napistu 0.3.1.dev1__py3-none-any.whl → 0.3.3__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

@@ -2,12 +2,16 @@ from __future__ import annotations
 
 import logging
 import math
+from pathlib import Path
+from typing import Union
 
 import numpy as np
 import pandas as pd
+from fs.errors import ResourceNotFound
 
 from napistu.network.napistu_graph_core import NapistuGraph
 from napistu.network.ig_utils import validate_edge_attributes
+from napistu.utils import load_json, save_json
 
 logger = logging.getLogger(__name__)
 
@@ -75,21 +79,17 @@ def precompute_distances(
     # interate through all partitions of "from" nodes and find their shortest and lowest weighted paths
     unique_partitions = vs_to_partition.index.unique().tolist()
 
-    precomputed_distances = (
-        pd.concat(
-            [
-                _calculate_distances_subset(
-                    napistu_graph,
-                    vs_to_partition,
-                    vs_to_partition.loc[uq_part],
-                    weights_vars=weights_vars,
-                )
-                for uq_part in unique_partitions
-            ]
-        )
-        .reset_index(drop=True)
-        .query("sc_id_origin != sc_id_dest")
-    )
+    precomputed_distances = pd.concat(
+        [
+            _calculate_distances_subset(
+                napistu_graph,
+                vs_to_partition,
+                vs_to_partition.loc[uq_part],
+                weights_vars=weights_vars,
+            )
+            for uq_part in unique_partitions
+        ]
+    ).query("sc_id_origin != sc_id_dest")
 
     # filter by path length and/or weight
     filtered_precomputed_distances = _filter_precomputed_distances(
@@ -97,11 +97,59 @@ def precompute_distances(
         max_steps=max_steps,
         max_score_q=max_score_q,
         path_weights_vars=["path_" + w for w in weights_vars],
-    )
+    ).reset_index(drop=True)
 
     return filtered_precomputed_distances
 
 
+def save_precomputed_distances(
+    precomputed_distances: pd.DataFrame, uri: Union[str, Path]
+) -> None:
+    """
+    Save a precomputed distances DataFrame to a JSON file.
+
+    Parameters
+    ----------
+    precomputed_distances : pd.DataFrame
+        The precomputed distances DataFrame to save
+    uri : Union[str, Path]
+        Path where to save the JSON file. Can be a local path or a GCS URI.
+
+    Raises
+    ------
+    OSError
+        If the file cannot be written to (permission issues, etc.)
+    """
+    save_json(str(uri), precomputed_distances.to_dict(orient="index"))
+
+
+def load_precomputed_distances(uri: Union[str, Path]) -> pd.DataFrame:
+    """
+    Load a precomputed distances DataFrame from a JSON file.
+
+    Parameters
+    ----------
+    uri : Union[str, Path]
+        Path to the JSON file to load
+
+    Returns
+    -------
+    pd.DataFrame
+        The reconstructed precomputed distances DataFrame
+
+    Raises
+    ------
+    FileNotFoundError
+        If the specified file does not exist
+    """
+    try:
+        data_dict = load_json(str(uri))
+    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,
     vs_to_partition: pd.DataFrame,

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
@@ -35,7 +33,9 @@ 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 +145,7 @@ 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 +1421,8 @@ 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
@@ -1812,8 +1812,8 @@ 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 +2257,7 @@ 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 +2281,6 @@ 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 +2293,7 @@ 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 +2506,9 @@ 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 +2532,8 @@ 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 +2541,9 @@ 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

{napistu-0.3.1.dev1.dist-info → napistu-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.1.dev1
+Version: 0.3.3
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett

