id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc
892	VERY IMPORTANT: doxygen source code browser	arango		"The ROMS source code is modified to facilitate [https://www.doxygen.nl/index.html doxygen] '''HTLM''' documentation, which is used extensively for generating information, dependencies, and visualizing the relationship between the components of modern source codes written with objective-oriented programming (OOP) principles in several computer languages (C, C++, Fortran, Java, Python, and so on).

It is a little more difficult to configure '''doxygen''' for Fortran source codes than C++. Still, thanks to David Robertson, we found satisfactory results with a sophisticated setup and minor smart changes to the 
ROMS source code layout.

The ROMS '''doxygen''' source code '''HTLM''' documentation is at [http://www.myroms.org/doxygen www.myroms.org/doxygen].

Here is a summary of the changes to the code:

* Change all occurrences of [[span(style=color: #FF0000, '''!>''')]] to [[span(style=color: #FF0000, '''!!^''')]], which are use to document the linearization of the nonlinear kernel to the tangent linear, representer, and adjoint kernels as a reference from the original. This avoids interference with '''doxygen''' native markdown syntax.

* Minor cosmetic changes to the following modules for '''analytical.F''', '''biology.F''', '''bbl.F''', '''propagator.F''', '''prsgrd.F''', '''step2d.F''', '''t3dmix.F''', and '''uv3dmix.F'''.  Basically, the '''MODULE''' declarations are moved to the various flavors of '''.h''' include files. The private subrotines with suffix '''_tile''' are renamed to eliminate identical routine names that are activated with C-preprocessing options.

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Below are examples of the graphical dependencies between code elements (directories and functions/routines).

[[Image(http://www.myroms.org/doxygen/dir_22f00cc7a3d072c17dcf325d075af7a5_dep_org.svg,750px)]]

[[Image(http://www.myroms.org/doxygen/namespacemod__netcdf_aef07e6f2f41a54f0809ea13b13c497cf_icgraph_org.svg, 750px)]]"	upgrade	closed	major	Release ROMS/TOMS 4.0	Nonlinear	3.9	Done