napistu 0.3.6__py3-none-any.whl → 0.4.0__py3-none-any.whl

{napistu-0.3.6.dist-info → napistu-0.4.0.dist-info}/RECORD

@@ -1,13 +1,13 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
-napistu/__main__.py,sha256=JnPRdK9Revwpi0pouC7ZIZAMEunh9NIFuaq91RlPaR0,28648
-napistu/consensus.py,sha256=jsWpoXOzmNklFKasgOa5NEqbhoZvsgY0rLMFQddi6Vo,69945
-napistu/constants.py,sha256=IhjZZgP0Yb3pPn5mV5SeTWiimRSG2hH02UX_Y6c_aOo,12388
+napistu/__main__.py,sha256=xwlbh_0Ig3a-yG6BIJRiDPSN9R2HnX2pEBvlodlO6h4,29015
+napistu/consensus.py,sha256=xWXiqIM6ot-SSPJZXTrVpohbINSCkZXBtRi-5REfk_g,69897
+napistu/constants.py,sha256=CA-8OnE8LudLSML8piIdfPyRwgdp143Yh9eVwk3uLTw,13377
 napistu/identifiers.py,sha256=e2-nTVzr5AINa0y1ER9218bKXyF2kAeJ9At22S4Z00o,33914
-napistu/indices.py,sha256=E_djN1XWc6l1lrFw_QnQXfZTKYTaUv8-jFPP7cHkY5A,9780
-napistu/sbml_dfs_core.py,sha256=ntZfuKrjf42MV1EXhKUro298a1aSd6t6M-tt141x634,71129
-napistu/sbml_dfs_utils.py,sha256=aXbQIlx7Yv7TH_7YxSuHZLsf6w2UXd_iOzpALKzg608,43506
+napistu/indices.py,sha256=Zjg3gE0JQ3T879lCPazYg-WXVE6hvcAr713ZKpJ32rk,9830
+napistu/sbml_dfs_core.py,sha256=3Z2Kg-aVnZMGK9iK-_vztY2ORgNpta8BUMuWEZg80iE,73125
+napistu/sbml_dfs_utils.py,sha256=hfTxPerJIKuPC_jpGRCGHE8XMagsHTEe1h2E99VEWL4,44980
 napistu/source.py,sha256=UGpN70bqbC9gnKmM0ivSdQYim9hfzgABeXoQKzRr9oU,13646
-napistu/utils.py,sha256=TcholWrFbRSu_sn9ODMA8y2YyAhekEKZjwf4S0WQNzI,33241
+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
@@ -21,19 +21,19 @@ 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
-napistu/ingestion/sbml.py,sha256=N7neMwjTEF7OMhAcNvQJ29V_d3PqMLjLOZqvJTlK9q0,24743
-napistu/ingestion/string.py,sha256=eLboW-dkaaiypwW6DxM3P1mGVweM3wqGsJPYKyImMAI,11713
-napistu/ingestion/trrust.py,sha256=ccjZc_eF3PdxxurnukiEo_e0-aKc_3z22NYbaJBtHdY,9774
+napistu/ingestion/sbml.py,sha256=l8Z98yWuOIRGns8G4UNnoQz7v_xmukZb_IZ_5ye34Ko,25296
+napistu/ingestion/string.py,sha256=go1WGTkoLJejX7GQWf9bFeInFGAw4jNSpS2B_Zr5f_s,11364
+napistu/ingestion/trrust.py,sha256=_6hIS48O3tRpMxX-FdIC57ekhCcV7J4owUzoaYnRqZo,9204
 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=5-hmH8_UrvDmGfeJ1283trkCtPOC3BEmtYPcMHuZyNY,18893
+napistu/matching/species.py,sha256=U8OfzmDN9dMwemdnzQdV19bWfjY8MLJ9-wf83siK1bM,18888
 napistu/mcp/__init__.py,sha256=EmtcdtYyfhXdxxPB5cY_pshXnFv6XZ5CtRU0JMHn3aQ,2074
 napistu/mcp/__main__.py,sha256=o9C4J3YHkfh_pQi-K9OC5bwFmsNWHuK2l8GL7M90uFc,8057
 napistu/mcp/client.py,sha256=Zyy7unFFq9XPBDrr2Hl7dMVDTGoZbtj_YFuUH18QScs,6350
@@ -54,26 +54,27 @@ 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=5_gtdVtKHp5z-jtPXkHlZRiTsuHdZeA3TVI9u4SXqrQ,24725
+napistu/ontologies/genodexito.py,sha256=ZZmb7V38BmFjy9VOGdxbD3-BD5tKGl5izr0nwO_eEdA,24967
 napistu/ontologies/mygene.py,sha256=RMFQTWsLkeYxmsOPxxmeIya2phdcUMcF5V2abaS8MVg,11109
-napistu/ontologies/renaming.py,sha256=bL15T0CswjM81NFVIVp-3CEsa1kxIIk2xJ2kE5eTeeg,6817
+napistu/ontologies/renaming.py,sha256=aZR5oxjeZhse026fuvFyQiKM8PVzbBT915J8AfXGv1M,7006
 napistu/rpy2/__init__.py,sha256=8WzSK_tmdcbyMUtb17OmqdQqbisqIBl8OQrDsaFDeX4,8356
 napistu/rpy2/callr.py,sha256=yFCGobZTVgH1vJc5h0njAflvFr6zmCWIP-uuLWnZL-g,3701
 napistu/rpy2/constants.py,sha256=3thZa4UUfpDpXaUzGcqfDEyEIQaf4a_C01-O2pciZ7c,2760
