napistu 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

napistu/source.py

@@ -223,7 +223,7 @@ def greedy_set_coverge_of_sources(
     Greedy Set Coverage of Sources
 
     Apply the greedy set coverge algorithm to find the minimal set of
-      sources which cover all entries
+    sources which cover all entries
 
     Parameters:
     source_df: pd.DataFrame

{napistu-0.3.4.dist-info → napistu-0.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.4
+Version: 0.3.6
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -43,7 +43,7 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: testcontainers; extra == "dev"
 Provides-Extra: mcp
-Requires-Dist: fastmcp<3.0.0,>=2.0.0; extra == "mcp"
+Requires-Dist: fastmcp<2.9.0,>=2.0.0; extra == "mcp"
 Requires-Dist: mcp<2.0.0,>=1.0.0; extra == "mcp"
 Requires-Dist: httpx>=0.24.0; extra == "mcp"
 Requires-Dist: beautifulsoup4<5.0.0,>=4.11.0; extra == "mcp"

{napistu-0.3.4.dist-info → napistu-0.3.6.dist-info}/RECORD

@@ -1,22 +1,22 @@
 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=10SuKl19koWvCaeM2k-5GDQxvJpKY3GaGFY_4VZivXw,12356
-napistu/identifiers.py,sha256=wsVriQdvPllA5uvh5CiREklA2tYW2MIB14dV7CPaMVU,34003
+napistu/__main__.py,sha256=JnPRdK9Revwpi0pouC7ZIZAMEunh9NIFuaq91RlPaR0,28648
+napistu/consensus.py,sha256=jsWpoXOzmNklFKasgOa5NEqbhoZvsgY0rLMFQddi6Vo,69945
+napistu/constants.py,sha256=IhjZZgP0Yb3pPn5mV5SeTWiimRSG2hH02UX_Y6c_aOo,12388
+napistu/identifiers.py,sha256=e2-nTVzr5AINa0y1ER9218bKXyF2kAeJ9At22S4Z00o,33914
 napistu/indices.py,sha256=E_djN1XWc6l1lrFw_QnQXfZTKYTaUv8-jFPP7cHkY5A,9780
-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/sbml_dfs_core.py,sha256=ntZfuKrjf42MV1EXhKUro298a1aSd6t6M-tt141x634,71129
+napistu/sbml_dfs_utils.py,sha256=aXbQIlx7Yv7TH_7YxSuHZLsf6w2UXd_iOzpALKzg608,43506
+napistu/source.py,sha256=UGpN70bqbC9gnKmM0ivSdQYim9hfzgABeXoQKzRr9oU,13646
 napistu/utils.py,sha256=TcholWrFbRSu_sn9ODMA8y2YyAhekEKZjwf4S0WQNzI,33241
 napistu/context/__init__.py,sha256=LQBEqipcHKK0E5UlDEg1ct-ymCs93IlUrUaH8BCevf0,242
 napistu/context/discretize.py,sha256=Qq7zg46F_I-PvQIT2_pEDQV7YEtUQCxKoRvT5Gu9QsE,15052
-napistu/context/filtering.py,sha256=oH1uNsf-_qSWRFtoxR8gDvCfZOzO3Ps40YO0qGAGXXs,13660
+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/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/bigg.py,sha256=f65--8ARe248eYCUJpFMF284Wz53sLyFyBuwelxHmJA,4340
 napistu/ingestion/constants.py,sha256=9UP47VImZ11q0kz17N3EJg2155USqLewwNWyKpA-cbA,8089
 napistu/ingestion/gtex.py,sha256=X0hSC1yrpf4xSJWFhpeNcnHwJzKDII2MvjfUqYA0JN8,3720
 napistu/ingestion/hpa.py,sha256=R27ExrryKQ4Crxv9ATXmBJCa-yd01TMOrDjkeBhIQac,5054
@@ -26,12 +26,12 @@ 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=YSWqaKm3I8bOixzvSA8fU4yfR2izddPYs4qJiqwjbxk,11678
+napistu/ingestion/string.py,sha256=eLboW-dkaaiypwW6DxM3P1mGVweM3wqGsJPYKyImMAI,11713
 napistu/ingestion/trrust.py,sha256=ccjZc_eF3PdxxurnukiEo_e0-aKc_3z22NYbaJBtHdY,9774
-napistu/ingestion/yeast.py,sha256=bwFBNxRq-dLDaddgBL1hpfZj0eQ56nBXyR_9n0NZT9Y,5233
+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=5GQCOFVvPPS7tCJodcSy51Fzh4c-biaP1dbbhgc8VLs,18818
+napistu/matching/interactions.py,sha256=XrzZvH1zgeaZLq3qhpsV0tx4BFgvNvkjM47l8ZUEOH4,18798
