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Get tests working on MacOS14 #1248

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luciansmith opened this issue Jan 28, 2025 · 1 comment
Open

Get tests working on MacOS14 #1248

luciansmith opened this issue Jan 28, 2025 · 1 comment
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@adelhpour

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@luciansmith
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Several tests fail on MacOS 14 right now, probably due to precision changes. The tests will need to be re-examined and perhaps fundamentally changed.

@adelhpour , since you work on the mac, I'm handing this to you!
luciansmith added a commit that referenced this issue Jan 28, 2025
@luciansmith
Don't run tests on MacOS14 after all.
e930f75 
Too many fail!  (See #1248)
@luciansmith
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Tests that fail:

2025-01-28T01:10:11.6431880Z The following tests FAILED:
2025-01-28T01:10:11.6432080Z 	414 - CApiRRTests.TestTwo_Cycles (Failed)
2025-01-28T01:10:11.6432190Z 	734 - SingularMatrixTests.RightSingularVector (Failed)
2025-01-28T01:10:11.6432270Z 	1430 - StateSavingTests.LOAD_VALID_FILE (ILLEGAL)
2025-01-28T01:10:11.6432330Z 	1495 - PythonTests (Failed)

The full PythonTests log:

2025-01-28T01:08:22.5230200Z 1495/3319 Test #1495: PythonTests .......................................................................................***Failed    1.84 sec
2025-01-28T01:08:22.5231910Z handling signal 5
2025-01-28T01:08:22.5233000Z Executing __main__.py located at "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py"
2025-01-28T01:08:22.5251610Z Adding roadrunner site-packages to sys.path:  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages
2025-01-28T01:08:22.5252440Z Using roadrunner at /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/__init__.py
2025-01-28T01:08:22.5253010Z Running test_rrtests at /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py
2025-01-28T01:08:22.5253710Z 
2025-01-28T01:08:22.5253710Z 
2025-01-28T01:08:22.5254050Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Remove_Compartment1.rrtest
2025-01-28T01:08:22.5254490Z Successfully loaded model.
2025-01-28T01:08:22.5254590Z 
2025-01-28T01:08:22.5254660Z Remove compartment compartment1
2025-01-28T01:08:22.5254960Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5255250Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5255530Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5255750Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5256010Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5256260Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5256520Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5256770Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5257050Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5257330Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5257630Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5257850Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5258070Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5258300Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5258510Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5258720Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5258940Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5259160Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5259390Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5259630Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5259850Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5260060Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5260280Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5260490Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5260710Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5260920Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5261220Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5261460Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5261680Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5261890Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5262180Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5262460Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5262680Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5262900Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5263120Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5263340Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5263560Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5263790Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5264110Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5264390Z PASS
2025-01-28T01:08:22.5264530Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5264750Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5264990Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5265210Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5265420Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5265700Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5265920Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5266130Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5266350Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5266570Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5266780Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5267040Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5267240Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5267460Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5267670Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5267810Z 
2025-01-28T01:08:22.5267820Z 
2025-01-28T01:08:22.5268100Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Comp.rrtest
2025-01-28T01:08:22.5268500Z Successfully loaded model.
2025-01-28T01:08:22.5268600Z 
2025-01-28T01:08:22.5268680Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5268890Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5269110Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5269370Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5269600Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5269740Z 
2025-01-28T01:08:22.5269740Z 
2025-01-28T01:08:22.5270020Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Two_Steps.rrtest
2025-01-28T01:08:22.5270430Z Successfully loaded model.
2025-01-28T01:08:22.5270530Z 
2025-01-28T01:08:22.5270610Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5270890Z Computing Steady State.  Distance to SteadyState: 9.420936253334844e-14
2025-01-28T01:08:22.5271160Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5271390Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5271660Z Computing Steady State.  Distance to SteadyState: 9.420936253334844e-14
2025-01-28T01:08:22.5271930Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5272200Z Check [Get Reaction Rates]                   reaction rates:  [0.01767925 0.01767925]
2025-01-28T01:08:22.5272440Z PASS
2025-01-28T01:08:22.5272570Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5272780Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5273070Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5273310Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5273530Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5273760Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5273990Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5274200Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5274410Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5274640Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5274860Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5275090Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5275330Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5275550Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5275690Z 
2025-01-28T01:08:22.5275700Z 
2025-01-28T01:08:22.5276000Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Bimolecular_end.rrtest
2025-01-28T01:08:22.5276430Z Successfully loaded model.
2025-01-28T01:08:22.5276530Z 
2025-01-28T01:08:22.5276620Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5276890Z Computing Steady State.  Distance to SteadyState: 4.931585212921501e-13
2025-01-28T01:08:22.5277240Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5277460Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5277730Z Computing Steady State.  Distance to SteadyState: 4.931585212921501e-13
2025-01-28T01:08:22.5278010Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5278230Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5278450Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5278760Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5278980Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5279190Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5279410Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5279630Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5279850Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5280080Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5280310Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5280530Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5280860Z Check [Get Reaction Rates]                   reaction rates:  [0.71717517 1.03482972 0.71717517 0.39952062 0.31765455]
2025-01-28T01:08:22.5281200Z PASS
2025-01-28T01:08:22.5281260Z 
2025-01-28T01:08:22.5281270Z 
2025-01-28T01:08:22.5281570Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/RatesOfChange.rrtest
2025-01-28T01:08:22.5282000Z Successfully loaded model.
2025-01-28T01:08:22.5282100Z 
2025-01-28T01:08:22.5282180Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5282320Z 
2025-01-28T01:08:22.5282330Z 
2025-01-28T01:08:22.5282630Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Add_Reactions2.rrtest
2025-01-28T01:08:22.5283050Z Successfully loaded model.
