Tutorial enhancements

[cbielow]

This PR enhances the pyOpenMS docs

• enhance glossary and links
• fix broken links
• update installation and build instructions for sphinx
• remove unused (and duplicated) page on hyperscore
• update domain specific terms in glossary

[matteopilz]

Any idea why the notebook test is failing? Is it because of the additional packages?

[cbielow]

not sure actually. I was trying to debug this locally, but the GH workflow is not entirely trivial and relies on GH magic, not locally executable bash scripts or alike.
Will keep trying...

[cbielow]

and the "new" packages are not actually 'extra'. They are part of some docs, which the respective developers seem to have used locally, but did not add to the requirements.txt. The packages were optional, so they just cause warnings when running sphinx-build, not errors.

[jpfeuffer]

It's either a corrupt package or an incomplete download. I would restart the build.

Where do we use ipython syntax?

[cbielow]

It's either a corrupt package or an incomplete download. I would restart the build.

IIRC there was a rebuild after my last commit and the error did not chance.
I've remove the hyperscore rst which was unreferenced according to sphinx (and git grep). Yet the build fails with
[NbConvertApp] WARNING | pattern 'docs/source/hyperscore.ipynb' matched no files, so it might be related to that.

Where do we use ipython syntax?

here: docs/source/user_guide/interfacing_ml_libraries.rst:.. code-block:: ipython3

[jpfeuffer]

Yep. I think the action is wrong. It tries to check all changed files. Deleted files are changed files as well but of course cannot be tested anymore.

I think the previous error with the download was a hiccup.

[jpfeuffer]

Ah hmm that is quite some overhead to install ipython just for colorizing two lines..
But if there is no alternative..

[cbielow]

ok, this seems to have done it. The list of changed files now excludes deleted files.