[Python 3.9] Improve isodesmic and add element balance constraints #2695

JacksonBurns · 2024-07-24T18:28:29Z

This PR replaces #2596 as described in this comment: #2687 (comment)

…nce species

…tion

hwpang · 2024-07-25T00:07:54Z

It seems that the tests for ubuntu have proceeded pretty far and mostly need some syntax updates?

JacksonBurns · 2024-07-25T15:26:18Z

@hwpang yes, this PR is almost working. There are test failures caused by the changes here, test failures from the resonance changes, and test failures from the original python 3.9 upgrade. I am going to try and find all the failures that are strictly this branch and fix them, merge this PR into the resonance branch, and then start tackling those (will probably need your help on that part!).

JacksonBurns · 2024-07-25T15:31:36Z

@hwpang I am trying to build locally so I can debug faster - which of these env variables are actually required?

          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH

JacksonBurns · 2024-07-25T16:44:13Z

The current test failures status:

=========================== short test summary info ============================
FAILED test/arkane/arkaneMainTest.py::TestArkaneExamples::test_arkane_examples - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/arkaneOutputTest.py::OutputTest::test_prettify - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/commonTest.py::TestArkaneSpecies::test_dump_yaml - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/commonTest.py::TestArkaneSpecies::test_create_and_load_yaml - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/statmechTest.py::TestStatmech::test_specifying_absolute_file_paths - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/statmechTest.py::TestStatmech::test_hinder_rotor_from_1d_array - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/statmechTest.py::TestStatmech::test_hindered_rotor_from_scan_logs - AttributeError: module 'numpy' has no attribute 'warnings'
FAILED test/arkane/encorr/isodesmicTest.py::TestSpeciesConstraints::test_calculating_constraints - TypeError: not all arguments converted during string formatting
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_find_error_canceling_reaction - TypeError: 'int' object is not iterable
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_multiple_error_canceling_reactions - TypeError: 'int' object is not iterable
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_calculate_target_enthalpy - TypeError: 'int' object is not iterable
FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_pdep_arrhenius - AttributeError: 'cantera.reaction.Reaction' object has no attribute 'rates'
FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_multi_pdep_arrhenius - AttributeError: 'cantera.reaction.Reaction' object has no attribute 'rates'
FAILED test/rmgpy/reactionTest.py::TestReactionToCantera::test_falloff - TypeError: __cinit__() got an unexpected keyword argument 'tbody'
FAILED test/rmgpy/speciesTest.py::TestSpecies::test_cantera - AttributeError: type object 'cantera.thermo.Species' has no attribute 'fromCti'
FAILED test/rmgpy/transportDataTest.py::TestTransportData::test_to_cantera - AttributeError: type object 'cantera.thermo.Species' has no attribute 'fromCti'
FAILED test/rmgpy/data/solvationTest.py::TestSoluteDatabase::test_saturation_density - AssertionError: assert 1.93 == 0
 +  where 1.93 = round(1.9298279226322848, 2)
 +    where 1.9298279226322848 = abs((6385.1498279226325 - 6383.22))
 +      where 6385.1498279226325 = get_liquid_saturation_density('Hexane', 400)
FAILED test/rmgpy/data/thermoTest.py::TestThermoDatabase::test_thermo_for_aromatic_radicals - ValueError: need more than 0 values to unpack
FAILED test/rmgpy/data/thermoTest.py::TestCyclicThermo::test_add_poly_ring_correction_thermo_data_from_heuristic_using_pyrene - AssertionError: assert 'Benzene' in []
