* Modify `cell kind` concept docs.
* Add `cell description` concept docs.
* Reorder the docs so that the recipe, cell kind and description, interconnectivity, hardware management, domain decomposition, and simulation are consecutive. Then start the more detailed cable cell docs. 

* Synced pages between Concepts, Python API and C++ API wherever possible
    * Recipe pages conform between the three section (concepts, python, c++)
    * Cell, Cable Cell and Cell * pages are rearranged and provided with some copy explaining the relationship between them.
* Moved Python API out of Concepts
* Renamed Concepts "How does Arbor work?"
* Added Python Module Index plus mock import of Arbor for RTD build (unfortunately won't show there)
* Broke out Interconnectivity (synapses) page.
* Reworked Single Cell Model page into a quick start, with lots of cross referencing.
* Tweaked logo.
* Added Spack to install options.
* Updated blurb.
* Documentation now follows EU capitalization rules.
* Assorted typofixes

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Add docs for Python wrapper to ReadTheDocs:

- Overview, Common Types, Hardware Management, Recipes, Domain Decomposition, Simulations, Metering
- Installing Arbor: Optional Requirements (Python), Buidling and Installing (Python Frontend), and Installation (Python Module)

Missing (, since not implemented yet): 

- probes
- arbor-sup 
- hint maps in domain_decomposition
- reset, events, empty schedule in event_generator
Also does not cover unit testing (since doc is user-centric).

Makes also defaults and units in wrapper consistent.

Fixes  #766

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

Add gap junctions and improve general model overview in docs.

* Replace Arbor Model::Common Types with Arbor Model::Concepts, that introduces the concept of cells, connections and gap junctions. 
* Add gap junction documentation to cpp:recipe
* Document the implicit rule forcing cells connected by gap junctions to be in the same cell group.
* Add documentation that discusses core concepts in Arbor models.

Update Hardware API documentation

* split the domain decomposition and hardware API docs into separate pages
* update hardware API to reflect new *libarbor* and *libarborenv*
* add basic documentation for `optional`, `any` and `unique_any` types.

Update the installation guide to reflect the latest supported tool,
compiler and library versions.

Remove the Python docs, because they documented features that have not
been implemented yet. The Python docs can be added incrementally as
features are implemented.

Start work on oupdating the documenetation for hardware interfaces and
domain decomposition.

akuesters authored 6 years ago and Benjamin Cumming committed 6 years ago

Update documentation for Python.

    splits the conceptual model ideas from the C++ docs into their own section
    has C++ and Python docs for recipes, domain decomposition, etc.

fixes #667

Added the following documentation (structure):

GETTING STARTED:

    Installing Arbor/Requirements/Optional Requirements/Python
    Installing Arbor/Building and Installing Arbor/Python Front End

MODEL BASICS:

    Overview
    Common Types
    Recipes
    Domain Decomposition
    Simulations

PYTHON:

    Overview
    Common Types
    Recipes
    Domain Decomposition
    Simulations

DEVELOPERS:

    Python Profiler
    Python Unit Testing

GETTING STARTED has two added sections of optional requirements using python and how to build the python front end.

MODEL BASICS describes Arbor's concepts in general (independent of programming language), thus general information on concepts in C++ API was moved here/ added.

PYTHON describes Arbor's python frontend in the same structure as MODEL BASICS and C++ API ( needs updates as soon as features are added/changed in new python PR).

DEVELOPERS section has two added sections for meter management and unit testing with python front end.

Further, some corrections in existing documentation (for obvious errors, e.g. duplicate text, not ending sentences) and referencing sections were done.