2025-01-28T01:08:22.5283160Z 
2025-01-28T01:08:22.5283210Z Add reaction J4
2025-01-28T01:08:22.5283360Z Set reversible attribute for J1
2025-01-28T01:08:22.5283550Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5283830Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5284110Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5284340Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5284580Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5284880Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5285130Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5285380Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5285650Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5285930Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5286140Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5286360Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5286580Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5286790Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5287010Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5287220Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5287440Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5287680Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5287910Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5288130Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5288350Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5288560Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5288770Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5288990Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5289250Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5289470Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5289690Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5289910Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5290130Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5290350Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5290680Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5290950Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5291170Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5291510Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5291730Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5291960Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5292180Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5292400Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5292710Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5292980Z PASS
2025-01-28T01:08:22.5293210Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5293440Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5293660Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5293880Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5294100Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5294310Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5294520Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5294730Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5294960Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5295170Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5295390Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5295610Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5295820Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5296030Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5296250Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5296380Z 
2025-01-28T01:08:22.5296390Z 
2025-01-28T01:08:22.5296750Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Event_timings_276.rrtest
2025-01-28T01:08:22.5297210Z Successfully loaded model.
2025-01-28T01:08:22.5297320Z 
2025-01-28T01:08:22.5297400Z Check [Check Monotonic Timepoints]           PASS
2025-01-28T01:08:22.5297640Z Check [Check Event Pre and Postfire Timepoints]PASS
2025-01-28T01:08:22.5297790Z 
2025-01-28T01:08:22.5297800Z 
2025-01-28T01:08:22.5298100Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Set_Kinetic_Law1.rrtest
2025-01-28T01:08:22.5298160Z Successfully loaded model.
2025-01-28T01:08:22.5298160Z 
2025-01-28T01:08:22.5298220Z Set kinetic law for J2
2025-01-28T01:08:22.5298310Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5298440Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5298520Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5298600Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5298700Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5298780Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5298880Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5298960Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5299090Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5299250Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5299320Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5299400Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5299480Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5299550Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5299630Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5299750Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5299830Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5299920Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5299990Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5300070Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5300150Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5300230Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5300300Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5300380Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5300450Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5300520Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5300660Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5300740Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5300820Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5300900Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5301030Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5301120Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5301200Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5301270Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5301350Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5301430Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5301510Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5301590Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5301760Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5301810Z PASS
2025-01-28T01:08:22.5301890Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5301970Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5302130Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5302210Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5302280Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5302360Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5302430Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5302510Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5302590Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5302670Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5302740Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5302820Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5302890Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5302960Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5303030Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5303040Z 
2025-01-28T01:08:22.5303040Z 
2025-01-28T01:08:22.5303360Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Remove_Parameter1.rrtest
2025-01-28T01:08:22.5303420Z Successfully loaded model.
2025-01-28T01:08:22.5303420Z 
2025-01-28T01:08:22.5303470Z Remove parameter test
2025-01-28T01:08:22.5303530Z Set boundary condition for S1
2025-01-28T01:08:22.5303680Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5303810Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5303890Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5303980Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5304070Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5304160Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5304320Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5304410Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5304550Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5304620Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5304690Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5304770Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5304850Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5304930Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5305000Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5305080Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5312960Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5320790Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5321190Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5321450Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5321690Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5321910Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5322130Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5322350Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5322560Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5322780Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5323010Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5323210Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5323430Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5323660Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5324030Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5324260Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5324770Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5325000Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5325230Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5325460Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5325690Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5325900Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5326350Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5326490Z PASS
2025-01-28T01:08:22.5326700Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5326920Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5327150Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5327360Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5327560Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5327780Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5327990Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5328200Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5328420Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5328620Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5328820Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5329170Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5329370Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5329590Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5329790Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5329800Z 
2025-01-28T01:08:22.5329810Z 
2025-01-28T01:08:22.5330620Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/jacobian_1.rrtest
2025-01-28T01:08:22.5330950Z Successfully loaded model.
2025-01-28T01:08:22.5330960Z 
2025-01-28T01:08:22.5331190Z Check [Amount/Concentration Jacobians]       PASS
2025-01-28T01:08:22.5331390Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5331600Z Check [Amount Jacobian]                      PASS
2025-01-28T01:08:22.5332340Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-16
2025-01-28T01:08:22.5333320Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5333600Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5333840Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5334070Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5334440Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5334670Z Check [Individual Amount Eigenvalues]        PASS
2025-01-28T01:08:22.5334920Z Check [Eigenvalue Amount Matrix]             PASS
2025-01-28T01:08:22.5335150Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5335370Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5335610Z Check [Unscaled Elasticity Amount Matrix]    PASS
2025-01-28T01:08:22.5335830Z Check [Scaled Elasticity Amount Matrix]      PASS
2025-01-28T01:08:22.5336060Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5336280Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5336500Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5336720Z Check [Check Default Time Step]              PASS
2025-01-28T01:08:22.5336950Z Check [Check Simulate Points vs Steps]       PASS
2025-01-28T01:08:22.5336960Z 
2025-01-28T01:08:22.5336970Z 
2025-01-28T01:08:22.5337800Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Futile_Cycle.rrtest
2025-01-28T01:08:22.5337980Z Successfully loaded model.
2025-01-28T01:08:22.5337990Z 
2025-01-28T01:08:22.5338220Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5338730Z Computing Steady State.  Distance to SteadyState: 2.220446049250313e-16
2025-01-28T01:08:22.5338970Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5339190Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5339550Z Computing Steady State.  Distance to SteadyState: 2.220446049250313e-16
2025-01-28T01:08:22.5339760Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5340210Z Check [Get Reaction Rates]                   reaction rates:  [1.47828597 3.71352547 2.23523949 1.47828597]
2025-01-28T01:08:22.5340340Z PASS
2025-01-28T01:08:22.5340540Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5340750Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5340970Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5341180Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5341390Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5341620Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5341840Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5342040Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5342260Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5342470Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5342710Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5343030Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5343250Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5343470Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5343480Z 
2025-01-28T01:08:22.5343480Z 
2025-01-28T01:08:22.5344290Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Test_3.rrtest
2025-01-28T01:08:22.5344480Z Successfully loaded model.