 napistu/matching/mount.py,sha256=8JEtiDIy7qdjWyDAs0vuVwEQkpwRf5ah4xMLZ4jKHag,19428
 napistu/matching/species.py,sha256=5-hmH8_UrvDmGfeJ1283trkCtPOC3BEmtYPcMHuZyNY,18893
 napistu/mcp/__init__.py,sha256=EmtcdtYyfhXdxxPB5cY_pshXnFv6XZ5CtRU0JMHn3aQ,2074
@@ -56,21 +56,21 @@ napistu/modify/constants.py,sha256=H6K6twzPlxt0yp6QLAxIx0Tp8YzYhtKKXPdmXi5V_QQ,3
 napistu/modify/curation.py,sha256=sQeSO53ZLdn14ww2GSKkoP0vJnDpAoSWb-YDjUf5hDQ,21743
 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/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/ig_utils.py,sha256=87vFuyLksYhfGoKBvjYeQt1yM_lg83m-14OaGbW64Wg,10478
+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=2N5ocGmibdBxIUVtv3H36iFWwkbys9ECCERFRlByhLc,69407
+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=S4ZaV0yVmI-o8sXfom5eXA3yy2IEbleYUyXEvnmVw98,17468
-napistu/network/precompute.py,sha256=_TyztdHucczZg1JacWuXfNp5NGRKBFMGfp8Imx7OBMM,9118
+napistu/network/paths.py,sha256=-dxRtaBRDYwuMw9DByGSn5OXFC3umDeO2zvVvD0TdWE,17452
+napistu/network/precompute.py,sha256=pIXCCE6Mf6HY8o-fiwUaOxvQ_9_mevK0vaC8fND4RZk,9141
 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
+napistu/ontologies/dogma.py,sha256=VVj6NKBgNym4SdOSu8g22OohALj7cbObhIJmdY2Sfy0,8860
 napistu/ontologies/genodexito.py,sha256=5_gtdVtKHp5z-jtPXkHlZRiTsuHdZeA3TVI9u4SXqrQ,24725
 napistu/ontologies/mygene.py,sha256=RMFQTWsLkeYxmsOPxxmeIya2phdcUMcF5V2abaS8MVg,11109
 napistu/ontologies/renaming.py,sha256=bL15T0CswjM81NFVIVp-3CEsa1kxIIk2xJ2kE5eTeeg,6817
@@ -81,13 +81,13 @@ 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-0.3.4.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.6.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
+tests/conftest.py,sha256=v8ZxJKqglEPlQ5ew3hM5eJQW2N0YhX9dOAaOQqdjyIc,4325
+tests/test_consensus.py,sha256=qnf6Ntc3q7oCji1aisH9Ziy6KbnQCf1REizinR8ier8,12454
 tests/test_constants.py,sha256=gJLDv7QMeeBiiupyMazj6mumk20KWvGMgm2myHMKKfc,531
 tests/test_context_discretize.py,sha256=5Mr9WqwHGYMO37M1TnMmSfC64UZ73mnoCiEM2IQHVDY,1667
-tests/test_context_filtering.py,sha256=0CWbmxKxerraJJgUqXiYHSYCfmRyOFvFRMG1u6mLbwI,9483
+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_gcs.py,sha256=p_uQWuY2TcGj3zV3qFC-GXBqj4St8YENR_XRpQ6UH5g,570
@@ -102,22 +102,22 @@ 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_ig_utils.py,sha256=uojDLtL7oT9S9NJrXL8kBEHHFq5DB1GnJQT0v-gHEBE,632
+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_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=xMGmZI9DxcWhJxuP7GCZEqtmcOvDRNK2LSia0x94v0U,9018
-tests/test_ontologies_genodexito.py,sha256=hBlunyEPiKskqagjWKW5Z6DJwKvpueYHJLwbfyeeAdo,2256
-tests/test_ontologies_mygene.py,sha256=BuBLm8VatzpK39-Ew_fFTK9ueLE4eqmKIDS5UKE59n8,1541
+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_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=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_sbml_dfs_core.py,sha256=Gef-wf0AI7adwS_CBUokiJCw7yyGzInwAUnAj7IRE-E,20311
+tests/test_sbml_dfs_utils.py,sha256=-EAW6N_elEOSQdsdRhnEdDhnZQH_weCGpnVOd2Xaepc,6963
 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-0.3.4.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,,
+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,,

