File tree restructure

[pritkc]

• Unified naming conventions throughout the project to align with the standard reference used by libCEED.
• Organized the documentation files within a nested doc/ folder.
• Updated paths in the config.py file for the C++ Doxygen documentation to reflect the new directory structure.
• Removed obsolete parameters in config.py to resolve deprecation warnings with lthe atest version.
• Adjusted paths in the Makefiles.
• Updated paths and improved contextual information in README.md
• Added necessary documentation and build-related files, such as doc/ and Makefile, to .gitignore .

resolves #16

[valeriabarra]

Hi @pritkc , thank you for your work. I would just remove these lines and for now leave only your line 14, where we exclude the doc/build path.

You also want to exclude the path that you have specified in your Doxyfile: in the HTML_OUTPUT variable, that is HTML_OUTPUT = doc/api_docs/cpp

Suggested change

	doc/source/.*
	!doc/source/*.rst
	!doc/source/conf.py
	# Include all non-build documentation files
	!doc/
	doc/api_docs/cpp

[valeriabarra]

Hi @jbrzensk , please make sure that you are ok with the proposed changes to the directory structure.

Basically, @pritkc is proposing to simplify the nomenclature for the different flavors directly as subdirectory names. E.g.:

src/mole_C++ -> src/cpp
src/mole_MATLAB -> src/matlab

And similarly, for the examples and test directories:

examples/examples_C++ -> examples/cpp
examples/examples_MATLAB -> examples/matlab

and

tests/tests_C++ -> tests/cpp
tests/tests_MATLAB -> tests/matlab

[jbrzensk]

Many of the MATLAB examples and all of the tests have the MOLE library location coded in, to run without adding the library to the MATLAB path.

If the folder locations are changed, each of the references in the code must also be updated.

[jbrzensk]

This folder no longer exists. The mole source directory is hard coded into all of the MATLAB examples. If you change the name, all the MATLAB files need the reference changed.

[jbrzensk]

Same here, the tests have the location of the source MATLAB hard coded. If you change the source location, they must be changed in the test files.

[jbrzensk]

Source location incorrect

[jbrzensk]

Source location incorrect

[jbrzensk]

Source location incorrect

[jbrzensk]

Source location incorrect

[jbrzensk]

The source location is incorrect. I am going to stop commenting here, because there are many filepath changes to be made.

[pritkc]

Hi @jbrzensk, thank you for catching that oversight! I noticed there are at least 32 instances that need updating. While we're discussing this, I’d appreciate your thoughts on whether adopting this unified nomenclature is worth any potential inconvenience for future legacy contributors.

[jbrzensk]

Are we including the generated doxygen files in the repository or letting the user create the doxygen files for C++?
What are the contents of doc/api/c++?

[valeriabarra]

Are we including the generated doxygen files in the repository or letting the user create the doxygen files for C++? What are the contents of doc/api/c++?

Hi @jbrzensk , yes, the main idea is to follow libCEED documentation model. We will have step-by-step instructions like libCEED does to explain how to build the documentation. And yes, it's a 2-step build process. First one builds the Doxygen API docs, by running, say, make with the desired target doxygen. This creates the XML files that will be then built in the User Manual by sphinx (through a plug-in that is called breathe).

[jbrzensk]

@valeriabarra I see you addressed this in the .gitignore comment above, sorry.
#17 (comment)