2025-01-28T01:08:22.5344660Z 
2025-01-28T01:08:22.5344930Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5345320Z Computing Steady State.  Distance to SteadyState: 8.326672684688674e-17
2025-01-28T01:08:22.5345550Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5345790Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5346030Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5346450Z Computing Steady State.  Distance to SteadyState: 8.326672684688674e-17
2025-01-28T01:08:22.5346700Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5346920Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5347170Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5347540Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5347760Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5347990Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5348250Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5348480Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5348740Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5349000Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5349230Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5349440Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5349880Z Check [Get Reaction Rates]                   reaction rates:  [0.42739481 0.2136974  0.2136974  0.2136974 ]
2025-01-28T01:08:22.5350100Z PASS
2025-01-28T01:08:22.5350340Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5350580Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5350820Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5367030Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5367270Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5367280Z 
2025-01-28T01:08:22.5367290Z 
2025-01-28T01:08:22.5367830Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Cycle_across_branches.rrtest
2025-01-28T01:08:22.5367900Z Successfully loaded model.
2025-01-28T01:08:22.5367910Z 
2025-01-28T01:08:22.5368000Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5368130Z Computing Steady State.  Distance to SteadyState: 1.0658141036401503e-14
2025-01-28T01:08:22.5368230Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5368310Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5368440Z Computing Steady State.  Distance to SteadyState: 1.0658141036401503e-14
2025-01-28T01:08:22.5368530Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5368700Z Check [Get Reaction Rates]                   reaction rates:  [1.76867681e+01 1.04306147e-14 1.76867681e+01]
2025-01-28T01:08:22.5368750Z PASS
2025-01-28T01:08:22.5368820Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5368900Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5368970Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5369050Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5369120Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5369200Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5369390Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5369460Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5369540Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5369620Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5369700Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5369780Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5369850Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5369930Z 
2025-01-28T01:08:22.5369930Z 
2025-01-28T01:08:22.5370240Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Add_Species1.rrtest
2025-01-28T01:08:22.5370310Z Successfully loaded model.
2025-01-28T01:08:22.5370310Z 
2025-01-28T01:08:22.5370360Z Add species S3
2025-01-28T01:08:22.5370460Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5370540Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5370610Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5370690Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5370760Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5370840Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5370970Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5371050Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5371140Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5371220Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5371300Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5371300Z 
2025-01-28T01:08:22.5371300Z 
2025-01-28T01:08:22.5371640Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Conserved_Cycle_and_Branch.rrtest
2025-01-28T01:08:22.5371700Z Successfully loaded model.
2025-01-28T01:08:22.5371710Z 
2025-01-28T01:08:22.5371790Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5371920Z Computing Steady State.  Distance to SteadyState: 2.3296701543181088e-14
2025-01-28T01:08:22.5372000Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5372080Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5372210Z Computing Steady State.  Distance to SteadyState: 2.3296701543181088e-14
2025-01-28T01:08:22.5372290Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5372370Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5372470Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5372550Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5372630Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5372700Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5372770Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5372850Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5373030Z Check [Get Reaction Rates]                   reaction rates:  [ 0.00000000e+00 -3.55271368e-15  1.42108547e-14]
2025-01-28T01:08:22.5373080Z PASS
2025-01-28T01:08:22.5373080Z 
2025-01-28T01:08:22.5373080Z 
2025-01-28T01:08:22.5373360Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Cycle.rrtest
2025-01-28T01:08:22.5373420Z Successfully loaded model.
2025-01-28T01:08:22.5373430Z 
2025-01-28T01:08:22.5373510Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5373640Z Computing Steady State.  Distance to SteadyState: 1.1443916996305594e-15
2025-01-28T01:08:22.5373720Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5373800Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5373930Z Computing Steady State.  Distance to SteadyState: 1.1443916996305594e-15
2025-01-28T01:08:22.5374010Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5374200Z Check [Get Reaction Rates]                   reaction rates:  [0.43742447 0.43742447 0.43742447]
2025-01-28T01:08:22.5374250Z PASS
2025-01-28T01:08:22.5374320Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5374390Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5374470Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5374550Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5374650Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5374740Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5374820Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5374890Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5374970Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5375050Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5375130Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5375210Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5375290Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5375360Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5375370Z 
2025-01-28T01:08:22.5375410Z 
2025-01-28T01:08:22.5375710Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Test_1.rrtest
2025-01-28T01:08:22.5375770Z Successfully loaded model.
2025-01-28T01:08:22.5375770Z 
2025-01-28T01:08:22.5375860Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5376010Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5376090Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5376170Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5376270Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5376350Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5376440Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5376530Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5376660Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5376750Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5376820Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5376900Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5377040Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5377130Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5377200Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5377280Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5377350Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5377430Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5377520Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5377600Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5377680Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5377760Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5377830Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5377910Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5377990Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5378060Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5378140Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5378220Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5378290Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5378370Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5378440Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5378640Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5378720Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5378800Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5378880Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5378970Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5379050Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5379190Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5379280Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5379450Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5379500Z PASS
2025-01-28T01:08:22.5379570Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5379650Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5379740Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5379810Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5379880Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5379960Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5380070Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5380150Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5380230Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5380300Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5380370Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5380450Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5380520Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5380600Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5380600Z 
2025-01-28T01:08:22.5380610Z 
2025-01-28T01:08:22.5380940Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Cycle_to_Input_and_Branch.rrtest
2025-01-28T01:08:22.5381000Z Successfully loaded model.
