Fix compiler warnings

[speth]

Changes proposed in this pull request

• Fix various compiler warnings. Almost all CI configurations are currently free of warnings for compiling both the main library as well as the test suite, with a couple of exceptions
  • The Intel compiler generates some warnings from within Eigen, and seems to be ignoring the compiler flags that are intended to ignore warnings from external/system libraries.
  • MSVC issues some warnings about symbols from yaml-cpp being marked as DLL export that MSVC thinks maybe shouldn't be.
• Fix deprecation warnings from Numpy about treating non-zero-D arrays a scalars
• Check that mass flow rate is set for FlowReactor. On macOS using openblas, not doing this before calling initialize would lead to a confusing LAPACK error.
• Update yaml-cpp submodule (to fix warnings related to C++17)
• Improve deprecation warnings issued from Python to include the name of the deprecated method, and to show the line where that function is called from (rather than the line with the call to warnings.warn
• Hide "expected" warnings in the pytest test suite
• Fix documentation typos and some Doxygen formatting issues
• Bump version to 3.0.0b1 (the corresponding commit will be tagged after this is merged). I'll hold off on merging this until after a couple of other currently-open PRs are merged.

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 #1519 (4fb1d76) into main (7a8174c) will decrease coverage by 0.02%.
The diff coverage is 54.76%.

@@            Coverage Diff             @@
##             main    #1519      +/-   ##
==========================================
- Coverage   70.51%   70.50%   -0.02%     
==========================================
  Files         376      376              
  Lines       59072    59075       +3     
  Branches    21217    21219       +2     
==========================================
- Hits        41653    41649       -4     
- Misses      14344    14348       +4     
- Partials     3075     3078       +3     

Impacted Files	Coverage Δ
include/cantera/kinetics/InterfaceKinetics.h	87.50% <ø> (ø)
include/cantera/numerics/AdaptivePreconditioner.h	96.29% <ø> (ø)
include/cantera/oneD/IonFlow.h	73.33% <ø> (ø)
include/cantera/thermo/ConstCpPoly.h	66.66% <ø> (ø)
...nclude/cantera/thermo/CoverageDependentSurfPhase.h	68.00% <ø> (ø)
include/cantera/thermo/GibbsExcessVPSSTP.h	12.50% <ø> (ø)
include/cantera/thermo/IdealGasPhase.h	89.74% <ø> (ø)
include/cantera/thermo/LatticePhase.h	87.50% <ø> (ø)
include/cantera/thermo/LatticeSolidPhase.h	38.70% <ø> (ø)
include/cantera/thermo/MargulesVPSSTP.h	100.00% <ø> (ø)
... and 30 more

... and 1 file with indirect coverage changes

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[ischoegl]

@speth ...see also #1520; I had already fixed most of the issues by the time this was opened; the other PR doesn't have the YAML fix though.

[ischoegl]

Thanks for merging #1520! Dropping 08275dc will resolve conflicts here (it is redundant to 745217c).

[ischoegl]

🎉 ... thanks, @speth. This all looks good to me!