napistu 0.3.7__py3-none-any.whl → 0.4.1__py3-none-any.whl

napistu/utils.py

@@ -7,24 +7,24 @@ import logging
 import os
 import pickle
 import re
+import requests
 import shutil
 import urllib.request as request
 import zipfile
 from contextlib import closing
 from itertools import starmap
 from textwrap import fill
-from typing import Any
-from typing import Union
-from typing import Optional
-from typing import List
+from typing import Any, List, Optional, Union
 from urllib.parse import urlparse
-import requests
+from pathlib import Path
 from requests.adapters import HTTPAdapter
 from requests.adapters import Retry
 
 import igraph as ig
 import numpy as np
 import pandas as pd
+import pyarrow as pa
+import pyarrow.parquet as pq
 from fs import open_fs
 from fs.copy import copy_dir
 from fs.copy import copy_file
@@ -604,6 +604,81 @@ def load_json(uri: str) -> Any:
         return json.loads(txt)
 
 
+def save_parquet(
+    df: pd.DataFrame, uri: Union[str, Path], compression: str = "snappy"
+) -> None:
+    """
+    Write a DataFrame to a single Parquet file.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        The DataFrame to save
+    uri : Union[str, Path]
+        Path where to save the Parquet file. Can be a local path or a GCS URI.
+        Recommended extensions: .parquet or .pq
+    compression : str, default 'snappy'
+        Compression algorithm. Options: 'snappy', 'gzip', 'brotli', 'lz4', 'zstd'
+
+    Raises
+    ------
+    OSError
+        If the file cannot be written to (permission issues, etc.)
+    """
+
+    uri_str = str(uri)
+
+    # Warn about non-standard extensions
+    if not any(uri_str.endswith(ext) for ext in [".parquet", ".pq"]):
+        logger.warning(
+            f"File '{uri_str}' doesn't have a standard Parquet extension (.parquet or .pq)"
+        )
+
+    target_base, target_path = get_target_base_and_path(uri_str)
+
+    with open_fs(target_base, create=True) as target_fs:
+        with target_fs.openbin(target_path, "w") as f:
+            # Convert to Arrow table and write as single file
+            table = pa.Table.from_pandas(df)
+            pq.write_table(
+                table,
+                f,
+                compression=compression,
+                use_dictionary=True,  # Efficient for repeated values
+                write_statistics=True,  # Enables query optimization
+            )
+
+
+def load_parquet(uri: Union[str, Path]) -> pd.DataFrame:
+    """
+    Read a DataFrame from a Parquet file.
+
+    Parameters
+    ----------
+    uri : Union[str, Path]
+        Path to the Parquet file to load
+
+    Returns
+    -------
+    pd.DataFrame
+        The DataFrame loaded from the Parquet file
+
+    Raises
+    ------
+    FileNotFoundError
+        If the specified file does not exist
+    """
+    try:
+        target_base, target_path = get_target_base_and_path(str(uri))
+
+        with open_fs(target_base) as target_fs:
+            with target_fs.openbin(target_path, "r") as f:
+                return pd.read_parquet(f, engine="pyarrow")
+
+    except ResourceNotFound as e:
+        raise FileNotFoundError(f"File not found: {uri}") from e
+
+
 def extract_regex_search(regex: str, query: str, index_value: int = 0) -> str:
     """
     Match an identifier substring and otherwise throw an error

{napistu-0.3.7.dist-info → napistu-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.7
+Version: 0.4.1
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -27,6 +27,7 @@ Requires-Dist: mygene<4.0.0,>=3.0.0
 Requires-Dist: numpy<3.0.0,>=1.24.0
 Requires-Dist: pandas<3.0.0,>=1.5.0
 Requires-Dist: pydantic<3.0.0,>=2.0.0
+Requires-Dist: pyarrow<20.0.0,>=15.0.0
 Requires-Dist: python-libsbml
 Requires-Dist: requests>=2.25.0
 Requires-Dist: scipy<2.0.0,>=1.10.0
@@ -51,7 +52,6 @@ Requires-Dist: markdown>=3.4.0; extra == "mcp"
 Requires-Dist: jupyter-client>=7.0.0; extra == "mcp"
 Requires-Dist: nbformat>=5.0.0; extra == "mcp"
 Provides-Extra: rpy2
-Requires-Dist: pyarrow<19.0.0,>=15.0.0; extra == "rpy2"
 Requires-Dist: rpy2<4.0.0,>=3.5.0; extra == "rpy2"
 Requires-Dist: rpy2-arrow<1.0.0,>=0.1.0; extra == "rpy2"
 Provides-Extra: scverse
@@ -61,7 +61,12 @@ Dynamic: license-file
 
