        ----------
     table_data : pd.DataFrame
         The table data to validate
     table_schema : dict
@@ -2542,9 +2506,9 @@ def _perform_sbml_dfs_table_validation(
     table_name : str
         Name of the table (for error messages)
 
-    Raises
-    ------
-    ValueError
+        Raises
+        ------
+        ValueError
         If the table does not conform to its schema:
         - Not a DataFrame
         - Wrong index name
@@ -2596,3 +2560,42 @@ def _perform_sbml_dfs_table_validation(
     # check for empty table
     if table_data.shape[0] == 0:
         raise ValueError(f"{table_name} contained no entries")
+
+
+def _filter_promiscuous_components(
+    bqb_has_parts_species: pd.DataFrame, max_promiscuity: int
+) -> pd.DataFrame:
+
+    # number of complexes a species is part of
+    n_complexes_involvedin = bqb_has_parts_species.value_counts(
+        [IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]
+    )
+    promiscuous_component_identifiers_index = n_complexes_involvedin[
+        n_complexes_involvedin > max_promiscuity
+    ].index
+    promiscuous_component_identifiers = pd.Series(
+        data=[True] * len(promiscuous_component_identifiers_index),
+        index=promiscuous_component_identifiers_index,
+        name="is_shared_component",
+        dtype=bool,
+    )
+
+    if len(promiscuous_component_identifiers) == 0:
+        return bqb_has_parts_species
+
+    filtered_bqb_has_parts = bqb_has_parts_species.merge(
+        promiscuous_component_identifiers,
+        left_on=[IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER],
+        right_index=True,
+        how="left",
+    )
+
+    filtered_bqb_has_parts["is_shared_component"] = (
+        filtered_bqb_has_parts["is_shared_component"].astype("boolean").fillna(False)
+    )
+    # drop identifiers shared as components across many species
+    filtered_bqb_has_parts = filtered_bqb_has_parts[
+        ~filtered_bqb_has_parts["is_shared_component"]
+    ].drop(["is_shared_component"], axis=1)
+
+    return filtered_bqb_has_parts

{napistu-0.3.2.dev1.dist-info → napistu-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.2.dev1
+Version: 0.3.4
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -19,7 +19,7 @@ Requires-Dist: Jinja2
 Requires-Dist: PyYAML<7.0.0,>=6.0.0
 Requires-Dist: click<9.0.0,>=8.0.0
 Requires-Dist: click-logging
-Requires-Dist: fs<3.0.0,>=2.4.0
+Requires-Dist: fs<3.0.0,>=2.4.16
 Requires-Dist: fs-gcsfs<2.0.0,>=1.5.0
 Requires-Dist: igraph
 Requires-Dist: matplotlib<4.0.0,>=3.5.0

