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We should replace cantera.Species.fromCti() calls with cantera.Species.from_yaml() calls #2676

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rwest opened this issue Jun 10, 2024 · 6 comments · May be fixed by #2751
Open
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We should replace cantera.Species.fromCti() calls with cantera.Species.from_yaml() calls #2676

rwest opened this issue Jun 10, 2024 · 6 comments · May be fixed by #2751
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Complexity: Low Good First Issue Topic: Cantera Type: Testing

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@rwest
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rwest commented Jun 10, 2024

Bug Description

The unit tests include the warning:

test/rmgpy/speciesTest.py::TestSpecies::test_cantera
  /home/runner/work/RMG-Py/RMG-Py/test/rmgpy/speciesTest.py:477: DeprecationWarning: XML_Node::build: 
  The CTI and XML input file formats are deprecated and will be removed in
  Cantera 3.0. Use 'cti2yaml.py' or 'ctml2yaml.py' to convert CTI or XML input
  files to the YAML format. See https://cantera.org/tutorials/legacy2yaml.html
  for more information.

The relevant part of RMG-Py/test/rmgpy/speciesTest.py is

        rmg_ct_species = rmg_species.to_cantera(use_chemkin_identifier=True)

        ct_species = ct.Species.fromCti(
            """species(name=u'Ar',
        atoms='Ar:1',
        thermo=(NASA([200.00, 1000.00],
                     [ 2.50000000E+00,  0.00000000E+00,  0.00000000E+00,
                       0.00000000E+00,  0.00000000E+00, -7.45375000E+02,
                       4.37967000E+00]),
                NASA([1000.00, 6000.00],
                     [ 2.50000000E+00,  0.00000000E+00,  0.00000000E+00,
                       0.00000000E+00,  0.00000000E+00, -7.45375000E+02,
                       4.37967000E+00])),
        transport=gas_transport(geom='atom',
                                diam=3.33,
                                well_depth=136.501,
                                dipole=2.0,
                                polar=1.0,
                                rot_relax=15.0))"""
        )
        assert type(rmg_ct_species) == type(ct_species)

We should replace the fromCti block with a from_yaml block with a syntax a bit like this (this example is obviously a different species)

ct.Species.from_yaml(
'''name: C6H5CH3
composition: {C: 7, H: 8}
thermo:
  model: NASA7
  temperature-ranges: [100.00, 1073.72, 5000.00]
  data:
  - [2.05719474e+00, 3.12152776E-02, 3.04758250E-05, -5.05435593E-08, 
     1.81542493E-11, 3.83493690E+03, 1.65378111E+01]
  - [9.30667130E+00, 3.36713230E-02, -1.41158452E-05, 2.69973752E-09, 
    -1.93204076E-13, 5.79813528E+02, -2.68610894E+01]'''
    )

Note the transportDataTest.py also has a fromCti call.

  • speciesTest.py
  • transportDataTest.py

How To Reproduce

Run the unit tests, specifically test/rmgpy/speciesTest.py

Expected Behavior

We wouldn't get deprecation warnings from Cantera.
@JacksonBurns
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Would this also require setting a new lower limit to the supported Cantera version inside the environment file? I assume that this new function has not been backported to all previous versions, and there would be some new cutoff.

@rwest
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rwest commented Jun 25, 2024

For a year now we have required Cantera 2.6, and from_yaml is documented in that version. (It already existed in 2.5.1 but was called fromYaml)

@rwest rwest mentioned this issue Jun 25, 2024
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@github-actions GitHub Actions
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This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Sep 24, 2024
@github-actions github-actions bot added the abandoned abandoned issue/PR as determined by actions bot label Oct 25, 2024
@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Oct 25, 2024
@JacksonBurns JacksonBurns reopened this Jan 22, 2025
@JacksonBurns
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The Python 3.9 upgrade is running into a challenge with Arm-Based Macs that could be solved by resolving this issue.

The juliacall overhaul required with Python 3.9 does not work when running in x86 emulation mode on Apple Silicon, so we would rather run in ARM native. Cantera 2.6 does not have arm-osx builds, but the latest versions of cantera do.

@JacksonBurns JacksonBurns removed stale stale issue/PR as determined by actions bot abandoned abandoned issue/PR as determined by actions bot labels Jan 22, 2025
@JacksonBurns JacksonBurns linked a pull request Jan 22, 2025 that will close this issue
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@JacksonBurns JacksonBurns linked a pull request Jan 22, 2025 that will close this issue
update cantera version to remove need for x86 emulation on arm mac #2751
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This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Apr 23, 2025
@JacksonBurns
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Updating the above comment - we can do the Python 3.9 upgrade w/o incrementing cantera, but not vice versa. Will try and get the Python 3.9 upgrade in first.

What I previously said about the missing builds was wrong, we were looking in the wrong channel.

Also important is that cantera 3.1.0 has a bug with reading surface files used in RMG. It has been resolved (Cantera/cantera#1845 (comment)) but not yet released (as of writing).

@github-actions github-actions bot removed the stale stale issue/PR as determined by actions bot label Apr 24, 2025
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update cantera version to remove need for x86 emulation on arm mac ReactionMechanismGenerator/RMG-Py
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