 # Napistu Python Library
 
+[![PyPI version](https://badge.fury.io/py/napistu.svg)](https://badge.fury.io/py/napistu)
 [![Documentation Status](https://readthedocs.org/projects/napistu/badge/?version=latest)](https://napistu.readthedocs.io/en/latest/?badge=latest)
+[![CI](https://github.com/napistu/napistu-py/actions/workflows/ci.yml/badge.svg)](https://github.com/napistu/napistu-py/actions/workflows/ci.yml)
+[![Release](https://github.com/napistu/napistu-py/actions/workflows/release.yml/badge.svg)](https://github.com/napistu/napistu-py/actions/workflows/release.yml)
+[![Deploy to Cloud Run](https://github.com/napistu/napistu-py/actions/workflows/deploy.yml/badge.svg)](https://github.com/napistu/napistu-py/actions/workflows/deploy.yml)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 This Python package hosts the majority of the algorithmic code for the [Napistu project](https://github.com/napistu/napistu).
 

{napistu-0.3.7.dist-info → napistu-0.4.1.dist-info}/RECORD

@@ -1,18 +1,18 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
-napistu/__main__.py,sha256=cml91Be1r_eyWeel_KNSWC-42AbMXWsrKZGf4PVgkaE,28997
+napistu/__main__.py,sha256=xwlbh_0Ig3a-yG6BIJRiDPSN9R2HnX2pEBvlodlO6h4,29015
 napistu/consensus.py,sha256=xWXiqIM6ot-SSPJZXTrVpohbINSCkZXBtRi-5REfk_g,69897
-napistu/constants.py,sha256=dbofeN0HKdmjYluyKuj6nfiL88j69otPhuw2krEhHz8,13240
+napistu/constants.py,sha256=8sp1l0cxu2rsnCrWBEEwhcBKvDtc4u0D0f_72zILLW0,13427
 napistu/identifiers.py,sha256=e2-nTVzr5AINa0y1ER9218bKXyF2kAeJ9At22S4Z00o,33914
 napistu/indices.py,sha256=Zjg3gE0JQ3T879lCPazYg-WXVE6hvcAr713ZKpJ32rk,9830
-napistu/sbml_dfs_core.py,sha256=3Z2Kg-aVnZMGK9iK-_vztY2ORgNpta8BUMuWEZg80iE,73125
-napistu/sbml_dfs_utils.py,sha256=M0qNbxWkVnPCeUYTBZAD5i4PgV66qu6JE36Eb1dKaMw,43617
+napistu/sbml_dfs_core.py,sha256=s0OyoHs-AjOcbZu1d3KNkW_PI7Rxbhu5ZLpfQeO4iY8,72639
+napistu/sbml_dfs_utils.py,sha256=w5dFcJFDKnKDK9jxPOCuCW8IccxdXmyNmP9vCUhVdf8,46184
 napistu/source.py,sha256=UGpN70bqbC9gnKmM0ivSdQYim9hfzgABeXoQKzRr9oU,13646
-napistu/utils.py,sha256=ckYaIYjUOy22A3ojS7wSUabq_A1rJMMOk6QLrcbr3sU,33560
+napistu/utils.py,sha256=PEAsLn7VGN8JlNJQcAMYpjF1gr2mWmb5IqBsypP9hi0,35768
 napistu/context/__init__.py,sha256=LQBEqipcHKK0E5UlDEg1ct-ymCs93IlUrUaH8BCevf0,242
 napistu/context/discretize.py,sha256=Qq7zg46F_I-PvQIT2_pEDQV7YEtUQCxKoRvT5Gu9QsE,15052
 napistu/context/filtering.py,sha256=l1oq-43ysSGqU9VmhTOO_pYT4DSMf20yxvktPC1MI0I,13696
 napistu/gcs/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
-napistu/gcs/constants.py,sha256=g6PaU99GY5XvaRHx4BGmWHUpcJ36-Zh_GzeNVOeHviM,2856
+napistu/gcs/constants.py,sha256=5hLp1pL7SHEiscLNKcdI4IeOP4vUaasBCIHJrEedl0o,2909
 napistu/gcs/downloads.py,sha256=SvGv9WYr_Vt3guzyz1QiAuBndeKPTBtWSFLj1-QbLf4,6348