{napistu-0.3.1.dev1.dist-info → napistu-0.3.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
-napistu/__main__.py,sha256=1O_ZyCqNeHcyuL4rbbz6R7_jnPOAamKtTNXZ68gSA7U,28624
+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=M-zGc85bo1DDRe7uvyeEMUoD9Qf59Qz53nx4R6PwHvk,12483
 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=TUPp2nzaxRWkHKsXrbFzgp0_p5CzEGAmA5cg3dOUm84,91794
 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=aEynTDdKK_WJbEqBd6Q8iihXzuk3rheurkPcnh9bYqQ,7651
+napistu/network/precompute.py,sha256=xDIHWxGWwDyEw1sF1bQKHVbunI8qmeJvo3Iv7wADUys,8960
 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-0.3.1.dev1.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.3.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
@@ -101,21 +101,21 @@ tests/test_matching_species.py,sha256=OuUWp0-X3WYXkc-g51XyOqhp4MgO8cJvUSqt8ZvqRa
 tests/test_mcp_config.py,sha256=GTu9vywqAHTYkolywdYS_BEIW3gBzs4A4qcneMSPpRk,7007
 tests/test_mcp_documentation_utils.py,sha256=OW0N2N_2IOktbYTcCWhhWz4bANi8IB60l1q3DJi8Ra4,810
 tests/test_mcp_server.py,sha256=bP3PWVQsEfX6-lAgXKP32njdg__o65n2WuLvkxTTHkQ,11215
-tests/test_net_propagation.py,sha256=9pKkUdduWejH4iKNCJXKFzAkdNpCfrMbiUWySgI_LH4,3244
 tests/test_network_data_handling.py,sha256=oBSZuB3IRG9bwmD6n8FY-UZLe2UqGzXpNSxVtkHRSvE,12605
 tests/test_network_ig_utils.py,sha256=uojDLtL7oT9S9NJrXL8kBEHHFq5DB1GnJQT0v-gHEBE,632
 tests/test_network_neighborhoods.py,sha256=8BV17m5X1OUd5FwasTTYUOkNYUHDPUkxOKH_VZCsyBE,631
 tests/test_network_net_create.py,sha256=VNFZTwQawAZQPDnVk_qFevgZErx5KyQZ24bMoZF4T4w,16462
+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=iyqvxdlt_LQdAoFr8x-NZUbq5VH4Xo64fTg3gyXiWEg,7245
+tests/test_network_precompute.py,sha256=W1tuHM-dd90nk0vUUNP_xZ7EhCKSjigI5ndm8oq8l0c,8869
 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.py,sha256=f25zj1NogYrmLluvBDboLameTuCiQ309433Qn3iPvhg,1483
 tests/test_sbml_dfs_core.py,sha256=z2dYl5-3ZvIsEeK_sHxm8VtWSdL81Eljz_9aeedlM6U,16806
 tests/test_sbml_dfs_utils.py,sha256=onFWdhrTix30XR1-CMrMXld37BYxEGi6TZrweugLDzI,505
 tests/test_sbo.py,sha256=x_PENFaXYsrZIzOZu9cj_Wrej7i7SNGxgBYYvcigLs0,308
@@ -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-0.3.1.dev1.dist-info/METADATA,sha256=xBdE_PoEkP5RZVbK_GFot3AW7gnZZDFLAcD7F9rdKfc,3418
-napistu-0.3.1.dev1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.1.dev1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.1.dev1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.1.dev1.dist-info/RECORD,,
+napistu-0.3.3.dist-info/METADATA,sha256=Y5HCnBOuVO0Rvc1S-P3llVgWJSeBR1hes6UTt0cyhB4,3413
+napistu-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.3.3.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.3.3.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.3.3.dist-info/RECORD,,

tests/test_network_precompute.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
+import pytest
 import os
+import tempfile
 
 import numpy as np
 import pandas as pd
@@ -214,11 +216,59 @@ def test_precomputed_distances_neighborhoods():
     assert upstream_disagreement_w_precompute.shape[0] == 0
 
 
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_precomputed_distances()
-    test_precomputed_distances_shortest_paths()
-    test_precomputed_distances_neighborhoods()
+@pytest.mark.skip_on_windows
+def test_precomputed_distances_serialization():
+    """
+    Test that validates the serialization -> deserialization approach works correctly.
+
+    Notes
+    -----
+    This function creates a sample DataFrame with the structure of precomputed
+    distances data, saves it to a temporary JSON file, loads it back, and
+    validates that all data is preserved correctly through the serialization
+    round-trip.
+    """
+    # Create a sample DataFrame that mimics the precomputed distances structure
+    sample_data = {
+        "sc_id_origin": {
+            1: "SC00000000",
+            3: "SC00000003",
+            4: "SC00000004",
+            5: "SC00000005",
+            6: "SC00000011",
+        },
+        "sc_id_dest": {
+            1: "SC00000001",
+            3: "SC00000001",
+            4: "SC00000001",
+            5: "SC00000001",
+            6: "SC00000001",
+        },
+        "path_length": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+        "path_upstream_weights": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+        "path_weights": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+    }
+
+    # Create original DataFrame
+    original_df = pd.DataFrame(sample_data)
+
+    # Create a temporary file path
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".json", delete=False
+    ) as tmp_file:
+        temp_path = tmp_file.name
+
+    try:
+        # Test serialization
+        precompute.save_precomputed_distances(original_df, temp_path)
+
+        # Test deserialization
+        loaded_df = precompute.load_precomputed_distances(temp_path)
+
+        # Validate that the loaded DataFrame is identical to the original
+        pd.testing.assert_frame_equal(original_df, loaded_df, check_like=True)
+
+    finally:
+        # Clean up the temporary file
+        if os.path.exists(temp_path):
+            os.remove(temp_path)

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"})