2025-01-28T01:08:22.5381000Z 
2025-01-28T01:08:22.5381080Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5381220Z Computing Steady State.  Distance to SteadyState: 1.486713723341161e-14
2025-01-28T01:08:22.5381300Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5381380Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5381570Z Computing Steady State.  Distance to SteadyState: 1.486713723341161e-14
2025-01-28T01:08:22.5381660Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5381850Z Check [Get Reaction Rates]                   reaction rates:  [ 0.02016805  0.84892892 -0.82876087 -0.02016805  1.67768978]
2025-01-28T01:08:22.5381930Z PASS
2025-01-28T01:08:22.5382010Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5382090Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5382160Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5382240Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5382310Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5382400Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5382470Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5382540Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5382630Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5382710Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5382790Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5382870Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5382950Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5382950Z 
2025-01-28T01:08:22.5382950Z 
2025-01-28T01:08:22.5383280Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Add_Event_Assignment1.rrtest
2025-01-28T01:08:22.5383380Z Successfully loaded model.
2025-01-28T01:08:22.5383380Z 
2025-01-28T01:08:22.5383440Z Add event assignment for S3
2025-01-28T01:08:22.5383520Z Check [Check Monotonic Timepoints]           PASS
2025-01-28T01:08:22.5383610Z Check [Check Event Pre and Postfire Timepoints]PASS
2025-01-28T01:08:22.5383620Z 
2025-01-28T01:08:22.5383620Z 
2025-01-28T01:08:22.5383960Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Multibranch1.rrtest
2025-01-28T01:08:22.5384010Z Successfully loaded model.
2025-01-28T01:08:22.5384020Z 
2025-01-28T01:08:22.5384100Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5384230Z Computing Steady State.  Distance to SteadyState: 9.930136612989092e-16
2025-01-28T01:08:22.5384330Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5384420Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5384550Z Computing Steady State.  Distance to SteadyState: 9.930136612989092e-16
2025-01-28T01:08:22.5384620Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5384890Z Check [Get Reaction Rates]                   reaction rates:  [2.98573132 0.5726622  2.41306912 0.37022645 2.04284268]
2025-01-28T01:08:22.5384950Z PASS
2025-01-28T01:08:22.5385030Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5385100Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5385190Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5385260Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5385340Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5385420Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5385490Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5385560Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5385640Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5385720Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5385800Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5385880Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5385960Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5386040Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5386040Z 
2025-01-28T01:08:22.5386050Z 
2025-01-28T01:08:22.5386400Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Add_Reactions1.rrtest
2025-01-28T01:08:22.5386470Z Successfully loaded model.
2025-01-28T01:08:22.5386480Z 
2025-01-28T01:08:22.5386530Z Add reaction reaction2
2025-01-28T01:08:22.5386630Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5386720Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5386800Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5386880Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5386950Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5387020Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5387100Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5387180Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5387260Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5387340Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5387420Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5387420Z 
2025-01-28T01:08:22.5387420Z 
2025-01-28T01:08:22.5387720Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Simple_Branch.rrtest
2025-01-28T01:08:22.5387780Z Successfully loaded model.
2025-01-28T01:08:22.5387790Z 
2025-01-28T01:08:22.5387920Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5388110Z Computing Steady State.  Distance to SteadyState: 1.6653345369377348e-16
2025-01-28T01:08:22.5388240Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5388310Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5388450Z Computing Steady State.  Distance to SteadyState: 1.6653345369377348e-16
2025-01-28T01:08:22.5388530Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5388800Z Check [Get Reaction Rates]                   reaction rates:  [1.52231259 1.19394147 0.32837112]
2025-01-28T01:08:22.5388840Z PASS
2025-01-28T01:08:22.5388920Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5388990Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5389070Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5389140Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5389210Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5389300Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5389370Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5389440Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5389570Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5389650Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5389730Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5389820Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5389890Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5389970Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5389970Z 
2025-01-28T01:08:22.5389970Z 
2025-01-28T01:08:22.5390270Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Two_Cycles.rrtest
2025-01-28T01:08:22.5390330Z Successfully loaded model.