 napistu/gcs/utils.py,sha256=eLSsvewWJdCguyj2k0ozUGP5BTemaE1PZg41Z3aY5kM,571
 napistu/ingestion/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
@@ -21,7 +21,7 @@ napistu/ingestion/constants.py,sha256=9UP47VImZ11q0kz17N3EJg2155USqLewwNWyKpA-cb
 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
-napistu/ingestion/napistu_edgelist.py,sha256=eVT9M7gmdBuGHcAYlvkD_zzvTtyzXufKWjwDiT8OxF4,3572
+napistu/ingestion/napistu_edgelist.py,sha256=4RLXsoIk_-Atu-Nqme_t1JpEpBET26VIY2Y_Hcd3sMw,3580
 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
@@ -31,7 +31,7 @@ napistu/ingestion/trrust.py,sha256=_6hIS48O3tRpMxX-FdIC57ekhCcV7J4owUzoaYnRqZo,9
 napistu/ingestion/yeast.py,sha256=7XwdkmgOnG1MYauKSk9nSK6fHemDrtXEPcS4ebs1_so,5268
 napistu/matching/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/matching/constants.py,sha256=j4XSOE9Bpma9F6apVJ1LijKOUPgRk8Geo_u_rvNtpSU,610
-napistu/matching/interactions.py,sha256=XrzZvH1zgeaZLq3qhpsV0tx4BFgvNvkjM47l8ZUEOH4,18798
+napistu/matching/interactions.py,sha256=NatrboXH0B7Jc2pics6mgmnVvp_bXFGBhVsYE1a-JKo,18992
 napistu/matching/mount.py,sha256=8JEtiDIy7qdjWyDAs0vuVwEQkpwRf5ah4xMLZ4jKHag,19428
 napistu/matching/species.py,sha256=U8OfzmDN9dMwemdnzQdV19bWfjY8MLJ9-wf83siK1bM,18888
 napistu/mcp/__init__.py,sha256=EmtcdtYyfhXdxxPB5cY_pshXnFv6XZ5CtRU0JMHn3aQ,2074
@@ -54,24 +54,26 @@ 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=qprylC2BbSk_vPWayYPVT8lwURXDMOlW5zNLV_wMFZ4,26755
+napistu/modify/gaps.py,sha256=CV-bdSfanhrnCIFVWfNuQJbtjvj4hsEwheKYR-Z3tNA,26844
 napistu/modify/pathwayannot.py,sha256=xuBSMDFWbg_d6-Gzv0Td3Q5nnFTa-Qzic48g1b1AZtQ,48081
 napistu/modify/uncompartmentalize.py,sha256=y5LkXn5x6u80dB_McfAIh88BxZGIAVFLujkP7sPNRh0,9690
 napistu/network/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
-napistu/network/constants.py,sha256=fC1njZDu6in1JiaZ1-T1_fhmmkcc2HKSUUomDVyQ7Dw,5789
-napistu/network/data_handling.py,sha256=mxplWwyXNrjZRN-jjWWUI9IZOqX69k8qSMDIrL9h0Og,14736
+napistu/network/constants.py,sha256=LPsMtbAoier9Qor9REA7UIx7vnBtDpxMbcv3yI-c-2s,6441
+napistu/network/data_handling.py,sha256=KncrAKjXI3169BgVE-SnY8FkpVF60JnUwfMHtbqvsTc,14725
 napistu/network/ig_utils.py,sha256=JSlf_sZtw3DiiSIiYJ2YqJFEP4hVJMwNRox2qYTA4zY,11470
-napistu/network/napistu_graph_core.py,sha256=2NbjiLcDcFWFyX1MuN17pobPDgoQFtcYWOwuPSFTT4g,10429
-napistu/network/neighborhoods.py,sha256=Q9HWUvf_J4a_4RQDKd7ywEy4cp3Wq2OPOfVsotDbEe0,56098
-napistu/network/net_create.py,sha256=aAw6kfHREpkMEcwQFgwU5CHg--b8YLO559surQLRXZI,69408
-napistu/network/net_propagation.py,sha256=89ZR4p2mGpkCCIemofZ53XbUjQsuNABxIc6UmF8A5n8,4935
-napistu/network/ng_utils.py,sha256=ijWDa5MTuULJpdV6dcVFGmLmtB_xy87jaUG7F5nvC_k,15240
-napistu/network/paths.py,sha256=-dxRtaBRDYwuMw9DByGSn5OXFC3umDeO2zvVvD0TdWE,17452