{napistu-0.3.2.dev1.dist-info → napistu-0.3.4.dist-info}/RECORD

@@ -1,10 +1,10 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/__main__.py,sha256=PbzIsFAoFHNQuSyi-ql-D7tQLEOuqgmTcgk0PY-OGeU,28636
 napistu/consensus.py,sha256=UbKKSLP1O46e3Rk8d_aqNlhRHeR3sZRztAgIm7-XK6Y,69960
-napistu/constants.py,sha256=Wb1eir8DKSAjukNPknNkKTS4kQSqZjTcTjFaOYNyrC8,15317
+napistu/constants.py,sha256=10SuKl19koWvCaeM2k-5GDQxvJpKY3GaGFY_4VZivXw,12356
 napistu/identifiers.py,sha256=wsVriQdvPllA5uvh5CiREklA2tYW2MIB14dV7CPaMVU,34003
 napistu/indices.py,sha256=E_djN1XWc6l1lrFw_QnQXfZTKYTaUv8-jFPP7cHkY5A,9780
-napistu/sbml_dfs_core.py,sha256=5t2TYQeuvZeBqR3_eX0oEfAVHyaWSYMLkEO7zmSpo4Y,91779
+napistu/sbml_dfs_core.py,sha256=w4hoggMAXJ4Np45_2j-l92vOZg134eYa5Sg7SIdCaFo,91804
 napistu/sbml_dfs_utils.py,sha256=LJo6WWTrmnE58ZLDuibeeHk88uCdfunWdja7XxdZpps,11525
 napistu/source.py,sha256=9uUJrkY4jHaKlzz5nNcQQ8wUAep2pfqhlHxHw1hmEkI,13648
 napistu/utils.py,sha256=TcholWrFbRSu_sn9ODMA8y2YyAhekEKZjwf4S0WQNzI,33241
@@ -17,7 +17,7 @@ napistu/gcs/downloads.py,sha256=SvGv9WYr_Vt3guzyz1QiAuBndeKPTBtWSFLj1-QbLf4,6348
 napistu/gcs/utils.py,sha256=eLSsvewWJdCguyj2k0ozUGP5BTemaE1PZg41Z3aY5kM,571
 napistu/ingestion/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/ingestion/bigg.py,sha256=q0HeVSO6pFftbrxxVfFGUtMvCoak9Wi9ngMggRfjFjo,4364
-napistu/ingestion/constants.py,sha256=JmIefW8qektzpJr5t0GBtcAq-4bVLougTrOAegm5bl8,5410
+napistu/ingestion/constants.py,sha256=9UP47VImZ11q0kz17N3EJg2155USqLewwNWyKpA-cbA,8089
 napistu/ingestion/gtex.py,sha256=X0hSC1yrpf4xSJWFhpeNcnHwJzKDII2MvjfUqYA0JN8,3720
 napistu/ingestion/hpa.py,sha256=R27ExrryKQ4Crxv9ATXmBJCa-yd01TMOrDjkeBhIQac,5054
 napistu/ingestion/identifiers_etl.py,sha256=6ppDUA6lEZurdmVbiFLOUzphYbr-hndMhtqsQnq_yAc,5009
@@ -25,8 +25,8 @@ napistu/ingestion/napistu_edgelist.py,sha256=eVT9M7gmdBuGHcAYlvkD_zzvTtyzXufKWjw
 napistu/ingestion/obo.py,sha256=AQkIPWbjA464Lma0tx91JucWkIwLjC7Jgv5VHGRTDkE,9601
 napistu/ingestion/psi_mi.py,sha256=5eJjm7XWogL9oTyGqR52kntHClLwLsTePKqCvUGyi-w,10111
 napistu/ingestion/reactome.py,sha256=Hn9X-vDp4o_HK-OtaQvel3vJeZ8_TC1-4N2rruK9Oks,7099
-napistu/ingestion/sbml.py,sha256=muLTo-LTeL9lvvdEOjnSg82PQM2jpRExkK0UyF1qea8,20262
-napistu/ingestion/string.py,sha256=8igOC3j8cPdG_pMl14Z2OZsbvHUldPTJOJOUD7IJ-Mc,11676
+napistu/ingestion/sbml.py,sha256=N7neMwjTEF7OMhAcNvQJ29V_d3PqMLjLOZqvJTlK9q0,24743
+napistu/ingestion/string.py,sha256=YSWqaKm3I8bOixzvSA8fU4yfR2izddPYs4qJiqwjbxk,11678
 napistu/ingestion/trrust.py,sha256=ccjZc_eF3PdxxurnukiEo_e0-aKc_3z22NYbaJBtHdY,9774