2025-01-28T01:08:22.5390330Z 
2025-01-28T01:08:22.5390420Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5390550Z Computing Steady State.  Distance to SteadyState: 3.614624287906422e-15
2025-01-28T01:08:22.5390630Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5390710Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5390840Z Computing Steady State.  Distance to SteadyState: 3.614624287906422e-15
2025-01-28T01:08:22.5390920Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5391110Z Check [Get Reaction Rates]                   reaction rates:  [0.57189637 0.57189637 0.57189637]
2025-01-28T01:08:22.5391160Z PASS
2025-01-28T01:08:22.5391280Z Check [Full Jacobian]                        Traceback from failed test: 
2025-01-28T01:08:22.5399790Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5399990Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5400290Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5400350Z     exec(code, run_globals)
2025-01-28T01:08:22.5400670Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5400760Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5401120Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5401180Z     func(rrInstance, testId)
2025-01-28T01:08:22.5401530Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 244, in checkFullJacobian
2025-01-28T01:08:22.5401610Z     checkMatrixVsUpcomingText(Jacobian)
2025-01-28T01:08:22.5401980Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5402310Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5402630Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5402710Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5402770Z *****FAIL*****
2025-01-28T01:08:22.5402860Z     Expected 8.52, but calculated 13.300000000000004
2025-01-28T01:08:22.5402940Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5403090Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5403160Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5403240Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5403380Z Check [Stoichiometry Matrix]                 Traceback from failed test: 
2025-01-28T01:08:22.5403660Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5403750Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5404220Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5404290Z     exec(code, run_globals)
2025-01-28T01:08:22.5404700Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5404810Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5405180Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5405240Z     func(rrInstance, testId)
2025-01-28T01:08:22.5405620Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 333, in checkStoichiometryMatrix
2025-01-28T01:08:22.5405690Z     checkMatrixVsUpcomingText(st)
2025-01-28T01:08:22.5406050Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5406120Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5406450Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5406520Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5406570Z *****FAIL*****
2025-01-28T01:08:22.5406630Z     Expected 0, but calculated 1.0
2025-01-28T01:08:22.5406710Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5406920Z Check [Link Matrix]                          Traceback from failed test: 
2025-01-28T01:08:22.5407210Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5407290Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5407540Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5407600Z     exec(code, run_globals)
2025-01-28T01:08:22.5407900Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5407990Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5408340Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5408520Z     func(rrInstance, testId)
2025-01-28T01:08:22.5408880Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 345, in checkLinkMatrix
2025-01-28T01:08:22.5408960Z     checkMatrixVsUpcomingText(st)
2025-01-28T01:08:22.5409320Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5409400Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5409780Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5409850Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5409900Z *****FAIL*****
2025-01-28T01:08:22.5409960Z     Expected -1, but calculated 0.0
2025-01-28T01:08:22.5410100Z Check [Unscaled Elasticity Matrix]           Traceback from failed test: 
2025-01-28T01:08:22.5410380Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5410660Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5410910Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5410970Z     exec(code, run_globals)
2025-01-28T01:08:22.5411270Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5411360Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5411710Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5411770Z     func(rrInstance, testId)
2025-01-28T01:08:22.5412180Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 385, in checkUnscaledElasticityMatrix
2025-01-28T01:08:22.5412260Z     checkMatrixVsUpcomingText(uee)
2025-01-28T01:08:22.5412720Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5412790Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5413100Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5413170Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5413220Z *****FAIL*****
2025-01-28T01:08:22.5413320Z     Expected 6.98818, but calculated 59.06533888870265
2025-01-28T01:08:22.5413470Z Check [Scaled Elasticity Matrix]             Traceback from failed test: 
2025-01-28T01:08:22.5413750Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5413830Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5414070Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5414130Z     exec(code, run_globals)
2025-01-28T01:08:22.5414510Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5414600Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5414950Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5415010Z     func(rrInstance, testId)
2025-01-28T01:08:22.5415380Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 397, in checkScaledElasticityMatrix
2025-01-28T01:08:22.5415460Z     checkMatrixVsUpcomingText(ee)
2025-01-28T01:08:22.5415820Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5415890Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5416200Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5416270Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5416320Z *****FAIL*****
2025-01-28T01:08:22.5416400Z     Expected 0, but calculated -0.08797976894619651
2025-01-28T01:08:22.5416550Z Check [Unscaled Concentration Control Matrix]Traceback from failed test: 
2025-01-28T01:08:22.5416820Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5416950Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5417200Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5417260Z     exec(code, run_globals)
2025-01-28T01:08:22.5417560Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5417710Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5418070Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5418130Z     func(rrInstance, testId)
2025-01-28T01:08:22.5418550Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 353, in checkUnscaledConcentrationControlMatrix
2025-01-28T01:08:22.5418620Z     checkMatrixVsUpcomingText(st)
2025-01-28T01:08:22.5418990Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5419060Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5419440Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5419530Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5419570Z *****FAIL*****
2025-01-28T01:08:22.5419670Z     Expected -0.0169507, but calculated 0.06482434067675279
2025-01-28T01:08:22.5419820Z Check [Scaled Concentration Control Matrix]  Traceback from failed test: 
2025-01-28T01:08:22.5420090Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5420170Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5420410Z File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5420470Z     exec(code, run_globals)
2025-01-28T01:08:22.5420770Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5420860Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5421270Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1690, in testAllRRTestFiles
2025-01-28T01:08:22.5421340Z     func(rrInstance, testId)
2025-01-28T01:08:22.5421830Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 362, in checkScaledConcentrationControlMatrix
2025-01-28T01:08:22.5421910Z     checkMatrixVsUpcomingText(st)
2025-01-28T01:08:22.5422290Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 148, in checkMatrixVsUpcomingText
2025-01-28T01:08:22.5422370Z     print(passMsg (errorFlag, msg))
2025-01-28T01:08:22.5422680Z File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 58, in passMsg
2025-01-28T01:08:22.5422750Z     for line in traceback.format_stack():
2025-01-28T01:08:22.5422800Z *****FAIL*****
2025-01-28T01:08:22.5422900Z     Expected -0.0123184, but calculated 0.005573598931636096
2025-01-28T01:08:22.5422980Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5423060Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5423070Z 
2025-01-28T01:08:22.5423070Z 
2025-01-28T01:08:22.5423380Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Remove_Parameter2.rrtest
2025-01-28T01:08:22.5423440Z Successfully loaded model.
2025-01-28T01:08:22.5423440Z 
2025-01-28T01:08:22.5423500Z Remove parameter test
2025-01-28T01:08:22.5423590Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5423810Z Computing Steady State.  Distance to SteadyState: 2.482534153247273e-16
2025-01-28T01:08:22.5423900Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5423980Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5424120Z Computing Steady State.  Distance to SteadyState: 2.482534153247273e-16
2025-01-28T01:08:22.5424190Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5424370Z Check [Get Reaction Rates]                   reaction rates:  [0.51491722 0.51491722 0.51491722 0.51491722]
2025-01-28T01:08:22.5424450Z PASS
2025-01-28T01:08:22.5424530Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5424600Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5424680Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5424760Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5424840Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5424920Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5424990Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5425070Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5425140Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5425260Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5425340Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5425420Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5425490Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5425500Z 
2025-01-28T01:08:22.5425500Z 
2025-01-28T01:08:22.5425800Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Gillespie.rrtest
2025-01-28T01:08:22.5425860Z Successfully loaded model.