tests/conftest.py

@@ -1,8 +1,11 @@
 from __future__ import annotations
 
+import functools
 import os
 import sys
+import threading
 
+import pytest
 
 from napistu import consensus
 from napistu import indices
@@ -109,3 +112,43 @@ def pytest_runtest_setup(item):
     # Skip tests that should run only on Unix
     if not is_unix and any(mark.name == "unix_only" for mark in item.iter_markers()):
         skip("Test runs only on Unix systems")
+
+
+def skip_on_timeout(timeout_seconds):
+    """Cross-platform decorator that skips a test if it takes longer than timeout_seconds"""
+
+    def decorator(func):
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            result = [None]
+            exception = [None]
+            finished = [False]
+
+            def target():
+                try:
+                    result[0] = func(*args, **kwargs)
+                    finished[0] = True
+                except Exception as e:
+                    exception[0] = e
+                    finished[0] = True
+
+            thread = threading.Thread(target=target)
+            thread.daemon = True
+            thread.start()
+            thread.join(timeout_seconds)
+
+            if not finished[0]:
+                # Thread is still running, timeout occurred
+                pytest.skip(f"Test skipped due to timeout ({timeout_seconds}s)")
+
+            if exception[0]:
+                raise exception[0]
+
+            return result[0]
+
+        return wrapper
+
+    return decorator
+
+
+pytest.skip_on_timeout = skip_on_timeout

tests/test_consensus.py

@@ -7,8 +7,10 @@ import pytest
 from napistu import consensus
 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
 
 test_path = os.path.abspath(os.path.join(__file__, os.pardir))
 test_data = os.path.join(test_path, "test_data")
@@ -246,6 +248,91 @@ def test_consensus_ontology_check():
     assert post_shared_onto_sp_set == {"chebi", "reactome", "uniprot"}
 
 
+def test_report_consensus_merges_reactions(tmp_path):
+    # Create two minimal SBML_dfs objects with a single reaction each, same r_id
+    r_id = "R00000001"
+    reactions = pd.DataFrame(
+        {
+            SBML_DFS.R_NAME: ["rxn1"],
+            SBML_DFS.R_IDENTIFIERS: [None],
+            SBML_DFS.R_SOURCE: [None],
+            SBML_DFS.R_ISREVERSIBLE: [False],
+        },
+        index=[r_id],
+    )
+    reactions.index.name = SBML_DFS.R_ID
+    reaction_species = pd.DataFrame(
+        {
+            SBML_DFS.R_ID: [r_id],
+            SBML_DFS.SC_ID: ["SC0001"],
+            SBML_DFS.STOICHIOMETRY: [1],
+            SBML_DFS.SBO_TERM: ["SBO:0000459"],
+        },
+        index=["RSC0001"],
+    )
+    reaction_species.index.name = SBML_DFS.RSC_ID
+    compartmentalized_species = pd.DataFrame(
+        {
+            SBML_DFS.SC_NAME: ["A [cytosol]"],
+            SBML_DFS.S_ID: ["S0001"],
+            SBML_DFS.C_ID: ["C0001"],
+            SBML_DFS.SC_SOURCE: [None],
+        },
+        index=["SC0001"],
+    )
+    compartmentalized_species.index.name = SBML_DFS.SC_ID
+    species = pd.DataFrame(
+        {
+            SBML_DFS.S_NAME: ["A"],
+            SBML_DFS.S_IDENTIFIERS: [None],
+            SBML_DFS.S_SOURCE: [None],
+        },
+        index=["S0001"],
+    )
+    species.index.name = SBML_DFS.S_ID
+    compartments = pd.DataFrame(
+        {
+            SBML_DFS.C_NAME: ["cytosol"],
+            SBML_DFS.C_IDENTIFIERS: [None],
+            SBML_DFS.C_SOURCE: [None],
+        },
+        index=["C0001"],
+    )
+    compartments.index.name = SBML_DFS.C_ID
+    sbml_dict = {
+        SBML_DFS.COMPARTMENTS: compartments,
+        SBML_DFS.SPECIES: species,
+        SBML_DFS.COMPARTMENTALIZED_SPECIES: compartmentalized_species,
+        SBML_DFS.REACTIONS: reactions,
+        SBML_DFS.REACTION_SPECIES: reaction_species,
+    }
+    sbml1 = sbml_dfs_core.SBML_dfs(sbml_dict, validate=False, resolve=False)
+    sbml2 = sbml_dfs_core.SBML_dfs(sbml_dict, validate=False, resolve=False)
+    sbml_dfs_dict = {"mod1": sbml1, "mod2": sbml2}
+
+    # Create a lookup_table that merges both reactions into a new_id
+    lookup_table = pd.DataFrame(
+        {
+            "model": ["mod1", "mod2"],
+            "r_id": [r_id, r_id],
+            "new_id": ["merged_rid", "merged_rid"],
+        }
+    )
+    # Use the reactions schema
+    table_schema = SBML_DFS_SCHEMA.SCHEMA[SBML_DFS.REACTIONS]
+
+    # Call the function and check that it runs and the merge_labels are as expected
+    consensus.report_consensus_merges(
+        lookup_table.set_index(["model", "r_id"])[
+            "new_id"
+        ],  # this is a Series with name 'new_id'
+        table_schema,
+        sbml_dfs_dict=sbml_dfs_dict,
+        n_example_merges=1,
+    )
+    # No assertion: this is a smoke test to ensure the Series output is handled without error
+
+
 ################################################
 # __main__
 ################################################
@@ -256,3 +343,4 @@ if __name__ == "__main__":
     test_source_tracking()
     test_passing_entity_data()
     test_consensus_ontology_check()
+    test_report_consensus_merges_reactions()