 napistu/ingestion/yeast.py,sha256=bwFBNxRq-dLDaddgBL1hpfZj0eQ56nBXyR_9n0NZT9Y,5233
 napistu/matching/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
@@ -54,7 +54,7 @@ napistu/mcp/utils.py,sha256=WB4c6s8aPZLgi_Wvhhq0DE8Cnz2QGff0V8hrF1feVRg,1296
 napistu/modify/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/modify/constants.py,sha256=H6K6twzPlxt0yp6QLAxIx0Tp8YzYhtKKXPdmXi5V_QQ,3689
 napistu/modify/curation.py,sha256=sQeSO53ZLdn14ww2GSKkoP0vJnDpAoSWb-YDjUf5hDQ,21743
-napistu/modify/gaps.py,sha256=nhoo30iQai16NzYYfHQ4PE42psWp5hA20Oq7yae1pzw,26743
+napistu/modify/gaps.py,sha256=qprylC2BbSk_vPWayYPVT8lwURXDMOlW5zNLV_wMFZ4,26755
 napistu/modify/pathwayannot.py,sha256=xuBSMDFWbg_d6-Gzv0Td3Q5nnFTa-Qzic48g1b1AZtQ,48081
 napistu/modify/uncompartmentalize.py,sha256=U5X4Q7Z-YIkC8_711x3sU21vTVdv9rKfauwz4JNzl6c,9690
 napistu/network/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
@@ -67,7 +67,7 @@ napistu/network/net_create.py,sha256=2N5ocGmibdBxIUVtv3H36iFWwkbys9ECCERFRlByhLc
 napistu/network/net_propagation.py,sha256=89ZR4p2mGpkCCIemofZ53XbUjQsuNABxIc6UmF8A5n8,4935
 napistu/network/ng_utils.py,sha256=ijWDa5MTuULJpdV6dcVFGmLmtB_xy87jaUG7F5nvC_k,15240
 napistu/network/paths.py,sha256=S4ZaV0yVmI-o8sXfom5eXA3yy2IEbleYUyXEvnmVw98,17468
-napistu/network/precompute.py,sha256=xDIHWxGWwDyEw1sF1bQKHVbunI8qmeJvo3Iv7wADUys,8960
+napistu/network/precompute.py,sha256=_TyztdHucczZg1JacWuXfNp5NGRKBFMGfp8Imx7OBMM,9118
 napistu/ontologies/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/ontologies/constants.py,sha256=GyOFvezSxDK1VigATcruTKtNhjcYaid1ggulEf_HEtQ,4345
 napistu/ontologies/dogma.py,sha256=jGZS-J3d29AoUOow-HVjfVZQJ87lnqO5L1aozieN1ec,8825
@@ -81,7 +81,7 @@ napistu/rpy2/rids.py,sha256=AfXLTfTdonfspgAHYO0Ph7jSUWv8YuyT8x3fyLfAqc8,3413
 napistu/scverse/__init__.py,sha256=Lgxr3iMQAkTzXE9BNz93CndNP5djzerLvmHM-D0PU3I,357
 napistu/scverse/constants.py,sha256=0iAkhyJUIeFGHdLLU3fCaEU1O3Oix4qAsxr3CxGTjVs,653
 napistu/scverse/loading.py,sha256=jqiE71XB-wdV50GyZrauFNY0Lai4bX9Fm2Gv80VR8t8,27016
-napistu-0.3.2.dev1.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.4.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/conftest.py,sha256=XVkd0tQywhnf2cgab7fIjBo3NlaTVX3cO8HaRS2jIwM,3190
 tests/test_consensus.py,sha256=3dJvvPsPG7bHbw_FY4Pm647N_Gt_Ud9157OKYfPCUd4,9502
@@ -108,16 +108,16 @@ tests/test_network_net_create.py,sha256=VNFZTwQawAZQPDnVk_qFevgZErx5KyQZ24bMoZF4
 tests/test_network_net_propagation.py,sha256=9pKkUdduWejH4iKNCJXKFzAkdNpCfrMbiUWySgI_LH4,3244
