Fix Failing CI because of `cclib` #2535

JacksonBurns · 2023-08-30T02:47:09Z

Motivation or Problem

The CI has been failing (see here) for a couple days because of the latest release of cclib (see here for reference), breaking unrelated PRs such as #2533

Description of Changes

Disallows 1.8.0 of cclib in the RMG environment.yml. This is intended as a temporary patch so PRs can keep working and I can do some work locally to find out why this version of cclib is failing, and potentially file a bug report with the maintainers.

Testing

Just using the CI here. As mentioned above, need to do some local debugging to try and find out why this is failing.

Reviewer Tips

Should be quick to merge (famous last words).

JacksonBurns · 2023-08-30T02:50:14Z

File diff for the cclib 1.8 vs 1.7.2 MOPAC parser class: cclib/cclib@v1.7.2...v1.8#diff-a710fa5d121b2ed984e78fcd7ed5a27924b0cad89d40e34e36d65f8039bc2285

codecov · 2023-08-30T05:33:16Z

Codecov Report

Merging #2535 (989060f) into main (8ba4c0d) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #2535   +/-   ##
=======================================
  Coverage   55.32%   55.32%           
=======================================
  Files         125      125           
  Lines       37139    37139           
=======================================
  Hits        20547    20547           
  Misses      16592    16592

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

github-actions · 2023-08-30T05:33:25Z

Regression Testing Results

⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:23
Current: Execution time (DD:HH:MM:SS): 00:00:01:37
Reference: Memory used: 2082.17 MB
Current: Memory used: 2078.06 MB

aromatics Passed Core Comparison ✅

Original model has 15 species.
Test model has 15 species. ✅
Original model has 11 reactions.
Test model has 11 reactions. ✅

aromatics Passed Edge Comparison ✅

Original model has 106 species.
Test model has 106 species. ✅
Original model has 358 reactions.
Test model has 358 reactions. ✅

Details

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:45
Current: Execution time (DD:HH:MM:SS): 00:00:03:12
Reference: Memory used: 2213.69 MB
Current: Memory used: 2218.70 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 215 reactions.
Test model has 215 reactions. ✅

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61
k(T):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1613 reactions.
Test model has 1610 reactions. ❌
The original model has 4 reactions that the tested model does not have. ❌
rxn: C[CH]CCCO(157) + CCCCCO[O](104) <=> CC=CCCO(183) + CCCCCOO(105) origin: Disproportionation
rxn: C[CH]CCCO(157) + CCCCCO[O](104) <=> C=CCCCO(184) + CCCCCOO(105) origin: Disproportionation
rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> CC=CCCO(183) + CCCCCO(130) origin: Disproportionation
rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> C=CCCCO(184) + CCCCCO(130) origin: Disproportionation
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCCCCO[O](104) + CCCCCO[O](104) <=> oxygen(1) + CCCCC=O(106) + CCCCCO(130) origin: Peroxyl_Termination

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](127) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61
k(T):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Details

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:46
Current: Execution time (DD:HH:MM:SS): 00:00:02:02
Reference: Memory used: 2217.66 MB
Current: Memory used: 2220.04 MB

nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 360 reactions. ✅

nitrogen Passed Edge Comparison ✅

Original model has 132 species.
Test model has 132 species. ✅
Original model has 997 reactions.
Test model has 997 reactions. ✅

Details

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:49
Current: Execution time (DD:HH:MM:SS): 00:00:03:18
Reference: Memory used: 2085.60 MB
Current: Memory used: 2080.56 MB

oxidation Passed Core Comparison ✅

Original model has 59 species.
Test model has 59 species. ✅
Original model has 694 reactions.
Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species.
Test model has 230 species. ✅
Original model has 1526 reactions.
Test model has 1526 reactions. ✅

Details

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:06
Current: Execution time (DD:HH:MM:SS): 00:00:01:20
Reference: Memory used: 2187.69 MB
Current: Memory used: 2170.78 MB

sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Details

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:41
Current: Execution time (DD:HH:MM:SS): 00:00:00:49
Reference: Memory used: 2308.40 MB
Current: Memory used: 2350.12 MB

superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:11
Current: Execution time (DD:HH:MM:SS): 00:00:03:48
Reference: Memory used: 2730.64 MB
Current: Memory used: 2739.12 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:07:43
Current: Execution time (DD:HH:MM:SS): 00:00:09:16
Reference: Memory used: 2709.47 MB
Current: Memory used: 2702.80 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 232 reactions.
Test model has 233 reactions. ❌
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](35) <=> [OH](21) + CC=O(61) origin: intra_H_migration

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species.
Test model has 206 species. ✅
Original model has 1508 reactions.
Test model has 1508 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](35) <=> C[CH]OO(62) origin: intra_H_migration
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](35) <=> [OH](21) + CC=O(61) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCO[O](34) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](94) + CCCC(C)[O](61) origin: Peroxyl_Disproportionation
tested:
rxn: CCCO[O](36) + CCCC(C)O[O](33) <=> oxygen(1) + CCC[O](91) + CCCC(C)[O](64) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61
k(T):	3.69	4.39	4.82	5.10	5.45	5.66	5.94	6.08

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.866,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Details

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

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rwest

Ok for temporary fix

rwest · 2024-03-20T19:33:10Z

Do we need a tag for "temporary" fixes? See #2638

JacksonBurns · 2024-03-21T18:03:24Z

I'm more inclined to just open and issue to track the temporary fixes that we should revert with long(er)-term solutions rather than a new label, since I think I tend to pay more attention to the issues personally.

do not allow cclib 1.8.0

989060f

JacksonBurns requested a review from rwest August 30, 2023 02:47

JacksonBurns self-assigned this Aug 30, 2023

rwest enabled auto-merge September 2, 2023 21:48

rwest disabled auto-merge September 2, 2023 21:48

rwest approved these changes Sep 2, 2023

View reviewed changes

rwest merged commit 2212786 into main Sep 2, 2023

rwest deleted the cclib-patch branch September 2, 2023 21:50

JacksonBurns mentioned this pull request Sep 5, 2023

correcting bidentate adsorption rate constant #2533

Merged

ChrisBNEU mentioned this pull request Mar 20, 2024

restrict newer versions of cclib #2638

Merged

JacksonBurns mentioned this pull request Jul 10, 2025

RMG-Py Version 3.3.0 #2826

Merged

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Fix Failing CI because of `cclib` #2535

Fix Failing CI because of `cclib` #2535

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JacksonBurns commented Aug 30, 2023

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codecov bot commented Aug 30, 2023 •

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github-actions bot commented Aug 30, 2023

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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Fix Failing CI because of cclib #2535

Fix Failing CI because of cclib #2535

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JacksonBurns commented Aug 30, 2023

Motivation or Problem

Description of Changes

Testing

Reviewer Tips

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Codecov Report

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github-actions bot commented Aug 30, 2023

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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Fix Failing CI because of `cclib` #2535

Fix Failing CI because of `cclib` #2535

codecov bot commented Aug 30, 2023 •

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