-napistu/network/precompute.py,sha256=pIXCCE6Mf6HY8o-fiwUaOxvQ_9_mevK0vaC8fND4RZk,9141
+napistu/network/neighborhoods.py,sha256=g5QeGaizSfW4nNe9YZY86g8q79EQmuvSwipaNPnOVqA,56121
+napistu/network/net_create.py,sha256=Ylt4osGWPfj9MSDPy67pOTmLERGtS3cStR94UaqmXes,59082
+napistu/network/net_create_utils.py,sha256=zajwaz2xAij_9fEnD77SgBw_EnNAnJ8jBCmmK2rk_bA,24672
+napistu/network/net_propagation.py,sha256=S70zl0W4aYu5RPf5PZh829xT1xUyeTdi3TcIaFeYMww,4924
+napistu/network/ng_core.py,sha256=dGnTUKR4WtnvaYMyIHqqF55FY4mJSa7wjA2LZ4cVB6U,11720
+napistu/network/ng_utils.py,sha256=c1tHXz_JcH01D5KovNQmRLTEVxpCkCe36otULq-liz8,15579
+napistu/network/paths.py,sha256=r6LVKVvX7i3ctBA5r-xvHfpH5Zsd0VDHUCtin2iag20,17453
+napistu/network/precompute.py,sha256=ibL0ByY7Wp5kEfIG3LUDpQKdvAeQX0DNkT_46g2YrGc,8367
 napistu/ontologies/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/ontologies/constants.py,sha256=GyOFvezSxDK1VigATcruTKtNhjcYaid1ggulEf_HEtQ,4345
 napistu/ontologies/dogma.py,sha256=VVj6NKBgNym4SdOSu8g22OohALj7cbObhIJmdY2Sfy0,8860
 napistu/ontologies/genodexito.py,sha256=ZZmb7V38BmFjy9VOGdxbD3-BD5tKGl5izr0nwO_eEdA,24967
+napistu/ontologies/id_tables.py,sha256=q_31eQwlkRNFzLOkJNT4Fp6ra6kkzFOByzgJu5WFh0U,8372
 napistu/ontologies/mygene.py,sha256=RMFQTWsLkeYxmsOPxxmeIya2phdcUMcF5V2abaS8MVg,11109
 napistu/ontologies/renaming.py,sha256=aZR5oxjeZhse026fuvFyQiKM8PVzbBT915J8AfXGv1M,7006
 napistu/rpy2/__init__.py,sha256=8WzSK_tmdcbyMUtb17OmqdQqbisqIBl8OQrDsaFDeX4,8356
@@ -81,9 +83,9 @@ 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-0.3.7.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.4.1.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/conftest.py,sha256=Tdw9-uYpnV1ZvdO9k9oto-JDEqMOTF05fsVps-EpmCE,6240
+tests/conftest.py,sha256=t-GHb0MvSsC-MyhkFpOy2K3t5fi7eaig_Rc2xEQC-t8,9678
 tests/test_consensus.py,sha256=Hzfrgp4SpkRDnEMVMD3f0UInSycndB8kKzC4wDDvRas,15076
 tests/test_constants.py,sha256=gJLDv7QMeeBiiupyMazj6mumk20KWvGMgm2myHMKKfc,531
 tests/test_context_discretize.py,sha256=5Mr9WqwHGYMO37M1TnMmSfC64UZ73mnoCiEM2IQHVDY,1667
@@ -101,33 +103,36 @@ 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_network_data_handling.py,sha256=oBSZuB3IRG9bwmD6n8FY-UZLe2UqGzXpNSxVtkHRSvE,12605
+tests/test_network_data_handling.py,sha256=4aS8z2AlKkVd-JhK4BQ8fjeiW8_bJ1hZ3cc71Jh7Glk,12716
 tests/test_network_ig_utils.py,sha256=Buoh570mNm5pcac3Hf6f3pevCjWfBwPfKuD8IkDLg58,2120
 tests/test_network_neighborhoods.py,sha256=8BV17m5X1OUd5FwasTTYUOkNYUHDPUkxOKH_VZCsyBE,631
-tests/test_network_net_create.py,sha256=LDjkA9boX8kH4wCLOpa0ENwN6JZU2c29w3qpYlhQ6Rs,16456
+tests/test_network_net_create.py,sha256=L0U91b4jVHDuC3DFo-_BUFVuv4GuSxZuLAo7r-7EJxY,12877
+tests/test_network_net_create_utils.py,sha256=0J6KIh2HBc4koFsvwMaul1QRtj5x92kR9HBdDZajnAw,18971
