Simplify creation of interface phases

[speth]

Changes proposed in this pull request

• Automatically import phases adjacent to an interface based on the adjacent-phases YAML field
• Make these phases available using the Solution.adjacent(name) or adjacent(index) methods of the C++ Solution class
• Make these phases available as the Solution.adjacent dict in Python (keyed by phase name)
• Write an adjacent-phases field when serializing interfaces to YAML
• Set the adjacent-phases field when converting mechansims from CK, CTI, or XML formats
• Deprecate the no-longer-used Phase::setRoot method
• Add the missing constructor Edge(filename, phasename)

If applicable, fill in the issue number this pull request is fixing

Closes Cantera/enhancements#103

If applicable, provide an example illustrating new features this pull request is introducing

Python:

tpb_a = ct.Interface("sofc.yaml", "tpb")
anode_surf, oxide_surf_a, anode_bulk = tpb_a.adjacent.values()
oxide_a, gas_a = oxide_surf_a.adjacent.values()

C++:

shared_ptr<Interface> soln = newInterface("stoichSolidKinetics.yaml", "reaction_surface");
shared_ptr<ThermoPhase> gas = soln->adjacent("air")->thermo();

Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review

[codecov]

Codecov Report

Merging #1169 (5e2e8d4) into main (fcff592) will increase coverage by 0.02%.
The diff coverage is 81.75%.

@@            Coverage Diff             @@
##             main    #1169      +/-   ##
==========================================
+ Coverage   65.35%   65.37%   +0.02%     
==========================================
  Files         315      317       +2     
  Lines       45999    46112     +113     
  Branches    19531    19603      +72     
==========================================
+ Hits        30062    30148      +86     
- Misses      13445    13461      +16     
- Partials     2492     2503      +11     

Impacted Files	Coverage Δ
include/cantera/base/YamlWriter.h	100.00% <ø> (ø)
include/cantera/thermo/EdgePhase.h	100.00% <ø> (ø)
include/cantera/thermo/Phase.h	84.61% <ø> (ø)
include/cantera/thermo/ThermoFactory.h	80.00% <ø> (ø)
src/thermo/Phase.cpp	81.12% <0.00%> (-0.39%)	⬇️
src/base/Solution.cpp	79.51% <72.85%> (-5.53%)	⬇️
src/base/Interface.cpp	87.87% <87.87%> (ø)
src/base/YamlWriter.cpp	98.31% <91.66%> (-0.78%)	⬇️
include/cantera/base/Interface.h	100.00% <100.00%> (ø)
include/cantera/base/Solution.h	93.33% <100.00%> (+4.44%)	⬆️
... and 8 more

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[ischoegl]

Thanks for this PR - this is a great addition, which should greatly simplify the instantiation of Interfaces + associated phases. Most of my comments are minor.

As a minor comment, the dictionary values aren't easy to parse in examples, e.g.

tpb_a = ct.Interface("sofc.yaml", "tpb")
anode_surf, oxide_surf_a, anode_bulk = tpb_a.adjacent.values()
oxide_a, gas_a = oxide_surf_a.adjacent.values()

While it can be assumed that users are familiar with what is listed in the input files, this assumes knowledge of a specific order of adjacent phases. I overall believe that a dictionary is the right choice here, but would suggest to access entries by key (this should facilitate understanding in the case of a user just downloading an example file without ever looking into the YAML source).

[ischoegl]

Thank you @speth, this looks good to me. As said, I believe this will greatly simplify the creation of Interfaces (at the least, it makes this much easier to understand for new users).

The only remaining thing will be to update the corresponding YAML tutorial on Cantera/cantera-website.