@@ -81,15 +82,15 @@ 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-0.3.6.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.4.0.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/conftest.py,sha256=v8ZxJKqglEPlQ5ew3hM5eJQW2N0YhX9dOAaOQqdjyIc,4325
-tests/test_consensus.py,sha256=qnf6Ntc3q7oCji1aisH9Ziy6KbnQCf1REizinR8ier8,12454
+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
 tests/test_context_filtering.py,sha256=5dwC2d-99CpLdnzzTf2NvEzsRuwiIj-YU8NFqwtWp0g,9485
 tests/test_curation.py,sha256=-Q2J0D7qs9PGjHZX-rM4NxRLLdwxoapytSo_98q9ItY,3864
-tests/test_gaps.py,sha256=mGGeyx1vUnmEOF__bsqfCYq9Y8a1P-9mefqna4Qgc_k,4062
+tests/test_gaps.py,sha256=GBRb0E0RUwhXz2PsnfTsGszKDsHHvH-E3x9hUZG1DhM,4550
 tests/test_gcs.py,sha256=p_uQWuY2TcGj3zV3qFC-GXBqj4St8YENR_XRpQ6UH5g,570
 tests/test_identifiers.py,sha256=9QlGCG27zposzEvazEuZqoMausNMLLuUwfA3FuYU1mc,8345
 tests/test_indices.py,sha256=e_8GSNzIT4JHGmelX9PseJzFXTxo-TQAus3r21AUt7I,4547
@@ -101,33 +102,35 @@ 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=VNFZTwQawAZQPDnVk_qFevgZErx5KyQZ24bMoZF4T4w,16462
+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=xMGmZI9DxcWhJxuP7GCZEqtmcOvDRNK2LSia0x94v0U,9018
+tests/test_network_precompute.py,sha256=zwJrKNC3s8rIrsyAQfQMYxbl8HZXUr7u09nMJ_K8jiU,9005
 tests/test_ontologies_genodexito.py,sha256=6fINyUiubHZqu7qxye09DQfJXw28ZMAJc3clPb-cCoY,2298
 tests/test_ontologies_mygene.py,sha256=VkdRcKIWmcG6V-2dpfvsBiOJN5dO-j0RqZNxtJRcyBU,1583
-tests/test_ontologies_renaming.py,sha256=k7bQzP24zG7W3fpULwk1me2sOWEWlxylr4Mhx1_gJJY,3740
+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=Gef-wf0AI7adwS_CBUokiJCw7yyGzInwAUnAj7IRE-E,20311
-tests/test_sbml_dfs_utils.py,sha256=-EAW6N_elEOSQdsdRhnEdDhnZQH_weCGpnVOd2Xaepc,6963
+tests/test_sbml_dfs_core.py,sha256=CH5OXNSAozWTl6qBvbHfgTG0NcgdlKJ_WcG0lTYBm3k,26217
+tests/test_sbml_dfs_utils.py,sha256=WLR-b7VQ7VW4d9rv0DePPd9l-CG-FkpsHTa3OOvrbXQ,8630
 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=JRJFmjDNZpjG59a-73JkTyGqa_a7Z8d0fE2cZt0CRII,22580
+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-0.3.6.dist-info/METADATA,sha256=vJqqDnZ9MU1mmU_qTFgGnBgaYx4zt-yqg26H6VDkqz0,3414
-napistu-0.3.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.6.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.6.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.6.dist-info/RECORD,,
+napistu-0.4.0.dist-info/METADATA,sha256=fejMxUkQvO_EqBaZIowvumw5KRzXsjZ9gGGX0tc-YkE,3397
+napistu-0.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.4.0.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.4.0.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.4.0.dist-info/RECORD,,

tests/conftest.py

@@ -5,15 +5,19 @@ import os
 import sys
 import threading
 
+import pandas as pd
 import pytest
+from pytest import fixture
+from pytest import skip
 
 from napistu import consensus
 from napistu import indices
-from napistu import sbml_dfs_core
-from napistu.ingestion import sbml
-from napistu.network import net_create
-from pytest import fixture
-from pytest import skip
+from napistu.identifiers import Identifiers
+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, MINI_SBO_FROM_NAME, SBOTERM_NAMES
 