FAILED test/rmgpy/data/thermoTest.py::TestMolecularManipulationInvolvedInThermoEstimation::test_bicyclic_decomposition_for_polyring_using_pyrene - assert [0, 0, 0, 0, 0] == [0, 6, 6, 6, 6]
  At index 1 diff: 0 != 6
  Full diff:
  - [0, 6, 6, 6, 6]
  + [0, 0, 0, 0, 0]
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_f_rules - ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (7, 6) + inhomogeneous part.
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_d_regularization_dims - Exception: Unable to calculate free energy for species 'C6H6-5': no thermo or statmech data available.
FAILED test/rmgpy/molecule/moleculeTest.py::TestMolecule::test_count_aromatic_rings - assert [2, 0] == [2, 1, 0]
  At index 1 diff: 0 != 1
  Right contains one more item: 0
  Full diff:
  - [2, 1, 0]
  ?     ---
  + [2, 0]
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_naphthyl - assert 2 == 4
 +  where 2 = len([Molecule(smiles="[c]1cccc2ccccc12"), Molecule(smiles="[C]1=C2C=CC=CC2=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_napthalene - assert 2 == 4
 +  where 2 = len([Molecule(smiles="Cc1cccc2ccccc12"), Molecule(smiles="CC1=CC=CC2=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene - assert 2 == 3
 +  where 2 = len([Molecule(smiles="Cc1cccc2c1ccc1ccccc12"), Molecule(smiles="CC1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene_radical - assert 2 == 9
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2c1ccc1ccccc12"), Molecule(smiles="[CH2]C1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_c13h11_rad - assert 2 == 6
 +  where 2 = len([Molecule(smiles="Cc1ccc([CH]c2ccccc2)cc1"), Molecule(smiles="CC1=CC=C([CH]C2=CC=CC=C2)C=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_aryne_3_rings - assert 4 == 5
 +  where 4 = len([Molecule(smiles="C1#Cc2c(ccc3ccccc23)C=C1"), Molecule(smiles="C1=C=C2C(=CC=1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=CC1=C2C=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_polycyclic_aromatic_with_non_aromatic_ring2 - assert 2 == 4
 +  where 2 = len([Molecule(smiles="C=C1C=Cc2cc3c(ccc4cc5ccccc5cc43)cc2C1=C"), Molecule(smiles="C=C1C=CC2=CC3=C(C=CC4=CC5=CC=CC=C5C=C43)C=C2C1=C")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycyclic_aromaticity_perception - ValueError: need more than 0 values to unpack
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycylic_aromaticity_perception2 - ValueError: need more than 0 values to unpack
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_clar_optimization - ValueError: not enough values to unpack (expected 4, got 2)
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenanthrene - assert 0 == 1
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenalene - assert 0 == 2
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_corannulene - assert 0 == 5
 +  where 0 = len([])
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM3::test_generate_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM3::test_load_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM6::test_generate_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM6::test_load_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM7::test_generate_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/mopacTest.py::TestMopacMolPM7::test_load_thermo_data - IndexError: list index out of range
FAILED test/rmgpy/qm/qmMainTest.py::TestQMCalculator::test_get_thermo_data_mopac - IndexError: list index out of range
FAILED test/rmgpy/qm/qmMainTest.py::TestQMCalculator::test_run_jobs - IndexError: list index out of range
