Fix Autodoc Generation

[ChristianLieven]

• [X] fix #490, #514
• [X] Enables automatic construction of API documentation using https://github.com/rtfd/sphinx-autoapi just like for cobrapy
• [X] add an entry to the next release

[codecov[bot]]

Codecov Report

Merging #608 into develop will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##           develop    #608   +/-   ##
=======================================
  Coverage     79.8%   79.8%           
=======================================
  Files           59      59           
  Lines         3109    3109           
  Branches       427     427           
=======================================
  Hits          2481    2481           
  Misses         555     555           
  Partials        73      73

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