 tests/test_network_ng_utils.py,sha256=CwDw4MKTPhVZXz2HA2XU2QjjBv8CXc1_yQ0drvkBkFw,724
 tests/test_network_paths.py,sha256=TWZnxY5bF3m6gahcxcYJGrBIawh2-_vUcec1LyPmXV8,1686
-tests/test_network_precompute.py,sha256=W1tuHM-dd90nk0vUUNP_xZ7EhCKSjigI5ndm8oq8l0c,8869
+tests/test_network_precompute.py,sha256=xMGmZI9DxcWhJxuP7GCZEqtmcOvDRNK2LSia0x94v0U,9018
 tests/test_ontologies_genodexito.py,sha256=hBlunyEPiKskqagjWKW5Z6DJwKvpueYHJLwbfyeeAdo,2256
 tests/test_ontologies_mygene.py,sha256=BuBLm8VatzpK39-Ew_fFTK9ueLE4eqmKIDS5UKE59n8,1541
 tests/test_ontologies_renaming.py,sha256=k7bQzP24zG7W3fpULwk1me2sOWEWlxylr4Mhx1_gJJY,3740
 tests/test_pathwayannot.py,sha256=bceosccNy9tgxQei_7j7ATBSSvBSxOngJvK-mAzR_K0,3312
 tests/test_rpy2_callr.py,sha256=UVzXMvYN3wcc-ikDIjH2sA4BqkbwiNbMm561BcbnbD4,2936
 tests/test_rpy2_init.py,sha256=APrNt9GEQV9va3vU5k250TxFplAoWFc-FJRFhM2GcDk,5927
-tests/test_sbml.py,sha256=-Lxr_Iu7zl15c98NLG-ty9d1V9lLYHsieKbU_s96F6s,471
-tests/test_sbml_dfs_core.py,sha256=z2dYl5-3ZvIsEeK_sHxm8VtWSdL81Eljz_9aeedlM6U,16806
-tests/test_sbml_dfs_utils.py,sha256=onFWdhrTix30XR1-CMrMXld37BYxEGi6TZrweugLDzI,505
+tests/test_sbml.py,sha256=f25zj1NogYrmLluvBDboLameTuCiQ309433Qn3iPvhg,1483
+tests/test_sbml_dfs_core.py,sha256=tFaLMMuVjTLuhL-wimvcBbodEp59dhyHvXZ-IlUGGeU,19222
+tests/test_sbml_dfs_utils.py,sha256=5lNzZ1NLOnFb_sZ0YWTgLzXy28yGNCtS_H8Q-W-T6Bw,2022
 tests/test_sbo.py,sha256=x_PENFaXYsrZIzOZu9cj_Wrej7i7SNGxgBYYvcigLs0,308
 tests/test_scverse_loading.py,sha256=bnU1lQSYYWhOAs0IIBoi4ZohqPokDQJ0n_rtkAfEyMU,29948
 tests/test_set_coverage.py,sha256=J-6m6LuOjcQa9pxRuWglSfJk4Ltm7kt_eOrn_Q-7P6Q,1604
@@ -126,8 +126,8 @@ tests/test_uncompartmentalize.py,sha256=nAk5kfAVLU9a2VWe2x2HYVcKqj-EnwmwddERIPRa
 tests/test_utils.py,sha256=JRJFmjDNZpjG59a-73JkTyGqa_a7Z8d0fE2cZt0CRII,22580
 tests/utils.py,sha256=SoWQ_5roJteFGcMaOeEiQ5ucwq3Z2Fa3AAs9iXHTsJY,749
 tests/test_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-napistu-0.3.2.dev1.dist-info/METADATA,sha256=go09DE0iiD9UQmhyGSTdq2iGLGgODt84uZ9vKbridIg,3418
-napistu-0.3.2.dev1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.2.dev1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.2.dev1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.2.dev1.dist-info/RECORD,,
+napistu-0.3.4.dist-info/METADATA,sha256=u0M0PcjZJds7ds-cV2MYar8maae9_ld_9FO--0G3xwA,3414
+napistu-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.3.4.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.3.4.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.3.4.dist-info/RECORD,,