tests/test_context_filtering.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import copy
 import pytest
 import pandas as pd
-from napistu import sbml_dfs_core
+from napistu import sbml_dfs_utils
 from napistu.constants import SBML_DFS
 from napistu.context.filtering import (
     filter_species_by_attribute,
@@ -208,7 +208,7 @@ def test_filter_reactions_with_disconnected_cspecies(sbml_dfs):
     first_reactions = list(sbml_dfs.reactions.index[:5])
 
     # 2. Find defining species in these reactions
-    reaction_species = sbml_dfs_core.add_sbo_role(sbml_dfs.reaction_species)
+    reaction_species = sbml_dfs_utils.add_sbo_role(sbml_dfs.reaction_species)
     defining_species = (
         reaction_species[reaction_species[SBML_DFS.R_ID].isin(first_reactions)]
         .query("sbo_role == 'DEFINING'")

tests/test_network_ig_utils.py

@@ -6,6 +6,15 @@ from napistu.network import ig_utils
 from napistu.network import net_create
 
 
+@pytest.fixture
+def multi_component_graph() -> ig_utils.ig.Graph:
+    """Creates a graph with multiple disconnected components of different sizes."""
+    g1 = ig_utils.ig.Graph.Ring(5)  # 5 vertices, 5 edges
+    g2 = ig_utils.ig.Graph.Tree(3, 2)  # 3 vertices, 2 edges
+    g3 = ig_utils.ig.Graph.Full(2)  # 2 vertices, 1 edge
+    return ig_utils.ig.disjoint_union([g1, g2, g3])
+
+
 def test_validate_graph_attributes(sbml_dfs):
 
     napistu_graph = net_create.process_napistu_graph(
@@ -21,3 +30,30 @@ def test_validate_graph_attributes(sbml_dfs):
     assert ig_utils.validate_vertex_attributes(napistu_graph, "node_type") is None
     with pytest.raises(ValueError):
         ig_utils.validate_vertex_attributes(napistu_graph, "baz")
+
+
+def test_filter_to_largest_subgraph(multi_component_graph):
+    """Tests that the function returns only the single largest component."""
+    largest = ig_utils.filter_to_largest_subgraph(multi_component_graph)
+    assert isinstance(largest, ig_utils.ig.Graph)
+    assert largest.vcount() == 5
+    assert largest.ecount() == 5
+
+
+def test_filter_to_largest_subgraphs(multi_component_graph):
+    """Tests that the function returns the top K largest components."""
+    # Test getting the top 2
+    top_2 = ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=2)
+    assert isinstance(top_2, list)
+    assert len(top_2) == 2
+    assert all(isinstance(g, ig_utils.ig.Graph) for g in top_2)
+    assert [g.vcount() for g in top_2] == [5, 3]
+
+    # Test getting more than the total number of components
+    top_5 = ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=5)
+    assert len(top_5) == 3
+    assert [g.vcount() for g in top_5] == [5, 3, 2]
+
+    # Test invalid top_k
+    with pytest.raises(ValueError):
+        ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=0)

tests/test_ontologies_genodexito.py

@@ -1,4 +1,6 @@
 import pandas as pd
+import pytest
+
 from napistu.ontologies.genodexito import Genodexito
 from napistu.ontologies.constants import (
     GENODEXITO_DEFS,
@@ -7,6 +9,7 @@ from napistu.ontologies.constants import (
 )
 
 
+@pytest.skip_on_timeout(5)
 def test_genodexito_mapping_operations():
     """Test Genodexito mapping table creation and operations."""
     # Initialize with test mode and Python method to avoid R dependencies

tests/test_ontologies_mygene.py

@@ -1,7 +1,10 @@
+import pytest
+
 from napistu.ontologies.mygene import create_python_mapping_tables
 from napistu.ontologies.constants import INTERCONVERTIBLE_GENIC_ONTOLOGIES
 
 
+@pytest.skip_on_timeout(5)
 def test_create_python_mapping_tables_yeast():
     """Test create_python_mapping_tables with yeast species."""
     # Test with a subset of mappings to keep test runtime reasonable