FAILED test/rmgpy/rmg/mainTest.py::TestRestartWithFilters::test_restart_with_filters - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/mainTest.py::TestRestartNoFilters::test_restart_no_filters - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestCoreEdgeReactionModel::test_thermo_filter_species - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestCoreEdgeReactionModel::test_thermo_filter_down - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestCoreEdgeReactionModel::test_check_for_existing_reaction_eliminates_identical_reactions - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestCoreEdgeReactionModel::test_check_for_existing_reaction_keeps_identical_reactions_with_duplicate_flag - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestCoreEdgeReactionModel::test_check_for_existing_reaction_eliminates_identical_reactions_without_duplicate_flag - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/rmg/modelTest.py::TestEnlarge::test_enlarge_3_react_edge - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/statmech/ndTorsionsTest.py::TestHinderedRotorClassicalND::test_hindered_rotor_nd - assert 4e-05 == 0
 +  where 4e-05 = round((2.8993250143510836 - 2.899287634962152), 5)
 +    where 2.8993250143510836 = abs(2.8993250143510836)
 +      where 2.8993250143510836 = <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)>(300.0)
 +        where <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)> = Mode(quantum=False).calc_partition_function
FAILED test/rmgpy/tools/generatereactionsTest.py::GenerateReactionsTest::test - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/tools/generatereactionsTest.py::GenerateReactionsTest::test_duplicate_reaction - AttributeError: 'list' object has no attribute 'getattr'
FAILED test/rmgpy/tools/generatereactionsTest.py::GenerateReactionsTest::test_library_reaction_enters_core - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/database/databaseTest.py::TestDatabase::test_kinetics - ValueError: need more than 0 values to unpack
ERROR test/database/databaseTest.py::TestDatabase::test_thermo - ValueError: need more than 0 values to unpack
ERROR test/database/databaseTest.py::TestDatabase::test_solvation - ValueError: need more than 0 values to unpack
ERROR test/database/databaseTest.py::TestDatabase::test_statmech - ValueError: need more than 0 values to unpack
ERROR test/database/databaseTest.py::TestDatabase::test_transport - ValueError: need more than 0 values to unpack
ERROR test/database/databaseTest.py::TestDatabase::test_metal_libraries - ValueError: need more than 0 values to unpack
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_execute - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_increases_reactions - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_seed_mechanism_creation - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_seed_edge_mechanism_creation - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_seed_library_creation - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_seed_edge_library_creation - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_seed_works - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_rmg_memory - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMain::test_make_cantera_input_file - AttributeError: 'list' object has no attribute 'getattr'
ERROR test/rmgpy/rmg/mainTest.py::TestMainFunctions::test_save_seed_modulus - FileExistsError: [Errno 17] File exists: '/home/runner/work/RMG-Py/RMG-Py/rmgpy/../test/rmgpy/test_data/mainTest/output'
ERROR test/rmgpy/rmg/mainTest.py::TestMainFunctions::test_max_iter - FileExistsError: [Errno 17] File exists: '/home/runner/work/RMG-Py/RMG-Py/rmgpy/../test/rmgpy/test_data/mainTest/output'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_species_conversion - TypeError: __cinit__() got an unexpected keyword argument 'tbody'
ERROR test/rmgpy/tools/canteramodelTest.py::RMGToCanteraTest::test_reaction_conversion - TypeError: __cinit__() got an unexpected keyword argument 'tbody'
= 56 failed, 1826 passed, 36 skipped, 2080058 warnings, 19 errors in 1204.42s (0:20:04) =
make: *** [Makefile:65: test-all] Error 1