 
 @fixture
@@ -28,13 +32,13 @@ def sbml_path():
 
 @fixture
 def sbml_model(sbml_path):
-    sbml_model = sbml.SBML(sbml_path)
+    sbml_model = SBML(sbml_path)
     return sbml_model
 
 
 @fixture
 def sbml_dfs(sbml_model):
-    sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
+    sbml_dfs = SBML_dfs(sbml_model)
     return sbml_dfs
 
 
@@ -56,20 +60,73 @@ def sbml_dfs_glucose_metabolism():
     test_data = os.path.join(test_path, "test_data")
     sbml_path = os.path.join(test_data, "reactome_glucose_metabolism.sbml")
 
-    sbml_model = sbml.SBML(sbml_path).model
-    sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
+    sbml_model = SBML(sbml_path)
+    sbml_dfs = SBML_dfs(sbml_model)
 
     return sbml_dfs
 
 
+@pytest.fixture
+def minimal_valid_sbml_dfs():
+    """Create a minimal valid SBML_dfs object for testing."""
+    blank_id = Identifiers([])
+    source = Source(init=True)
+
+    sbml_dict = {
+        SBML_DFS.COMPARTMENTS: pd.DataFrame(
+            {
+                SBML_DFS.C_NAME: ["cytosol"],
+                SBML_DFS.C_IDENTIFIERS: [blank_id],
+                SBML_DFS.C_SOURCE: [source],
+            },
+            index=pd.Index(["C00001"], name=SBML_DFS.C_ID),
+        ),
+        SBML_DFS.SPECIES: pd.DataFrame(
+            {
+                SBML_DFS.S_NAME: ["ATP"],
+                SBML_DFS.S_IDENTIFIERS: [blank_id],
+                SBML_DFS.S_SOURCE: [source],
+            },
+            index=pd.Index(["S00001"], name=SBML_DFS.S_ID),
+        ),
+        SBML_DFS.COMPARTMENTALIZED_SPECIES: pd.DataFrame(
+            {
+                SBML_DFS.SC_NAME: ["ATP [cytosol]"],
+                SBML_DFS.S_ID: ["S00001"],
+                SBML_DFS.C_ID: ["C00001"],
+                SBML_DFS.SC_SOURCE: [source],
+            },
+            index=pd.Index(["SC00001"], name=SBML_DFS.SC_ID),
+        ),
+        SBML_DFS.REACTIONS: pd.DataFrame(
+            {
+                SBML_DFS.R_NAME: ["test_reaction"],
+                SBML_DFS.R_IDENTIFIERS: [blank_id],
+                SBML_DFS.R_SOURCE: [source],
+                SBML_DFS.R_ISREVERSIBLE: [False],
+            },
+            index=pd.Index(["R00001"], name=SBML_DFS.R_ID),
+        ),
+        SBML_DFS.REACTION_SPECIES: pd.DataFrame(
+            {
+                SBML_DFS.R_ID: ["R00001"],
+                SBML_DFS.SC_ID: ["SC00001"],
+                SBML_DFS.STOICHIOMETRY: [1.0],
+                SBML_DFS.SBO_TERM: ["SBO:0000011"],
+            },
+            index=pd.Index(["RSC00001"], name=SBML_DFS.RSC_ID),
+        ),
+    }
+
+    return SBML_dfs(sbml_dict)
+
+
 @fixture
 def napistu_graph(sbml_dfs):
     """
     Pytest fixture to create a NapistuGraph from sbml_dfs with directed=True and topology weighting.
     """
-    return net_create.process_napistu_graph(
-        sbml_dfs, directed=True, weighting_strategy="topology"
-    )
+    return process_napistu_graph(sbml_dfs, directed=True, weighting_strategy="topology")
 
 
 @fixture
@@ -77,11 +134,112 @@ def napistu_graph_undirected(sbml_dfs):
     """
     Pytest fixture to create a NapistuGraph from sbml_dfs with directed=False and topology weighting.
     """
-    return net_create.process_napistu_graph(
+    return process_napistu_graph(
         sbml_dfs, directed=False, weighting_strategy="topology"
     )
 