2025-01-28T01:08:22.5425860Z 
2025-01-28T01:08:22.5425940Z Check [Gillespie Seed]                       PASS
2025-01-28T01:08:22.5426010Z Check [Gillespie Value]                      PASS
2025-01-28T01:08:22.5426090Z Check [Gillespie Fixed Time Interval]        PASS
2025-01-28T01:08:22.5426100Z 
2025-01-28T01:08:22.5426100Z 
2025-01-28T01:08:22.5426390Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Remove_Rules1.rrtest
2025-01-28T01:08:22.5426460Z Successfully loaded model.
2025-01-28T01:08:22.5426460Z 
2025-01-28T01:08:22.5426510Z Remove rules for S1
2025-01-28T01:08:22.5426570Z Set boundary condition for S1
2025-01-28T01:08:22.5426660Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5426830Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5426920Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5427000Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5427100Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5427190Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5427290Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5427370Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5427510Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5427590Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5427660Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5427740Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5427820Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5427900Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5427970Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5428050Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5428120Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5428200Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5428290Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5428420Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5428500Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5428580Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5428660Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5428730Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5428800Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5428910Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5428990Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5429070Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5429140Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5429220Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5429360Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5429440Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5429520Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5429600Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5429680Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5429790Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5429870Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5429950Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5430120Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5430170Z PASS
2025-01-28T01:08:22.5430250Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5430320Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5430400Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5430480Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5430550Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5430630Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5430700Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5430780Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5430850Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5430920Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5431000Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5431120Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5431200Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5431270Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5431340Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5431350Z 
2025-01-28T01:08:22.5431350Z 
2025-01-28T01:08:22.5431620Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/oscli.rrtest
2025-01-28T01:08:22.5431690Z Successfully loaded model.
2025-01-28T01:08:22.5431690Z 
2025-01-28T01:08:22.5431770Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5431870Z Computing Steady State.  Distance to SteadyState: 0.0
2025-01-28T01:08:22.5431950Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5432020Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5432120Z Computing Steady State.  Distance to SteadyState: 0.0
2025-01-28T01:08:22.5432190Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5432320Z Check [Get Reaction Rates]                   reaction rates:  [8. 0. 8. 8.]
2025-01-28T01:08:22.5432360Z PASS
2025-01-28T01:08:22.5432440Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5432510Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5432590Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5432690Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5432770Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5432850Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5432920Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5433000Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5433080Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5433160Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5433290Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5433370Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5433380Z 
2025-01-28T01:08:22.5433380Z 
2025-01-28T01:08:22.5433690Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/variable_time_step.rrtest
2025-01-28T01:08:22.5433750Z Successfully loaded model.
2025-01-28T01:08:22.5433760Z 
2025-01-28T01:08:22.5433830Z Check [Get Variable End Time]                PASS
2025-01-28T01:08:22.5433840Z 
2025-01-28T01:08:22.5433840Z 
2025-01-28T01:08:22.5434150Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Absolute_Tolerance1.rrtest
2025-01-28T01:08:22.5434210Z Successfully loaded model.
2025-01-28T01:08:22.5434250Z 
2025-01-28T01:08:22.5434290Z PASS
2025-01-28T01:08:22.5434300Z 
2025-01-28T01:08:22.5434300Z 
2025-01-28T01:08:22.5434600Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/MultiBranch2.rrtest
2025-01-28T01:08:22.5434660Z Successfully loaded model.
2025-01-28T01:08:22.5434660Z 
2025-01-28T01:08:22.5434750Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5434880Z Computing Steady State.  Distance to SteadyState: 3.429337716954387e-15
2025-01-28T01:08:22.5434960Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5435020Z Traceback (most recent call last):
2025-01-28T01:08:22.5435330Z   File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 196, in _run_module_as_main
2025-01-28T01:08:22.5435410Z     return _run_code(code, main_globals, None,
2025-01-28T01:08:22.5435660Z   File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
2025-01-28T01:08:22.5435720Z     exec(code, run_globals)
2025-01-28T01:08:22.5436030Z   File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/__main__.py", line 27, in <module>
2025-01-28T01:08:22.5436160Z     test_rrtests.testAllRRTestFiles(test_data_dir)
2025-01-28T01:08:22.5436530Z   File "/Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_rrtests.py", line 1710, in testAllRRTestFiles
2025-01-28T01:08:22.5436620Z     raise FailedTestsError(summary)
2025-01-28T01:08:22.5436790Z test_rrtests.testAllRRTestFiles.<locals>.FailedTestsError: Total failed tests:	 7
2025-01-28T01:08:22.5436850Z Total unknown tests:	 0
2025-01-28T01:08:22.5436910Z Total passed tests:	 754
2025-01-28T01:08:22.5436990Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5437120Z Computing Steady State.  Distance to SteadyState: 3.429337716954387e-15
2025-01-28T01:08:22.5437200Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5437420Z Check [Get Reaction Rates]                   reaction rates:  [ 0.82617423  0.58364214 -0.24253209  0.24096501  0.82460714 -0.00156709]
2025-01-28T01:08:22.5437470Z PASS
2025-01-28T01:08:22.5437540Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5437620Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5437700Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5437770Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5437860Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5437930Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5438040Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5438120Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5438200Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5438270Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5438350Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5438430Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5438510Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5438630Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5438640Z 
2025-01-28T01:08:22.5438640Z 
2025-01-28T01:08:22.5438930Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Test_2.rrtest
2025-01-28T01:08:22.5438990Z Successfully loaded model.
