Docs update

[kkaris]

The readthedocs documentation is in need of another round of updates:

• Link to new notebooks in root README
• terarium_client.py - extend docstrings for all functions
• sources:
  • amr:
    • __init__.py: sanity_check_amr() - missing docstring
    • regnet.py: add file header
    • stockflow.py: stock_to_concept() - extend docstring
    • flux_span.py: reproduce_ode_semantics() - extend docstring
  • sbml/api.py: extend docstring for the functions listed in __all__
  • biomodels.py: query_biomodels() - extend docstring
  • acsets/stockflow.py - add docstrings to template_model_from_stockflow_ascet_json
  • acsets/decapodes - modules added and methods in __all__ have docstrings added
  • util.py - module missing
• metamodel:
  • decapodes.py: - module missing, functions and classes need docstrings
  • template_model.py: add/extend docstrings for exposed functions/classes
  • templates.py: add/extend docstrings for exposed functions/classes
  • ops.py: get_term_roles() and deactivate_templates() - extend docstrings
  • comparison.py: add/extend docstrings
  • search.py: extend docstrings
  • io.py: extend docstrings
• modeling:
  • __init__.py: Add docstrings to Model, Transition, Variable and ModelParameter classes
  • amr:
    • petrinet.py: add docstring for ModelSpecification basemodel?
    • ops.py: add/extend docstrings - copy the docstrings of the wrapped functions
    • regnet.py: extend method docstrings for AMRRegNetModel. Add docstring for ModelSpecification basemodel?
  • acsets
    • stockflow.py: add docstring
  • bilayer.py: extend docstrings
• [ ] dkg:
  • [ ] __init__.py: extend docstring
  • [ ] askemo:
    • [ ] askemo_climate.py: module missing
    • [ ] client.py: Add AskemEntity, extend docstrings for Neo4jClient methods
• examples.py Add module - contains among other things example Decapode and DecaExpr json structures

Other documentation to look at

• Rest API docs (under mira/dkg/)
  • model.py
    • /add_transition: add_transition_query Body - add example values
    • Base model AMRComparisonQuery - Extend example list

[kkaris]

New Todo's:

• Add/extend bilayer docstrings
• Go through rest API docs and see if text needs updating
• Skip dkg

[kkaris]

A bunch of classes are excluded from the docs for the templates module, mira.metamodel.templates, see docs/source/metamodel.rst:

Templates (:py:mod:`mira.metamodel.templates`)
----------------------------------------------
.. automodule:: mira.metamodel.templates
    :members:
    :exclude-members: Concept, ControlledConversion, NaturalConversion, Provenance, Template, NaturalDegradation, NaturalProduction, GroupedControlledConversion
    :show-inheritance:

Should we include them now that we anticipate automated reading of the documentation?