Link C++ and Python SolutionArray implementations

[ischoegl]

Changes proposed in this pull request

Follow-up to #1385.

• Expose C++ core SolutionArray to Python (as SolutionArrayBase)
• Load YAML and HDF SolutionArray formats from Python
• Add support for additional extra types in C++ SolutionArray that are already available in Python, e.g. entries with types string, long int, vector<double> and vector<long int> (internal handling leverages AnyValue)
• Link C++ and Python versions of SolutionArray
• Deprecate Python h5py support and associated dedicated functions; continue support for pre-existing HDF format with core C++ HDF routines; disable creation of new HDF files with legacy format.

With this change, all data available for SolutionArray are stored by the C++ core object, with the Python SolutionArray serving as an external API. At the same time, all property calculations are still handled by the Python interface, although states are being updated in the C++ core.

Due to the size of the PR, some additional features are postponed for a follow-up:

• Save/restore from CSV data (see read_csv does not work for species name with a comma #1372)
• Backport selected SolutionArray.write_hdf capabilities for SolutionArray.save: e.g. default group names
• Implement SolutionArray::show() with ascii pandas-style formatting.
• Make Python SolutionArray picklable/copyable (via YAML)
• Initial ReactorNet.save implementation for single-reactor networks
• Allow for replacing groups in HDF via H5Ldelete see SO post, which is exposed in HighFive as unlink (see declaration)

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

Resolves Cantera/enhancements#137

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

While the way data are handled internally is completely refactored, most changes are completely under the hood, with SolutionArray.save and SolutionArray.restore being an exception.

In [1]: import cantera as ct
   ...: gas = ct.Solution("h2o2.yaml")
   ...: arr = ct.SolutionArray(gas, (5), extra={"spam": [1, 2, 3, 4, 5]})
   ...: arr.save("test.yaml", "entry", description="SolutionArray saved as YAML")
   ...: arr.save("test.h5", "entry", description="SolutionArray saved as HDF")

In [2]: a = ct.SolutionArray(gas)
   ...: a.restore("test.yaml", "entry")
Out[2]:
{'description': 'SolutionArray saved as YAML',
 'generator': 'Cantera SolutionArray',
 'cantera-version': '3.0.0a3',
 'git-commit': "'6b3079996'",
 'date': 'Wed Feb  1 07:13:13 2023'}

In [3]: b = ct.SolutionArray(gas)
   ...: b.restore("test.h5", "entry")
Out[3]:
{'cantera-version': '3.0.0a3',
 'date': 'Wed Feb  1 07:13:13 2023',
 'description': 'SolutionArray saved as HDF',
 'generator': 'Cantera SolutionArray',
 'git-commit': "'6b3079996'"}

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 #1426 (750521f) into main (b076ed9) will increase coverage by 0.26%.
The diff coverage is 80.29%.

@@            Coverage Diff             @@
##             main    #1426      +/-   ##
==========================================
+ Coverage   69.61%   69.87%   +0.26%     
==========================================
  Files         373      373              
  Lines       55846    56686     +840     
  Branches    18338    18883     +545     
==========================================
+ Hits        38875    39609     +734     
- Misses      14516    14564      +48     
- Partials     2455     2513      +58     

Impacted Files	Coverage Δ
include/cantera/base/AnyMap.h	79.41% <ø> (ø)
src/oneD/Domain1D.cpp	76.21% <0.00%> (ø)
src/oneD/Boundary1D.cpp	55.41% <60.00%> (ø)
include/cantera/base/AnyMap.inl.h	53.62% <64.00%> (+1.89%)	⬆️
src/base/AnyMap.cpp	83.24% <67.50%> (-0.57%)	⬇️
interfaces/cython/cantera/onedim.py	89.38% <70.58%> (+1.24%)	⬆️
src/base/Storage.cpp	80.89% <75.11%> (+23.57%)	⬆️
src/base/SolutionArray.cpp	78.17% <77.10%> (+2.54%)	⬆️
interfaces/cython/cantera/composite.py	89.07% <96.89%> (-1.02%)	⬇️
interfaces/cython/cantera/solutionbase.pyx	89.66% <98.66%> (+3.44%)	⬆️
... and 5 more

... and 2 files with indirect coverage changes

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[ischoegl]

@speth - thank you for the review! I believe that everything is addressed; I also rebased to #1455.

[speth]

Thanks for the updates, @ischoegl. I have just a couple of remaining comments.

[ischoegl]

@speth ... I adopted both suggestions/requests.

[speth]

Thanks, @ischoegl! I think this is good to go. I'm going to ignore the transient failure of the "coverage" builder, as we already have the coverage testing results.