Map out structure of domzgr.F90

[jdha]

Produce skeleton of domzgr.F90 routines to hang the python package on.

[oceandie]

HI guys,

I generated the NEMO4.0.4-DOMAINcfg tool call tree documentation using doxygen ( https://www.doxygen.nl/index.html ) with graphviz ( http://www.graphviz.org ).
The output of these software is a bunch of html files that would be nice to include in our pyNEMO documentation.

As far I understood (from @malmans2 ’s notes), our documentation will be automatically generated and managed by Sphynx.
How would you recommend I include my doxygen html documentation in our project?

[oceandie]

As @malmans2 noted, we're not going to upload NEMO code on GitHub - so doc for FORTRAN DOMAINcfg needs to be generated only once. He suggests to put it into pyDOMCFG/docs/_static (maskes sense to me as well) and then just add a reference to it (I am not sure I understand this correctly - you mean in the index?).

@malmans2 also asked about graphviz, since there is an extension for sphinx: https://www.sphinx-doc.org/en/master/usage/extensions/graphviz.html: Would a single .dot file work or we need an html tree?

The .dot file can be embedded using:
.. graphviz:: external.dot

I checked and when running doxygen with graphviz no *.dot files are produced - so I think we might discard this option ....

[malmans2]

Actually, let me check if there's some kind of extension, because if you just link to the FORTRAN index.html then I doubt all links will work...

[malmans2]

Nevermind, maybe it just works.
I would try to place the DOMAINcfg html directory under static, then use a link that opens a new tab. For example, use something like this this to define the link

.. |DOMAINcfg_link| raw:: html

   <a href="./_static/DOMAINcfg_html/index.html" target="_blank">NEMO4.0.4-DOMAINcfg tool call tree</a>

then you can show the reference with:

|DOMAINcfg_link|

I guess you could either place the link in our docs/index.rst, or create a separate .rst with a few words about it under docs/developers

[oceandie]

Naive question: why the doc (https://pydomcfg.readthedocs.io/en/latest/) is not updated with my last merged modfications?

[malmans2]

I can see the call graph. Did you try to force refresh?