Auto generate API documentation

[eboileau]

Aims/objectives.

To document the API, and the code in general. This should go to https://dieterich-lab.github.io/scimodom/.

A clear and concise description of todo items.

Add/format docstrings, add to docs.

[HaraldWilhelmi]

Consider to switch from Flask to FastAPI. That gives a OpenAPI documentation with very little effort.

[HaraldWilhelmi]

Explored that option a bit:

Going to FastAPI is more difficult than I thought. Either we should not do it - or -
prepare this step as follows:

• The code uses Flask CLI commands. IMHO this is unnecessary. The CLI commands could be transformed to standalone commands, removing this Flask dependency completely.
• Both plugins/cli.py and api/public.py contain SQLAchemy code directly interacting with the database. IMHO all the database related stuff should be moved to something like scimodom/services/data.py so that we have a single spot where concentrate all performance relevant database code and separate it e.g. from validation of user input and decoding/encoding of data for Rest calls.