 
+@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_consensus.py

@@ -5,12 +5,13 @@ import os
 import pandas as pd
 import pytest
 from napistu import consensus
+from napistu import identifiers
 from napistu import indices
 from napistu import source
 from napistu import sbml_dfs_core
 from napistu.ingestion import sbml
 from napistu.modify import pathwayannot
-from napistu.constants import SBML_DFS, SBML_DFS_SCHEMA
+from napistu.constants import SBML_DFS, SBML_DFS_SCHEMA, SCHEMA_DEFS, IDENTIFIERS, BQB
 
 test_path = os.path.abspath(os.path.join(__file__, os.pardir))
 test_data = os.path.join(test_path, "test_data")
@@ -21,11 +22,16 @@ def test_reduce_to_consensus_ids():
 
     # test aggregating by IDs, by moving from compartmentalized_species -> species
 
-    sbml_model = sbml.SBML(sbml_path).model
-    comp_species_df = sbml.setup_cspecies(sbml_model)
-    comp_species_df.index.names = ["s_id"]
+    sbml_model = sbml.SBML(sbml_path)
+    comp_species_df = sbml_model._define_cspecies()
+    comp_species_df.index.names = [SBML_DFS.S_ID]
     consensus_species, species_lookup = consensus.reduce_to_consensus_ids(
-        comp_species_df, {"pk": "s_id", "id": "s_Identifiers"}
+        comp_species_df,
+        {
+            SCHEMA_DEFS.PK: SBML_DFS.S_ID,
+            SCHEMA_DEFS.ID: SBML_DFS.S_IDENTIFIERS,
+            SCHEMA_DEFS.TABLE: SBML_DFS.SPECIES,
+        },
     )
 
     assert isinstance(consensus_species, pd.DataFrame)
@@ -333,6 +339,68 @@ def test_report_consensus_merges_reactions(tmp_path):
     # No assertion: this is a smoke test to ensure the Series output is handled without error
 
 
+def test_build_consensus_identifiers_handles_merges_and_missing_ids():
+
+    # Three entities:
+    # - 'A' with identifier X
+    # - 'B' with no identifiers
+    # - 'C' with identifier X (should merge with 'A')
+    df = pd.DataFrame(
+        {
+            "s_id": ["A", "B", "C"],
+            "s_Identifiers": [
+                identifiers.Identifiers(
+                    [
+                        {
+                            IDENTIFIERS.ONTOLOGY: "test",
+                            IDENTIFIERS.IDENTIFIER: "X",
+                            IDENTIFIERS.BQB: BQB.IS,
+                        }
+                    ]
+                ),
+                identifiers.Identifiers([]),
+                identifiers.Identifiers(
+                    [
+                        {
+                            IDENTIFIERS.ONTOLOGY: "test",
+                            IDENTIFIERS.IDENTIFIER: "X",
+                            IDENTIFIERS.BQB: BQB.IS,
+                        }
+                    ]
+                ),
+            ],
+        }
+    ).set_index("s_id")
+
+    schema = SBML_DFS_SCHEMA.SCHEMA[SBML_DFS.SPECIES]
+
+    indexed_cluster, cluster_consensus_identifiers = (
+        consensus.build_consensus_identifiers(df, schema)
+    )
+
+    # All entities should be assigned to a cluster
+    assert set(indexed_cluster.index) == set(df.index)
+    assert not indexed_cluster.isnull().any()
+    # There should be a consensus identifier for each cluster
+    assert set(cluster_consensus_identifiers.index) == set(indexed_cluster.values)
+
+    # Entities 'A' and 'C' should be merged (same cluster)
+    assert indexed_cluster.loc["A"] == indexed_cluster.loc["C"]
+    # Entity 'B' should be in a different cluster
+    assert indexed_cluster.loc["B"] != indexed_cluster.loc["A"]
+
+    # The consensus identifier for the merged cluster should include identifier X
+    merged_cluster_id = indexed_cluster.loc["A"]
+    ids_obj = cluster_consensus_identifiers.loc[merged_cluster_id, schema["id"]]
+    assert any(i["identifier"] == "X" for i in getattr(ids_obj, "ids", []))
+
+    # The consensus identifier for the entity with no identifiers should be empty
+    noid_cluster_id = indexed_cluster.loc["B"]
+    ids_obj_noid = cluster_consensus_identifiers.loc[noid_cluster_id, schema["id"]]
+    assert hasattr(ids_obj_noid, "ids")
+    assert len(getattr(ids_obj_noid, "ids", [])) == 0
+
+
 ################################################
 # __main__
 ################################################
@@ -344,3 +412,4 @@ if __name__ == "__main__":
     test_passing_entity_data()
     test_consensus_ontology_check()
     test_report_consensus_merges_reactions()
+    test_build_consensus_identifiers_handles_merges_and_missing_ids()

