[DOC] Proofreading of the OpenMS documentation

[enetz]

The OpenMS documentation is being written by many people in chunks that are usually written once together with a class and then rarely double-checked or proofread. Some typos, grammatical errors and suboptimal formulations remain in the documentation and should be fixed.

To start fixing this, build OpenMS from GitHub with the documentation. Read the built doc in OpenMS_build/doc/index.html . It should look similar to this: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html (hint: here you will also find how to build OpenMS ;) )

Please look for:

• typos and other grammatical errors
• improve readability and completeness of descriptions by editing the doxygen source code (not the HTML!) in OpenMS/doc and doxygen descriptions in C++ class files.
• any other quirks that you encounter

Rebuild the documentation and double-check the updated documentation locally before submitting a pull request with your fixes.

[timosachsenberg]

Is there an easy way to find undocumented public methods? And Maybe an automated way to prioritize them by usage in tools and library?

[greengypsy]

Yes, there is a flag you need to turn on in the Doxyfile (WARN_IF_UNDOCUMENTED).

[timosachsenberg]

Hmm these might be protected (hence the underscore). Having at least the public ones documented would already be great. Is there an option to fine tune warnings or would we need to do some post filtering (e.g. check warnings if they contain only protected or privat methods by checking for substring _(

[greengypsy]

I can't find any way to filter these to only public ones. A script might need to be created to filter the results are the doxyfile is run.