we are not compatible with the latest version, will be resolved in this PR: #2639

JacksonBurns · 2024-07-25T17:03:10Z

This batch of commits should resolve a great number of these, hopefully

JacksonBurns · 2024-07-25T18:27:31Z

Down to 25 failures:

=========================== short test summary info ============================
FAILED test/arkane/arkaneMainTest.py::TestArkaneExamples::test_arkane_examples - TypeError: concatenate() got an unexpected keyword argument 'lb'
FAILED test/arkane/encorr/isodesmicTest.py::TestSpeciesConstraints::test_calculating_constraints - TypeError: not all arguments converted during string formatting
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_find_error_canceling_reaction - TypeError: concatenate() got an unexpected keyword argument 'lb'
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_multiple_error_canceling_reactions - TypeError: concatenate() got an unexpected keyword argument 'lb'
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_calculate_target_enthalpy - TypeError: concatenate() got an unexpected keyword argument 'lb'
FAILED test/rmgpy/data/solvationTest.py::TestSoluteDatabase::test_saturation_density - AssertionError: assert 1.93 == 0
 +  where 1.93 = round(1.9298279226322848, 2)
 +    where 1.9298279226322848 = abs((6385.1498279226325 - 6383.22))
 +      where 6385.1498279226325 = get_liquid_saturation_density('Hexane', 400)
FAILED test/rmgpy/data/thermoTest.py::TestCyclicThermo::test_add_poly_ring_correction_thermo_data_from_heuristic_using_pyrene - AssertionError: assert 'Benzene' in []
FAILED test/rmgpy/data/thermoTest.py::TestMolecularManipulationInvolvedInThermoEstimation::test_bicyclic_decomposition_for_polyring_using_pyrene - assert [0, 0, 0, 0, 0] == [0, 6, 6, 6, 6]
  At index 1 diff: 0 != 6
  Full diff:
  - [0, 6, 6, 6, 6]
  + [0, 0, 0, 0, 0]
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_f_rules - ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (7, 6) + inhomogeneous part.
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_d_regularization_dims - Exception: Unable to calculate free energy for species 'C6H6-5': no thermo or statmech data available.
FAILED test/rmgpy/molecule/moleculeTest.py::TestMolecule::test_count_aromatic_rings - assert [2, 0] == [2, 1, 0]
  At index 1 diff: 0 != 1
  Right contains one more item: 0
  Full diff:
  - [2, 1, 0]
  ?     ---
  + [2, 0]
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_naphthyl - assert 2 == 4
 +  where 2 = len([Molecule(smiles="[c]1cccc2ccccc12"), Molecule(smiles="[C]1=C2C=CC=CC2=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_napthalene - assert 2 == 4
 +  where 2 = len([Molecule(smiles="Cc1cccc2ccccc12"), Molecule(smiles="CC1=CC=CC2=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene - assert 2 == 3
 +  where 2 = len([Molecule(smiles="Cc1cccc2c1ccc1ccccc12"), Molecule(smiles="CC1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene_radical - assert 2 == 9
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2c1ccc1ccccc12"), Molecule(smiles="[CH2]C1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_c13h11_rad - assert 2 == 6
 +  where 2 = len([Molecule(smiles="Cc1ccc([CH]c2ccccc2)cc1"), Molecule(smiles="CC1=CC=C([CH]C2=CC=CC=C2)C=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_aryne_3_rings - assert 4 == 5
 +  where 4 = len([Molecule(smiles="C1#Cc2c(ccc3ccccc23)C=C1"), Molecule(smiles="C1=C=C2C(=CC=1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=CC1=C2C=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_polycyclic_aromatic_with_non_aromatic_ring2 - assert 2 == 4
 +  where 2 = len([Molecule(smiles="C=C1C=Cc2cc3c(ccc4cc5ccccc5cc43)cc2C1=C"), Molecule(smiles="C=C1C=CC2=CC3=C(C=CC4=CC5=CC=CC=C5C=C43)C=C2C1=C")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycyclic_aromaticity_perception - assert 2 == 6
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2ccccc12"), Molecule(smiles="C=C1C=CC=C2C=C[CH]C=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycylic_aromaticity_perception2 - assert 6 == 7
 +  where 6 = len([Molecule(smiles="[CH2]C=C1C=CC(=C)c2ccccc21"), Molecule(smiles="[CH2]c1ccc(C=C)c2ccccc12"), Molecule(smiles="C=C[C]1C=CC(=C)c2ccccc21"), Molecule(smiles="C=CC1=C[CH]C(=C)c2ccccc21"), Molecule(smiles="[CH2]C1=CC=C(C=C)c2ccccc21"), Molecule(smiles="[CH2]C=C1C=CC(=C)C2=C1C=CC=C2")])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_clar_optimization - ValueError: not enough values to unpack (expected 4, got 2)
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenanthrene - assert 0 == 1
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenalene - assert 0 == 2
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_corannulene - assert 0 == 5
 +  where 0 = len([])
FAILED test/rmgpy/statmech/ndTorsionsTest.py::TestHinderedRotorClassicalND::test_hindered_rotor_nd - assert 4e-05 == 0
 +  where 4e-05 = round((2.8993250143510827 - 2.899287634962152), 5)
 +    where 2.8993250143510827 = abs(2.8993250143510827)
 +      where 2.8993250143510827 = <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)>(300.0)
 +        where <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)> = Mode(quantum=False).calc_partition_function
== 25 failed, 1876 passed, 36 skipped, 2083535 warnings in 1696.85s (0:28:16) ==
make: *** [Makefile:65: test-all] Error 1

JacksonBurns · 2024-07-26T15:48:18Z

These are the remaining test failures:

