Deprecate redundant kinetics methods in Python API

[ischoegl]

Changes proposed in this pull request

• Deprecate redundant / unpythonic methods that mimic the C-API (all alternative methods already exist):
  • Kinetics.reaction_type(i) -> Kinetics.reaction(i).reaction_type
  • Kinetics.is_reversible(i) -> Kinetics.reaction(i).reversible
  • Kinetics.reaction_equation(i) -> Kinetics.reaction(i).equation
  • Kinetics.reactants(i) -> Kinetics.reaction(i).reactant_string
  • Kinetics.products(i) -> Kinetics.reaction(i).product_string
• Improve rendering of Reaction.__repr__, where essential information was lost in Eliminate unnecessary specialized Reaction types #1183
• Fix indentation and blank lines for Sphinx docstring deprecation information

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

After #1183, several reactions no longer show specialized information (which is held by the ReactionRate), where specifically no identifiable information is shown for Chebyshev and pressure-dependent-Arrhenius (Plog) (as well as the new Blowers-Masel and two-temperature-plasma types), e.g.

in [1]: import cantera as ct
   ...: gas = ct.Solution("test/data/kineticsfromscratch.yaml")
   ...: gas.reactions()
Out[1]: 
[<Reaction: H2 + O <=> H + OH>,
 <ThreeBodyReaction: 2 O + M <=> O2 + M>,
 <FalloffReaction: 2 OH (+M) <=> H2O2 (+M)>,
 <Reaction: H2 + O2 <=> 2 OH>,
 <Reaction: HO2 <=> O + OH>,
 <ThreeBodyReaction: H + O2 + O2 <=> HO2 + O2>,
 <Reaction: H2 + O <=> H + OH>,
 <FalloffReaction: 2 OH (+M) <=> H2O2 (+M)>,
 <FalloffReaction: H + HO2 (+M) <=> H2 + O2 (+M)>,
 <FalloffReaction: H + HO2 (+M) <=> H2 + O2 (+M)>,
 <ChemicallyActivatedReaction: H2O + OH (+M) <=> H2 + HO2 (+M)>,
 <Reaction: H + O => H + O>,
 <Reaction: O + OH => O + OH>]

This PR reformats Reaction.__repr__ to always include information for the rate specialization.

In [1]: import cantera as ct
   ...: gas = ct.Solution("test/data/kineticsfromscratch.yaml")
   ...: gas.reactions()
Out[1]: 
[H2 + O <=> H + OH    <Reaction(Arrhenius)>,
 2 O + M <=> O2 + M    <ThreeBodyReaction(Arrhenius)>,
 2 OH (+M) <=> H2O2 (+M)    <FalloffReaction(Troe)>,
 H2 + O2 <=> 2 OH    <Reaction(pressure-dependent-Arrhenius)>,
 HO2 <=> O + OH    <Reaction(Chebyshev)>,
 H + O2 + O2 <=> HO2 + O2    <ThreeBodyReaction(Arrhenius)>,
 H2 + O <=> H + OH    <Reaction(Blowers-Masel)>,
 2 OH (+M) <=> H2O2 (+M)    <FalloffReaction(Lindemann)>,
 H + HO2 (+M) <=> H2 + O2 (+M)    <FalloffReaction(SRI)>,
 H + HO2 (+M) <=> H2 + O2 (+M)    <FalloffReaction(Tsang)>,
 H2O + OH (+M) <=> H2 + HO2 (+M)    <ChemicallyActivatedReaction(Lindemann)>,
 H + O => H + O    <Reaction(two-temperature-plasma)>,
 O + OH => O + OH    <Reaction(two-temperature-plasma)>]

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 #1202 (0889b09) into main (041559d) will decrease coverage by 0.02%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1202      +/-   ##
==========================================
- Coverage   65.41%   65.38%   -0.03%     
==========================================
  Files         318      318              
  Lines       46085    46095      +10     
  Branches    19604    19604              
==========================================
- Hits        30145    30139       -6     
- Misses      13426    13442      +16     
  Partials     2514     2514              

Impacted Files	Coverage Δ
src/base/application.h	69.76% <0.00%> (-15.95%)	⬇️
src/base/global.cpp	70.58% <0.00%> (-4.26%)	⬇️
include/cantera/base/global.h	81.81% <0.00%> (-2.40%)	⬇️
src/base/application.cpp	63.98% <0.00%> (-1.26%)	⬇️
src/kinetics/Kinetics.cpp	72.47% <0.00%> (-0.46%)	⬇️
include/cantera/cython/wrappers.h	85.15% <0.00%> (-0.33%)	⬇️
src/kinetics/Reaction.cpp	81.07% <0.00%> (+0.17%)	⬆️
src/kinetics/Falloff.cpp	85.39% <0.00%> (+0.74%)	⬆️
include/cantera/base/logger.h	78.57% <0.00%> (+5.84%)	⬆️

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[speth]

Looks good to me -- I just had one minor suggestion, but I don't think it affects much either way.

Longer term, I'd like to eliminate these from C++ as well, though that would require updating the C / Matlab / Fortran APIs, which currently have no notion of a Reaction object.

[bryanwweber]

Thanks @ischoegl! A few small comments.

[bryanwweber]

Thanks @ischoegl looks good to me! I'll wait for @speth to approve as well, since he also left a review.

[bryanwweber]

Ah, I see @speth approved. Feel free to once the checks are all green.