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YAML format documentation #91

Merged
merged 45 commits into from
Mar 11, 2020
Merged

YAML format documentation #91

merged 45 commits into from
Mar 11, 2020

Commits on Dec 13, 2019

  1. Add link to YAML reference documentation

    @speth
    speth committed Dec 13, 2019
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  2. Fix broken link to class ThermoPhase documentation 

    Needed to be updated after setting Doxygen to use subdirectories
    @speth
    speth committed Dec 13, 2019
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Commits on Mar 9, 2020

  1. Remove CTI-specific content from the 'science' section 

    Useful content that was not already in the CTI tutorial has been
relocated to that section.
    @speth
    speth committed Mar 9, 2020
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  2. Add skeleton for YAML version of "Defining Phases"

    @speth
    speth committed Mar 9, 2020
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  3. Add rudimentary YAML syntax tutorial

    @speth
    speth committed Mar 9, 2020
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  4. Add documentation for YAML phase declarations

    @speth
    speth committed Mar 9, 2020
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  5. more succinct "state" docs

    @speth
    speth committed Mar 9, 2020
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  6. Add docs for YAML elements and species entries

    @speth
    speth committed Mar 9, 2020
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  7. Remove reference to never-implemented "skip" option for reactions

    @speth
    speth committed Mar 9, 2020
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  8. Make local copy of dev docs available

    @speth
    speth committed Mar 9, 2020
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  9. Add documentation for YAML reaction definitions

    @speth
    speth committed Mar 9, 2020
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  10. Fix href target search to work for development API docs 

    Sphinx now generates HTML containing additional CSS class names for
this text, e.g. "sig-name descname", so the old search pattern no longer
works.
    @speth
    speth committed Mar 9, 2020
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  11. Remove unused references from CTI tutorial

    @speth
    speth committed Mar 9, 2020
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  12. Complete the YAML format tutorial

    @speth
    speth committed Mar 9, 2020
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  13. Remove incorrect documentation regarding "stoichiometric liquid" 

    I don't think the CTI `stoichiometric_liquid` class has ever supported a
transport model.
    @speth
    speth committed Mar 9, 2020
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  14. Add links to relevant YAML docs from "Science" section

    @speth
    speth committed Mar 9, 2020
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  15. Link YAML users' guide from dev docs page

    @speth
    speth committed Mar 9, 2020
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  16. Add YAML API docs to ref_targets 

    The YAML API is mostly not functions, but handled as Sphinx sections. So
they are added to ref_targets
    @bryanwweber @speth
    bryanwweber authored and speth committed Mar 9, 2020
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  17. Get the YAML API docs by scraping GitHub 

    Since we clone the 2.4 branch of the repo that doesn't have these docs
    @bryanwweber @speth
    bryanwweber authored and speth committed Mar 9, 2020
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  18. Use ref targets for YAML documentation

    @speth
    speth committed Mar 9, 2020
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  19. Fix references to reST sections with capitalized names 

    All names are normalized to lowercase within docutils
    @speth
    speth committed Mar 9, 2020
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  20. Fix duplicated labels in YAML docs

    @speth
    speth committed Mar 9, 2020
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  21. Change CSS for literal strings to make them stand out more

    @speth
    speth committed Mar 9, 2020
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  22. Fix math formatting in Python / Matlab tutorials

    @speth
    speth committed Mar 9, 2020
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  23. Use one blank line before section headers

    @speth
    speth committed Mar 9, 2020
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  24. Re-order composition and state paragraphs

    @speth
    speth committed Mar 9, 2020
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  25. Add ck2yaml tutorial

    @speth
    speth committed Mar 9, 2020
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  26. Add basic tutorial for cti2yaml and ctml2yaml

    @speth
    speth committed Mar 9, 2020
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  27. Add short descriptions for all models listed in the YAML tutorial

    @speth
    speth committed Mar 9, 2020
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  28. Document dependency on ruamel.yaml

    @speth
    speth committed Mar 9, 2020
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  29. Clarify that main documentation page is for stable version

    @speth
    speth committed Mar 9, 2020
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  30. Add Q / vapor-fraction to list of valid state variables

    @speth
    speth committed Mar 9, 2020
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  31. Fix bad formatting caused by incorrect indentation

    @speth
    speth committed Mar 9, 2020
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  32. Eliminate Latin abbreviations i.e. and e.g.

    @speth
    speth committed Mar 9, 2020
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  33. Avoid impression that charge can be inferred from species name

    @speth
    speth committed Mar 9, 2020
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Commits on Mar 10, 2020

  1. Minor formatting / typo / wording updates

    @speth
    speth committed Mar 10, 2020
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  2. Extend description of Arrhenius expression

    @speth
    speth committed Mar 10, 2020
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  3. Fix missing and incorrect use of \mathrm

    @speth
    speth committed Mar 10, 2020
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  4. Replace dangling "chapter" reference from old CTI guide

    @speth
    speth committed Mar 10, 2020
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  5. Put YAML format first

    @speth
    speth committed Mar 10, 2020
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  6. Revise description of Arrhenius expressions in YAML docs

    @speth
    speth committed Mar 10, 2020
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  7. Always use just "R" for the universal gas constant

    @speth
    speth committed Mar 10, 2020
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  8. Bold YAML file terminology

    @speth
    speth committed Mar 10, 2020
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  9. Formatting changes for chemically-activated reactions

    @speth
    speth committed Mar 10, 2020
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  10. Document --quiet and --extra options of ck2yaml

    @speth
    speth committed Mar 10, 2020
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