=========================== short test summary info ============================
FAILED test/arkane/encorr/isodesmicTest.py::TestSpeciesConstraints::test_calculating_constraints - TypeError: not all arguments converted during string formatting
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_calculate_target_enthalpy - AttributeError: 'TestErrorCancelingScheme' object has no attribute 'pyo'
FAILED test/rmgpy/data/solvationTest.py::TestSoluteDatabase::test_saturation_density - AssertionError: assert 1.93 == 0
 +  where 1.93 = round(1.9298279226322848, 2)
 +    where 1.9298279226322848 = abs((6385.1498279226325 - 6383.22))
 +      where 6385.1498279226325 = get_liquid_saturation_density('Hexane', 400)
FAILED test/rmgpy/data/thermoTest.py::TestCyclicThermo::test_add_poly_ring_correction_thermo_data_from_heuristic_using_pyrene - AssertionError: assert 'Benzene' in []
FAILED test/rmgpy/data/thermoTest.py::TestMolecularManipulationInvolvedInThermoEstimation::test_bicyclic_decomposition_for_polyring_using_pyrene - assert [0, 0, 0, 0, 0] == [0, 6, 6, 6, 6]
  At index 1 diff: 0 != 6
  Full diff:
  - [0, 6, 6, 6, 6]
  + [0, 0, 0, 0, 0]
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_f_rules - ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (7, 6) + inhomogeneous part.
FAILED test/rmgpy/data/kinetics/familyTest.py::TestTreeGeneration::test_d_regularization_dims - Exception: Unable to calculate free energy for species 'C6H6-5': no thermo or statmech data available.
FAILED test/rmgpy/molecule/moleculeTest.py::TestMolecule::test_count_aromatic_rings - assert [2, 0] == [2, 1, 0]
  At index 1 diff: 0 != 1
  Right contains one more item: 0
  Full diff:
  - [2, 1, 0]
  ?     ---
  + [2, 0]
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_naphthyl - assert 2 == 4
 +  where 2 = len([Molecule(smiles="[c]1cccc2ccccc12"), Molecule(smiles="[C]1=C2C=CC=CC2=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_napthalene - assert 2 == 4
 +  where 2 = len([Molecule(smiles="Cc1cccc2ccccc12"), Molecule(smiles="CC1=CC=CC2=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene - assert 2 == 3
 +  where 2 = len([Molecule(smiles="Cc1cccc2c1ccc1ccccc12"), Molecule(smiles="CC1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene_radical - assert 2 == 9
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2c1ccc1ccccc12"), Molecule(smiles="[CH2]C1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_c13h11_rad - assert 2 == 6
 +  where 2 = len([Molecule(smiles="Cc1ccc([CH]c2ccccc2)cc1"), Molecule(smiles="CC1=CC=C([CH]C2=CC=CC=C2)C=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_aryne_3_rings - assert 4 == 5
 +  where 4 = len([Molecule(smiles="C1#Cc2c(ccc3ccccc23)C=C1"), Molecule(smiles="C1=C=C2C(=CC=1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=CC1=C2C=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_polycyclic_aromatic_with_non_aromatic_ring2 - assert 2 == 4
 +  where 2 = len([Molecule(smiles="C=C1C=Cc2cc3c(ccc4cc5ccccc5cc43)cc2C1=C"), Molecule(smiles="C=C1C=CC2=CC3=C(C=CC4=CC5=CC=CC=C5C=C43)C=C2C1=C")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycyclic_aromaticity_perception - assert 2 == 6
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2ccccc12"), Molecule(smiles="C=C1C=CC=C2C=C[CH]C=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycylic_aromaticity_perception2 - assert 6 == 7
 +  where 6 = len([Molecule(smiles="[CH2]C=C1C=CC(=C)c2ccccc21"), Molecule(smiles="[CH2]c1ccc(C=C)c2ccccc12"), Molecule(smiles="C=C[C]1C=CC(=C)c2ccccc21"), Molecule(smiles="C=CC1=C[CH]C(=C)c2ccccc21"), Molecule(smiles="[CH2]C1=CC=C(C=C)c2ccccc21"), Molecule(smiles="[CH2]C=C1C=CC(=C)C2=C1C=CC=C2")])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_clar_optimization - ValueError: not enough values to unpack (expected 4, got 2)
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenanthrene - assert 0 == 1
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenalene - assert 0 == 2
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_corannulene - assert 0 == 5
 +  where 0 = len([])
FAILED test/rmgpy/statmech/ndTorsionsTest.py::TestHinderedRotorClassicalND::test_hindered_rotor_nd - assert 4e-05 == 0
 +  where 4e-05 = round((2.8993250143510827 - 2.899287634962152), 5)
 +    where 2.8993250143510827 = abs(2.8993250143510827)
 +      where 2.8993250143510827 = <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)>(300.0)
 +        where <bound method HinderedRotorClassicalND.calc_partition_function of Mode(quantum=False)> = Mode(quantum=False).calc_partition_function
== 22 failed, 1879 passed, 36 skipped, 3939723 warnings in 2297.49s (0:38:17) ==
make: *** [Makefile:65: test-all] Error 1

@hwpang I think these test failures are because of the changes in this PR, could you take a look?