 tests/test_network_net_propagation.py,sha256=9pKkUdduWejH4iKNCJXKFzAkdNpCfrMbiUWySgI_LH4,3244
-tests/test_network_ng_utils.py,sha256=CwDw4MKTPhVZXz2HA2XU2QjjBv8CXc1_yQ0drvkBkFw,724
+tests/test_network_ng_core.py,sha256=w-iNBTtenennJhaLFauk952pEsk7W0-Fa8lPvIRqHyY,628
+tests/test_network_ng_utils.py,sha256=QVVuRnvCRfTSIlGdwQTIF9lr0wOwoc5gGeXAUY_AdgE,713
 tests/test_network_paths.py,sha256=TWZnxY5bF3m6gahcxcYJGrBIawh2-_vUcec1LyPmXV8,1686
-tests/test_network_precompute.py,sha256=8HqTSXdxdXuQqNewP3xxsps9UEtw6OVgPN_lUywXiNg,9012
+tests/test_network_precompute.py,sha256=zwJrKNC3s8rIrsyAQfQMYxbl8HZXUr7u09nMJ_K8jiU,9005
 tests/test_ontologies_genodexito.py,sha256=6fINyUiubHZqu7qxye09DQfJXw28ZMAJc3clPb-cCoY,2298
+tests/test_ontologies_id_tables.py,sha256=CpwpbmQvTc1BaVd6jbDKHAVE2etwN0vx93nC8jpnMlE,7265
 tests/test_ontologies_mygene.py,sha256=VkdRcKIWmcG6V-2dpfvsBiOJN5dO-j0RqZNxtJRcyBU,1583
 tests/test_ontologies_renaming.py,sha256=pawp3pV1hxW8nskWc4f2YHwMUqTilEEBD2BtpcSay5Q,3839
 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_rpy2_callr.py,sha256=V4a-QH5krgYOQRgqzksMzIkGAFjBqKOAqgprxrH6bE0,2904
+tests/test_rpy2_init.py,sha256=T3gnxC1O7XNvYM2P4018ikpPPAy-kwQLm7Erj0RfA-4,5895
 tests/test_sbml.py,sha256=f25zj1NogYrmLluvBDboLameTuCiQ309433Qn3iPvhg,1483
-tests/test_sbml_dfs_core.py,sha256=CH5OXNSAozWTl6qBvbHfgTG0NcgdlKJ_WcG0lTYBm3k,26217
-tests/test_sbml_dfs_utils.py,sha256=-EAW6N_elEOSQdsdRhnEdDhnZQH_weCGpnVOd2Xaepc,6963
+tests/test_sbml_dfs_core.py,sha256=nnLPpZTVtCznOBohk7CX67x6sMqktJWt-sZMWQKoaDs,26521
+tests/test_sbml_dfs_utils.py,sha256=gWIhzUEtQlOR9c1TiCyhlSAELmWnBSncn6vCEqH5hl0,11029
 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
 tests/test_source.py,sha256=hT0IlpexR5zP0OhWl5BBaho9d1aCYQlFZLwRIRRnw_Y,1969
 tests/test_uncompartmentalize.py,sha256=nAk5kfAVLU9a2VWe2x2HYVcKqj-EnwmwddERIPRax8c,1289
-tests/test_utils.py,sha256=ls0zETdSeupuWCsnycWbgBVwLs2aXLgrAO1jyEBrfao,23190
+tests/test_utils.py,sha256=qPSpV-Q9b6vmdycgaDmQqtcvzKnAVnN9j5xJ9x-T6bg,23959
 tests/utils.py,sha256=SoWQ_5roJteFGcMaOeEiQ5ucwq3Z2Fa3AAs9iXHTsJY,749
 tests/test_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-napistu-0.3.7.dist-info/METADATA,sha256=59xinCTQICD-lrDm7UR5wdnScq6LHsXy553S6vCRk4Q,3414
-napistu-0.3.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.7.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.7.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.7.dist-info/RECORD,,
+napistu-0.4.1.dist-info/METADATA,sha256=zl_710wCsatB3lKZAgHba-MLEOPSDOyrxs3b5FB6toA,4078
+napistu-0.4.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.4.1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.4.1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.4.1.dist-info/RECORD,,