2025-01-28T01:08:22.5438990Z 
2025-01-28T01:08:22.5439070Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5439210Z Computing Steady State.  Distance to SteadyState: 8.326672684688674e-17
2025-01-28T01:08:22.5439290Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5439370Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5439470Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5439630Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5439710Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5439850Z Computing Steady State.  Distance to SteadyState: 2.0396099332657776e-16
2025-01-28T01:08:22.5439930Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5440000Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5440080Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5440160Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5440230Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5440310Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5440380Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5440460Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5440550Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5440620Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5440790Z Check [Get Reaction Rates]                   reaction rates:  [0.42076503 0.21038251 0.21038251 0.21038251]
2025-01-28T01:08:22.5440840Z PASS
2025-01-28T01:08:22.5440920Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5441040Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5441140Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5441220Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5441290Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5441370Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5441440Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5441530Z Check [Amount/Concentration Jacobians]       PASS
2025-01-28T01:08:22.5441600Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5441670Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5441680Z 
2025-01-28T01:08:22.5441680Z 
2025-01-28T01:08:22.5441990Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Remove_Species1.rrtest
2025-01-28T01:08:22.5442050Z Successfully loaded model.
2025-01-28T01:08:22.5442050Z 
2025-01-28T01:08:22.5442100Z Remove species S4
2025-01-28T01:08:22.5442180Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5442310Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5442390Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5442620Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5442770Z Check [Get Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5453420Z Check [Get Initial Floating Species Concs]   PASS
2025-01-28T01:08:22.5453620Z Check [Set Species Initial Concentrations By Index]PASS
2025-01-28T01:08:22.5453710Z Check [Set Species Initial Concentrations]   PASS
2025-01-28T01:08:22.5453860Z Computing Steady State.  Distance to SteadyState: 1.962615573354719e-17
2025-01-28T01:08:22.5453940Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5454010Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5454340Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5454420Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5454500Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5454570Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5454650Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5454730Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5454810Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5454890Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5454970Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5455040Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5455190Z Check [Floating Species Ids]                 PASS
2025-01-28T01:08:22.5455280Z Check [Boundary Species Ids]                 PASS
2025-01-28T01:08:22.5455360Z Check [Global Parameter Ids]                 PASS
2025-01-28T01:08:22.5455440Z Check [Compartment Ids]                      PASS
2025-01-28T01:08:22.5455510Z Check [Reaction Ids]                         PASS
2025-01-28T01:08:22.5455590Z Check [Species Initial Concentration Ids]    PASS
2025-01-28T01:08:22.5455670Z Check [Get Eigenvalue Ids]                   PASS
2025-01-28T01:08:22.5455740Z Check [Get Rates Of Change Ids]              PASS
2025-01-28T01:08:22.5455820Z Check [Set Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5455960Z Computing Steady State.  Distance to SteadyState: 1.3877787807814457e-17
2025-01-28T01:08:22.5456050Z Check [Get Steady State Selection List 2]    PASS
2025-01-28T01:08:22.5456130Z Check [Set Time Course Selection List]       PASS
2025-01-28T01:08:22.5456210Z Check [Get Time Course Selection List]       PASS
2025-01-28T01:08:22.5456280Z Check [Compute Steady State Values]          PASS
2025-01-28T01:08:22.5456360Z Check [Floating Species Concentrations]      PASS
2025-01-28T01:08:22.5456440Z Check [Boundary Species Concentrations]      PASS
2025-01-28T01:08:22.5456600Z Check [Get Global Parameter Values]          PASS
2025-01-28T01:08:22.5456780Z Check [Get Reaction Rates]                   reaction rates:  [0.07151526 0.07151526 0.07151526 0.07151526]
2025-01-28T01:08:22.5456820Z PASS
2025-01-28T01:08:22.5456900Z Check [Get Reaction Rates By Index]          PASS
2025-01-28T01:08:22.5456970Z Check [Number of Dependent Species]          PASS
2025-01-28T01:08:22.5457060Z Check [Number of Independent Species]        PASS
2025-01-28T01:08:22.5457130Z Check [Number Of Rate Rules]                 PASS
2025-01-28T01:08:22.5457200Z Check [Get Rates Of Change]                  PASS
2025-01-28T01:08:22.5457280Z Check [Get Reaction Rates Ex]                PASS
2025-01-28T01:08:22.5457350Z Check [Get Rates of Change Ex]               PASS
2025-01-28T01:08:22.5457430Z Check [Get Rates of Change By Index]         PASS
2025-01-28T01:08:22.5457500Z Check [Get Control Coefficient]              PASS
2025-01-28T01:08:22.5457580Z Check [Check RK4 Output]                     PASS
2025-01-28T01:08:22.5457650Z Check [Check RK45 Output]                    PASS
2025-01-28T01:08:22.5457720Z Check [Test Reset]                           PASS
2025-01-28T01:08:22.5457790Z Check [Test ResetAll]                        PASS
2025-01-28T01:08:22.5457890Z Check [Test ResetToOrigin]                   PASS
2025-01-28T01:08:22.5457960Z Check [Test SetValues]                       PASS
2025-01-28T01:08:22.5457960Z 
2025-01-28T01:08:22.5458060Z 
2025-01-28T01:08:22.5458370Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/SimpleUniUni.rrtest
2025-01-28T01:08:22.5458440Z Successfully loaded model.