FAILED test/arkane/encorr/isodesmicTest.py::TestSpeciesConstraints::test_calculating_constraints - TypeError: not all arguments converted during string formatting
FAILED test/arkane/encorr/isodesmicTest.py::TestErrorCancelingScheme::test_calculate_target_enthalpy - AttributeError: 'TestErrorCancelingScheme' object has no attribute 'pyo'

@xiaoruiDong I think these test failures are due to the changes in the resonance calculation. I will list the here, but we should resolve them in #2694.

FAILED test/rmgpy/data/solvationTest.py::TestSoluteDatabase::test_saturation_density - AssertionError: assert 1.93 == 0
 +  where 1.93 = round(1.9298279226322848, 2)
 +    where 1.9298279226322848 = abs((6385.1498279226325 - 6383.22))
 +      where 6385.1498279226325 = get_liquid_saturation_density('Hexane', 400)
FAILED test/rmgpy/data/thermoTest.py::TestCyclicThermo::test_add_poly_ring_correction_thermo_data_from_heuristic_using_pyrene - AssertionError: assert 'Benzene' in []
FAILED test/rmgpy/data/thermoTest.py::TestMolecularManipulationInvolvedInThermoEstimation::test_bicyclic_decomposition_for_polyring_using_pyrene - assert [0, 0, 0, 0, 0] == [0, 6, 6, 6, 6]
  At index 1 diff: 0 != 6
  Full diff:
  - [0, 6, 6, 6, 6]
  + [0, 0, 0, 0, 0]

...

FAILED test/rmgpy/molecule/moleculeTest.py::TestMolecule::test_count_aromatic_rings - assert [2, 0] == [2, 1, 0]
  At index 1 diff: 0 != 1
  Right contains one more item: 0
  Full diff:
  - [2, 1, 0]
  ?     ---
  + [2, 0]
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_naphthyl - assert 2 == 4
 +  where 2 = len([Molecule(smiles="[c]1cccc2ccccc12"), Molecule(smiles="[C]1=C2C=CC=CC2=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_napthalene - assert 2 == 4
 +  where 2 = len([Molecule(smiles="Cc1cccc2ccccc12"), Molecule(smiles="CC1=CC=CC2=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene - assert 2 == 3
 +  where 2 = len([Molecule(smiles="Cc1cccc2c1ccc1ccccc12"), Molecule(smiles="CC1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_methyl_phenanthrene_radical - assert 2 == 9
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2c1ccc1ccccc12"), Molecule(smiles="[CH2]C1=CC=CC2=C1C=CC1=CC=CC=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_c13h11_rad - assert 2 == 6
 +  where 2 = len([Molecule(smiles="Cc1ccc([CH]c2ccccc2)cc1"), Molecule(smiles="CC1=CC=C([CH]C2=CC=CC=C2)C=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_aryne_3_rings - assert 4 == 5
 +  where 4 = len([Molecule(smiles="C1#Cc2c(ccc3ccccc23)C=C1"), Molecule(smiles="C1=C=C2C(=CC=1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=Cc1ccccc12"), Molecule(smiles="C1#CC2=C(C=C1)C=CC1=C2C=CC=C1")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_polycyclic_aromatic_with_non_aromatic_ring2 - assert 2 == 4
 +  where 2 = len([Molecule(smiles="C=C1C=Cc2cc3c(ccc4cc5ccccc5cc43)cc2C1=C"), Molecule(smiles="C=C1C=CC2=CC3=C(C=CC4=CC5=CC=CC=C5C=C43)C=C2C1=C")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycyclic_aromaticity_perception - assert 2 == 6
 +  where 2 = len([Molecule(smiles="[CH2]c1cccc2ccccc12"), Molecule(smiles="C=C1C=CC=C2C=C[CH]C=C12")])
FAILED test/rmgpy/molecule/resonanceTest.py::ResonanceTest::test_false_negative_polycylic_aromaticity_perception2 - assert 6 == 7
 +  where 6 = len([Molecule(smiles="[CH2]C=C1C=CC(=C)c2ccccc21"), Molecule(smiles="[CH2]c1ccc(C=C)c2ccccc12"), Molecule(smiles="C=C[C]1C=CC(=C)c2ccccc21"), Molecule(smiles="C=CC1=C[CH]C(=C)c2ccccc21"), Molecule(smiles="[CH2]C1=CC=C(C=C)c2ccccc21"), Molecule(smiles="[CH2]C=C1C=CC(=C)C2=C1C=CC=C2")])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_clar_optimization - ValueError: not enough values to unpack (expected 4, got 2)
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenanthrene - assert 0 == 1
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_phenalene - assert 0 == 2
 +  where 0 = len([])
FAILED test/rmgpy/molecule/resonanceTest.py::ClarTest::test_corannulene - assert 0 == 5
 +  where 0 = len([])