tests/conftest.py

@@ -17,7 +17,7 @@ from napistu.sbml_dfs_core import SBML_dfs
 from napistu.source import Source
 from napistu.ingestion.sbml import SBML
 from napistu.network.net_create import process_napistu_graph
-from napistu.constants import SBML_DFS
+from napistu.constants import SBML_DFS, MINI_SBO_FROM_NAME, SBOTERM_NAMES
 
 
 @fixture
@@ -139,6 +139,107 @@ def napistu_graph_undirected(sbml_dfs):
     )
 
 
+@pytest.fixture
+def reaction_species_examples():
+    """
+    Pytest fixture providing a dictionary of example reaction species DataFrames for various test cases.
+    """
+
+    d = dict()
+    d["valid_interactor"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.INTERACTOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.INTERACTOR],
+            ],
+            SBML_DFS.SC_ID: ["sc1", "sc2"],
+            SBML_DFS.STOICHIOMETRY: [0, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["invalid_interactor"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.INTERACTOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT],
+            ],
+            SBML_DFS.SC_ID: ["sc1", "sc2"],
+            SBML_DFS.STOICHIOMETRY: [0, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["sub_and_prod"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.REACTANT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT],
+            ],
+            SBML_DFS.SC_ID: ["sub", "prod"],
+            SBML_DFS.STOICHIOMETRY: [-1, 1],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["stimulator"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.REACTANT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR],
+            ],
+            SBML_DFS.SC_ID: ["sub", "prod", "stim"],
+            SBML_DFS.STOICHIOMETRY: [-1, 1, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["all_entities"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.REACTANT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.CATALYST],
+            ],
+            SBML_DFS.SC_ID: ["sub", "prod", "stim", "cat"],
+            SBML_DFS.STOICHIOMETRY: [-1, 1, 0, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["no_substrate"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.INHIBITOR],
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.CATALYST],
+            ],
+            SBML_DFS.SC_ID: ["prod", "stim1", "stim2", "inh", "cat"],
+            SBML_DFS.STOICHIOMETRY: [1, 0, 0, 0, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["single_species"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT]],
+            SBML_DFS.SC_ID: ["lone_prod"],
+            SBML_DFS.STOICHIOMETRY: [1],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    d["activator_and_inhibitor_only"] = pd.DataFrame(
+        {
+            SBML_DFS.SBO_TERM: [
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR],  # activator
+                MINI_SBO_FROM_NAME[SBOTERM_NAMES.INHIBITOR],  # inhibitor
+            ],
+            SBML_DFS.SC_ID: ["act", "inh"],
+            SBML_DFS.STOICHIOMETRY: [0, 0],
+        }
+    ).set_index(SBML_DFS.SBO_TERM)
+
+    return d
+
+
 # Define custom markers for platforms
 def pytest_configure(config):
     config.addinivalue_line("markers", "skip_on_windows: mark test to skip on Windows")

tests/test_network_data_handling.py

@@ -6,6 +6,7 @@ import igraph as ig
 import pandas as pd
 
 from napistu.network import data_handling, net_create
+from napistu.network.constants import GRAPH_WIRING_APPROACHES
 
 
 # Fixtures
@@ -226,7 +227,7 @@ def test_add_results_table_to_graph(sbml_dfs_glucose_metabolism):
     """Test adding results table to graph."""
     # Create a test graph using create_napistu_graph
     graph = net_create.create_napistu_graph(
-        sbml_dfs_glucose_metabolism, directed=True, graph_type="regulatory"
+        sbml_dfs_glucose_metabolism, directed=True, wiring_approach="regulatory"
     )
 
     # Add some test data to sbml_dfs
@@ -300,7 +301,9 @@ def test_add_graph_species_attribute(sbml_dfs_glucose_metabolism):
     """Test adding species attributes to graph."""
     # Create a test graph using create_napistu_graph
     graph = net_create.create_napistu_graph(
-        sbml_dfs_glucose_metabolism, directed=True, graph_type="regulatory"
+        sbml_dfs_glucose_metabolism,
+        directed=True,
+        wiring_approach=GRAPH_WIRING_APPROACHES.REGULATORY,
     )
 
     # Add test data to sbml_dfs