Rewrite Jupyter Notebook examples as Python examples

[speth]

Changes proposed in this pull request

• Rewrite (most) examples from https://github.com/Cantera/cantera-jupyter as pure Python examples to be parsed by Sphinx Gallery. There are a few exceptions:
  • Skip 1D_pfr_surfchem.ipynb, It is almost wholly superseded by the FlowReactor-based version (1D_pfr_surfchem.py). The only exception is the "adiabatic" case, but this is problematic because the original reaction kinetics are only valid at a single temperature.
  • The useful comments and features from batch_reactor_ignition_delay_NTC.ipynb and nonideal_shock_tube.ipynb are incorporated into the existing NonIdealShockTube.py example.
  • lithium_ion_battery.ipynb was used to update the existing lithium_ion_battery.py, mainly by including the extended model description.
  • flame_speed_with_sensitivity_analysis.ipynb was used to update the existing flamespeed_sensitivity.py
  • twin_premixed_flame_axisymmetric.ipynb was used to update the existing premixed_counterflow_twin_flame.py.
  • I'm not quite sure what to do with ck2yaml_demo.ipynb. Bringing this back into the main repository would bring back in a bunch of CK input data that we deliberately removed, and I'm not sure how useful it is in general compared to the ck2yaml tutorial already in the Users' Guide.. Per @ischoegl's comment below, this example is not being migrated.
• Fix a documentation typo in the PFR model description as noted in the Users' Group

For all the examples that included diagrams, I re-drew the PNGs in Adobe Illustrator and saved them as SVGs, to avoid having to commit these moderately large binary files into the repo, and because the vector versions just look nicer.

I've added co-author credit in the commit message for the original authors of the Jupyter examples.

Note that this already incorporates the fix to the 1D packed bed example from Cantera/cantera-jupyter#47.

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

• I believe this is the last major step in addressing Reorganize website source material to simplify updating enhancements#178.

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

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

[ischoegl]

I'm 👍 with removing ck2yaml_demo.ipynb, even though I had created it to document how the input files were created in the first place. Perhaps we can preserve some of this history with some annotations in the yaml files we distribute? At the same time, I don't have strong opinions either way.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.69%. Comparing base (0c89553) to head (923af6f).
Report is 17 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1681      +/-   ##
==========================================
+ Coverage   72.76%   75.69%   +2.93%     
==========================================
  Files         378      443      +65     
  Lines       56986    60975    +3989     
  Branches    20691     9551   -11140     
==========================================
+ Hits        41468    46158    +4690     
+ Misses      12463    11786     -677     
+ Partials     3055     3031      -24     

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[ischoegl]

Thanks for your work on this, @speth. Merging the notebooks back into samples is greatly appreciated!