There are a handful of other failures which we can resolve in #2687

xiaoruiDong · 2024-07-26T16:03:37Z

@JacksonBurns Will take a look

JacksonBurns · 2024-08-05T13:05:43Z

Above commits are intended to resolve the two outstanding test failures unique to this PR. If successful, will merge this PR and resolve the resonance issues in the base.

JacksonBurns · 2024-08-05T18:03:44Z

@hwpang I think I have fixed the errors that were unique to this PR. Going to merge.

@xiaoruiDong I will tag you in the next PR and we pick this up from there.

hwpang and others added 22 commits July 24, 2024 14:20

Update year in license

ca0091a

imports sorting by formatter

bd60215

Add improvements by @amarkpayne

d90e4fb

Add constraints for element balance

b78765f

Add pyutilib to catch ApplicationError

1b052aa

Formatting by formatter

a929f2c

Catch TypeError

57faf2f

WIP

6938a88

Modify based on review comment

bd7f2b5

Better way to initialize empty list

bbc0030

Improve code readability to get enumerated constraints

7fa4cf1

Constraint cation/anion/neutral target to cation/anion/neutral refere…

b28281d

…nce species

Add warning for easy debugging

3544b2f

Switch to use scipy

24bf4e5

Remove unused imports and correct obj fnc

59e0cf1

Remove unused package, add version constraint to scipy

fd96df6

Remove options of solver

e75c15e

Add comment to make test more readable

46e930f

Use keyword variable

a61e34b

Add comment

05a7d49

Add comment to test

e3cc59e

remove lpsolve55 from environments, tests, functions, docstrings, & docs

bb44414

JacksonBurns mentioned this pull request Jul 24, 2024

Improve isodesmic and add element balance constraints #2596

Closed

JacksonBurns added 2 commits July 24, 2024 15:23

convert helper function args to kwargs for partial to work, hide func…

d47a1f5

…tion

re-try running M1 macs on native hardware rather than x86 emulation

54efa64

JacksonBurns changed the title ~~Improve isodesmic and add element balance constraints - Python 3.9~~ [Python 3.9] Improve isodesmic and add element balance constraints Jul 24, 2024

ugh, typo

12f2968

JacksonBurns added 2 commits July 24, 2024 21:04

pass constraints as a tuple

5407567

fix return type for clar call

baf260a

update return types in cython header

db6e632

yet more incorrect return types

91d74cd

JacksonBurns added 7 commits July 25, 2024 12:49

use python warnings module instead of removed numpy warnings passthrough

fb19d02

fix incorrect use of getattr

f30b04a

add back the cclib version restriction

ff4ef4e

we are not compatible with the latest version, will be resolved in this PR: #2639

allow empty return to be properly excepted

28d2fbf

fix usage of n for iteration

be69fb2

make dict_keys -> str conversion explicit so it will run

5e7b266

re-limit the version of cantera to undo the API breaks

551926d

JacksonBurns and others added 2 commits July 25, 2024 14:29

incorrect placement of parens

c1d6902

make tuple cast more explicit

10e79c2

JacksonBurns mentioned this pull request Aug 4, 2024

[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (juliaup and pythoncall), Add Tests for Arkane Network Algorithms #2687

Closed

JacksonBurns added 2 commits August 5, 2024 09:02

explicit cast of set to str

46b9c92

remove disused pyomo components

9092cd5

fix usage of warning

4f8f268

JacksonBurns marked this pull request as ready for review August 5, 2024 18:03

JacksonBurns merged commit 56efc1a into feat/resonance_scipy Aug 5, 2024
2 of 8 checks passed

JacksonBurns deleted the feat/isodesmic_scipy branch August 5, 2024 18:04

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[Python 3.9] Improve isodesmic and add element balance constraints #2695

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[Python 3.9] Improve isodesmic and add element balance constraints #2695

[Python 3.9] Improve isodesmic and add element balance constraints #2695

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