tests/test_gaps.py

@@ -3,21 +3,32 @@ import numpy as np
 import warnings
 
 from napistu.sbml_dfs_core import SBML_dfs
-from napistu.constants import SBML_DFS
-from napistu.constants import MINI_SBO_FROM_NAME
 from napistu.identifiers import Identifiers
-
+from napistu.source import Source
 from napistu.modify import gaps
+from napistu.constants import BQB
+from napistu.constants import IDENTIFIERS
+from napistu.constants import ONTOLOGIES
+from napistu.constants import MINI_SBO_FROM_NAME
+from napistu.constants import SBML_DFS
+from napistu.ingestion.constants import EXCHANGE_COMPARTMENT, COMPARTMENTS
 
 
 # Minimal compartments table
 def _create_sbml_dfs_missing_transport_rxns():
 
+    blank_id = Identifiers([])
+    blank_source = Source(init=True)
+
     compartments = pd.DataFrame(
         {
-            SBML_DFS.C_NAME: ["mitochondria", "nucleus", "cytosol"],
-            SBML_DFS.C_IDENTIFIERS: [None],
-            SBML_DFS.C_SOURCE: [None],
+            SBML_DFS.C_NAME: [
+                COMPARTMENTS.MITOCHONDRIA,
+                COMPARTMENTS.NUCLEUS,
+                EXCHANGE_COMPARTMENT,
+            ],
+            SBML_DFS.C_IDENTIFIERS: [blank_id],
+            SBML_DFS.C_SOURCE: [blank_source],
         },
         index=["c_mito", "c_nucl", "c_cytosol"],
     ).rename_axis(SBML_DFS.C_ID)
@@ -30,15 +41,15 @@ def _create_sbml_dfs_missing_transport_rxns():
                 Identifiers(
                     [
                         {
-                            "ontology": "uniprot",
-                            "identifier": "PFAKE1",
-                            "bqb": "BQB_IS",
-                            "url": None,
+                            IDENTIFIERS.ONTOLOGY: ONTOLOGIES.UNIPROT,
+                            IDENTIFIERS.IDENTIFIER: "PFAKE1",
+                            IDENTIFIERS.BQB: BQB.IS,
+                            IDENTIFIERS.URL: None,
                         }
                     ]
                 )
             ],
-            SBML_DFS.S_SOURCE: [None],
+            SBML_DFS.S_SOURCE: [blank_source],
         },
         index=["s_A"],
     ).rename_axis(SBML_DFS.S_ID)
@@ -49,7 +60,7 @@ def _create_sbml_dfs_missing_transport_rxns():
             SBML_DFS.SC_NAME: ["A [mitochondria]", "A [nucleus]"],
             SBML_DFS.S_ID: ["s_A", "s_A"],
             SBML_DFS.C_ID: ["c_mito", "c_nucl"],
-            SBML_DFS.SC_SOURCE: [None],
+            SBML_DFS.SC_SOURCE: [blank_source],
         },
         index=["sc_A_mito", "sc_A_nucl"],
     ).rename_axis(SBML_DFS.SC_ID)
@@ -58,8 +69,8 @@ def _create_sbml_dfs_missing_transport_rxns():
     reactions = pd.DataFrame(
         {
             SBML_DFS.R_NAME: ["A [mito] -> A [mito]", "A [nucl] -> A [nucl]"],
-            SBML_DFS.R_IDENTIFIERS: [None],
-            SBML_DFS.R_SOURCE: [None],
+            SBML_DFS.R_IDENTIFIERS: [blank_id],
+            SBML_DFS.R_SOURCE: [blank_source],
             SBML_DFS.R_ISREVERSIBLE: [True, True],
         },
         index=["r_A_mito", "r_A_nucl"],
@@ -105,7 +116,7 @@ def test_add_transportation_reactions():
 
     sbml_dfs = _create_sbml_dfs_missing_transport_rxns()
     sbml_dfs_w_transport = gaps.update_sbml_df_with_exchange(
-        np.array(["s_A"]), sbml_dfs, exchange_compartment="cytosol"
+        np.array(["s_A"]), sbml_dfs, exchange_compartment=EXCHANGE_COMPARTMENT
     )
     assert sbml_dfs_w_transport.reactions.shape[0] == 4, "Should add 2 reactions"
     assert sbml_dfs_w_transport.reactions[

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