2025-01-28T01:08:22.5458440Z 
2025-01-28T01:08:22.5458520Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5458600Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5458600Z 
2025-01-28T01:08:22.5458610Z 
2025-01-28T01:08:22.5458900Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Four_Steps.rrtest
2025-01-28T01:08:22.5458990Z Successfully loaded model.
2025-01-28T01:08:22.5459000Z 
2025-01-28T01:08:22.5459080Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5459210Z Computing Steady State.  Distance to SteadyState: 2.482534153247273e-16
2025-01-28T01:08:22.5459290Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5459370Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5459500Z Computing Steady State.  Distance to SteadyState: 2.482534153247273e-16
2025-01-28T01:08:22.5459580Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5459780Z Check [Get Reaction Rates]                   reaction rates:  [0.51491722 0.51491722 0.51491722 0.51491722]
2025-01-28T01:08:22.5459830Z PASS
2025-01-28T01:08:22.5459900Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5459980Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5460060Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5460140Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5460220Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5460290Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5460360Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5460440Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5460520Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5460590Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5460680Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5460750Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5460830Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5460830Z 
2025-01-28T01:08:22.5460840Z 
2025-01-28T01:08:22.5461160Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/reversible_Jacobian.rrtest
2025-01-28T01:08:22.5461290Z Successfully loaded model.
2025-01-28T01:08:22.5461290Z 
2025-01-28T01:08:22.5461430Z Computing Steady State.  Distance to SteadyState: 2.7194799110210365e-16
2025-01-28T01:08:22.5461500Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5461580Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5461660Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5461740Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5461810Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5461890Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5461970Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5462050Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5462050Z 
2025-01-28T01:08:22.5462060Z 
2025-01-28T01:08:22.5462360Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Conserved_Cycle.rrtest
2025-01-28T01:08:22.5462430Z Successfully loaded model.
2025-01-28T01:08:22.5462430Z 
2025-01-28T01:08:22.5462510Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5462640Z Computing Steady State.  Distance to SteadyState: 4.440892098500626e-16
2025-01-28T01:08:22.5462720Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5462800Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5462970Z Computing Steady State.  Distance to SteadyState: 4.440892098500626e-16
2025-01-28T01:08:22.5463050Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5463120Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5463200Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5463270Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5463350Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5463470Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5463560Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5463630Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5463710Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5463780Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5463870Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5463950Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5464030Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5464110Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5464240Z Check [Get Reaction Rates]                   reaction rates:  [2.03087238 2.03087238]
2025-01-28T01:08:22.5464320Z PASS
2025-01-28T01:08:22.5464400Z Check [Test ResetConservedTotal]             PASS
2025-01-28T01:08:22.5464400Z 
2025-01-28T01:08:22.5464410Z 
2025-01-28T01:08:22.5464710Z Starting Test on  /Users/runner/work/roadrunner/build-roadrunner/lib/site-packages/roadrunner/tests/test_data/Three_Steps.rrtest
2025-01-28T01:08:22.5464770Z Successfully loaded model.
2025-01-28T01:08:22.5464770Z 
2025-01-28T01:08:22.5464850Z Check [Set Steady State Selection List]      PASS
2025-01-28T01:08:22.5464980Z Computing Steady State.  Distance to SteadyState: 4.002966042486721e-16
2025-01-28T01:08:22.5465060Z Check [Get Steady State Selection List]      PASS
2025-01-28T01:08:22.5465140Z Check [Species Concentrations]               PASS
2025-01-28T01:08:22.5465270Z Computing Steady State.  Distance to SteadyState: 4.002966042486721e-16
2025-01-28T01:08:22.5465340Z Check [Steady State Fluxes]                  PASS
2025-01-28T01:08:22.5465490Z Check [Get Reaction Rates]                   reaction rates:  [0.78422515 0.78422515 0.78422515]
2025-01-28T01:08:22.5465540Z PASS
2025-01-28T01:08:22.5465620Z Check [Full Jacobian]                        PASS
2025-01-28T01:08:22.5465690Z Check [Reduced Jacobian]                     PASS
2025-01-28T01:08:22.5465810Z Check [Individual Eigenvalues]               PASS
2025-01-28T01:08:22.5465890Z Check [Eigenvalue Matrix]                    PASS
2025-01-28T01:08:22.5465960Z Check [Reduced Eigenvalue Matrix]            PASS
2025-01-28T01:08:22.5466040Z Check [Stoichiometry Matrix]                 PASS
2025-01-28T01:08:22.5466120Z Check [Reduced Stoichiometry Matrix]         PASS
2025-01-28T01:08:22.5466190Z Check [Link Matrix]                          PASS
2025-01-28T01:08:22.5466270Z Check [Unscaled Elasticity Matrix]           PASS
2025-01-28T01:08:22.5466350Z Check [Scaled Elasticity Matrix]             PASS
2025-01-28T01:08:22.5466430Z Check [Unscaled Concentration Control Matrix]PASS
2025-01-28T01:08:22.5466500Z Check [Scaled Concentration Control Matrix]  PASS
2025-01-28T01:08:22.5466580Z Check [Unscaled Flux Control Matrix]         PASS
2025-01-28T01:08:22.5466660Z Check [Scaled Flux Control Matrix]           PASS
2025-01-28T01:08:22.5466710Z PASS
2025-01-28T01:08:22.5466760Z Total failed tests:	 7
2025-01-28T01:08:22.5466820Z Total unknown tests:	 0
2025-01-28T01:08:22.5466870Z Total passed tests:	 754

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