tests/test_network_precompute.py

@@ -179,8 +179,11 @@ def test_precomputed_distances_neighborhoods():
                 right_on=join_key,
                 how="outer",
             )
-            .fillna(False)
         )
+        for col in ["in_precompute", "in_otf"]:
+            neighbor_comparison[col] = (
+                neighbor_comparison[col].astype("boolean").fillna(False)
+            )
         comparison_l.append(neighbor_comparison.assign(focal_sc_id=key))
 
     comparison_df = pd.concat(comparison_l)

tests/test_sbml.py

@@ -1,17 +1,48 @@
 from __future__ import annotations
 
-import pandas as pd
 from napistu import sbml_dfs_core
 from napistu.ingestion import sbml
+import pytest
+from pydantic import ValidationError
 
 
 def test_sbml_dfs(sbml_path):
     sbml_model = sbml.SBML(sbml_path)
-    _ = sbml_model.model
+    _ = sbml_dfs_core.SBML_dfs(sbml_model)
 
-    dfs = sbml_dfs_core.SBML_dfs(sbml_model)
-    dfs.validate()
 
-    assert type(dfs.get_cspecies_features()) is pd.DataFrame
-    assert type(dfs.get_species_features()) is pd.DataFrame
-    assert type(dfs.get_identifiers("species")) is pd.DataFrame
+def test_compartment_aliases_validation_positive():
+    """
+    Tests that a valid compartment aliases dictionary passes validation.
+    """
+    valid_aliases = {
+        "extracellular": ["ECM", "extracellular space"],
+        "cytosol": ["cytoplasm"],
+    }
+    # This should not raise an exception
+    sbml.CompartmentAliasesValidator.model_validate(valid_aliases)
+
+
+def test_compartment_aliases_validation_negative():
+    """
+    Tests that an invalid compartment aliases dictionary raises a ValidationError.
+    """
+    invalid_aliases = {
+        "extracellular": ["ECM"],
+        "not_a_real_compartment": ["fake"],
+    }
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate(invalid_aliases)
+
+
+def test_compartment_aliases_validation_bad_type():
+    """
+    Tests that a validation error is raised for incorrect data types.
+    """
+    # Test with a non-dict input
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate(["extracellular"])
+
+    # Test with incorrect value types in the dictionary
+    with pytest.raises(ValidationError):
+        sbml.CompartmentAliasesValidator.model_validate({"extracellular": "ECM"})

tests/test_sbml_dfs_core.py

@@ -10,7 +10,14 @@ from napistu.ingestion import sbml
 from napistu.modify import pathwayannot
 
 from napistu import identifiers as napistu_identifiers
-from napistu.constants import SBML_DFS, SBOTERM_NAMES
+from napistu.constants import (
+    SBML_DFS,
+    SBOTERM_NAMES,
+    BQB_DEFINING_ATTRS,
+    BQB_DEFINING_ATTRS_LOOSE,
+    BQB,
+    IDENTIFIERS,
+)
 from napistu.sbml_dfs_core import SBML_dfs
 
 
@@ -493,3 +500,84 @@ def test_remove_entity_data_nonexistent(sbml_dfs_w_data, caplog):
 
