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

[rwest]

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]

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]

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)

[github-actions]

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.

[JacksonBurns]

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.