Read and write idXML files using pyopenms

[jonasscheid]

Added

• io.idxml: Write support for idXML files, including merging an existing idXML with a PSMList 🎉
• Docs: Add intersphinx links to other package documentation pages.

Changed

• io.idxml: Use pyOpenMS instead of Pyteomics for reading idXML (~5x faster⚡)
• Fixed Black formatting throughout project

[jonasscheid]

Black reformatting mostly responsible for the number of files changed 😁
The PR also includes now tests for reading and writing idXML.

Ready to review @RalfG

[ypriverol]

@jonasscheid thanks for this PR, we have an issue in quantms that depends on this PR. @RalfG we have tested the previous version and it is really not working. Can you help us and give priority to this PR and a new version of ms2rescore for me to test 😜. Thanks in advance.

[jonasscheid]

@ypriverol Can you test if the reader and writer do a proper job for you? Would be good to know before this can be merged

[RalfG]

Great work, @jonasscheid! I did some benchmarking, and this implementation is about 5x faster at reading idXML than the previous version 🚀

Some more minor points that require attention and a bigger one (modification parsing) that did not seem to be working yet.