     # Validate the model is still valid
     sbml_dfs_w_data.validate()
+
+
+def test_filter_to_characteristic_species_ids():
+
+    species_ids_dict = {
+        SBML_DFS.S_ID: ["large_complex"] * 6
+        + ["small_complex"] * 2
+        + ["proteinA", "proteinB"]
+        + ["proteinC"] * 3
+        + [
+            "promiscuous_complexA",
+            "promiscuous_complexB",
+            "promiscuous_complexC",
+            "promiscuous_complexD",
+            "promiscuous_complexE",
+        ],
+        IDENTIFIERS.ONTOLOGY: ["complexportal"]
+        + ["HGNC"] * 7
+        + ["GO"] * 2
+        + ["ENSG", "ENSP", "pubmed"]
+        + ["HGNC"] * 5,
+        IDENTIFIERS.IDENTIFIER: [
+            "CPX-BIG",
+            "mem1",
+            "mem2",
+            "mem3",
+            "mem4",
+            "mem5",
+            "part1",
+            "part2",
+            "GO:1",
+            "GO:2",
+            "dna_seq",
+            "protein_seq",
+            "my_cool_pub",
+        ]
+        + ["promiscuous_complex"] * 5,
+        IDENTIFIERS.BQB: [BQB.IS]
+        + [BQB.HAS_PART] * 7
+        + [BQB.IS] * 2
+        + [
+            # these are retained if BQB_DEFINING_ATTRS_LOOSE is used
+            BQB.ENCODES,
+            BQB.IS_ENCODED_BY,
+            # this should always be removed
+            BQB.IS_DESCRIBED_BY,
+        ]
+        + [BQB.HAS_PART] * 5,
+    }
+
+    species_ids = pd.DataFrame(species_ids_dict)
+
+    characteristic_ids_narrow = sbml_dfs_core.filter_to_characteristic_species_ids(
+        species_ids,
+        defining_biological_qualifiers=BQB_DEFINING_ATTRS,
+        max_complex_size=4,
+        max_promiscuity=4,
+    )
+
+    EXPECTED_IDS = ["CPX-BIG", "GO:1", "GO:2", "part1", "part2"]
+    assert characteristic_ids_narrow[IDENTIFIERS.IDENTIFIER].tolist() == EXPECTED_IDS
+
+    characteristic_ids_loose = sbml_dfs_core.filter_to_characteristic_species_ids(
+        species_ids,
+        # include encodes and is_encoded_by as equivalent to is
+        defining_biological_qualifiers=BQB_DEFINING_ATTRS_LOOSE,
+        max_complex_size=4,
+        # expand promiscuity to default value
+        max_promiscuity=20,
+    )
+
+    EXPECTED_IDS = [
+        "CPX-BIG",
+        "GO:1",
+        "GO:2",
+        "dna_seq",
+        "protein_seq",
+        "part1",
+        "part2",
+    ] + ["promiscuous_complex"] * 5
+    assert characteristic_ids_loose[IDENTIFIERS.IDENTIFIER].tolist() == EXPECTED_IDS

tests/test_sbml_dfs_utils.py

@@ -1,6 +1,9 @@
 from __future__ import annotations
 
+import pandas as pd
+
 from napistu import sbml_dfs_utils
+from napistu.constants import BQB, BQB_DEFINING_ATTRS, BQB_DEFINING_ATTRS_LOOSE
 
 
 def test_id_formatter():
@@ -14,9 +17,47 @@ def test_id_formatter():
     assert list(input_vals) == inv_ids
 
 
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_id_formatter()
+def test_get_characteristic_species_ids():
+    """
+    Test get_characteristic_species_ids function with both dogmatic and non-dogmatic cases.
+    """
+    # Create mock species identifiers data
+    mock_species_ids = pd.DataFrame(
+        {
+            "s_id": ["s1", "s2", "s3", "s4", "s5"],
+            "identifier": ["P12345", "CHEBI:15377", "GO:12345", "P67890", "P67890"],
+            "ontology": ["uniprot", "chebi", "go", "uniprot", "chebi"],
+            "bqb": [
+                "BQB_IS",
+                "BQB_IS",
+                "BQB_HAS_PART",
+                "BQB_HAS_VERSION",
+                "BQB_ENCODES",
+            ],
+        }
+    )
+
+    # Create mock SBML_dfs object
+    class MockSBML_dfs:
+        def get_identifiers(self, entity_type):
+            return mock_species_ids
+
+    mock_sbml = MockSBML_dfs()
+
+    # Test dogmatic case (default)
+    expected_bqbs = BQB_DEFINING_ATTRS + [BQB.HAS_PART]  # noqa: F841
+    dogmatic_result = sbml_dfs_utils.get_characteristic_species_ids(mock_sbml)
+    expected_dogmatic = mock_species_ids.query("bqb in @expected_bqbs")
+
+    pd.testing.assert_frame_equal(dogmatic_result, expected_dogmatic, check_like=True)
+
+    # Test non-dogmatic case
+    expected_bqbs = BQB_DEFINING_ATTRS_LOOSE + [BQB.HAS_PART]  # noqa: F841
+    non_dogmatic_result = sbml_dfs_utils.get_characteristic_species_ids(
+        mock_sbml, dogmatic=False
+    )
+    expected_non_dogmatic = mock_species_ids.query("bqb in @expected_bqbs")
+
+    pd.testing.assert_frame_equal(
+        non_dogmatic_result, expected_non_dogmatic, check_like=True
+    )