user

This directory contains MOOSE user documentation.

The documentation is encoded in the Markdown format. Each of the Markdown
files is converted here to a corresponding HTML file for viewing in a browser,
and can be converted to many other formats. To learn more about the Markdown
format itself, go to the other 'markdown' directory one level up, in the
main 'Docs' directory.

Here are some of the important files:
	- index.html:
			If you just want to read the documentation, open this file in 
			your browser, and start exploring! This file links to all the 
			other user documents. All the user documents are listed below as
			well, as *.markdown files.
	- markdown/pymoose2walkthrough.markdown:
			"Getting started with python scripting for MOOSE"
	- markdown/MooseGuiDocs.markdown:
			"MOOSEGUI: Graphical interface for MOOSE"
	- markdown/Nkit2Documentation.markdown:
			"Neuronal simulations in MOOSEGUI". THIS IS CURRENTLY NOT INCLUDED
	- markdown/Kkit12Documentation.markdown:
			"Kinetikit 12: Interface for chemical kinetic models in MOOSEGUI"
	- markdown/RdesigneurDocumentation:markdown:
			"Reaction Diffusion and Electrical SIGnaling in NEURons):Interface
			 to the multiscale modeling capabilities in MOOSE"
	- markdown/moosebuiltindocs.markdown:
			"MOOSE class and function documentation"
			This file is auto-generated by the 'py/digestbuiltindocs.py' 
			Python script (see below).
	- py/digestbuiltindocs.py: This Python script compiles all the inline
			documentation for MOOSE classes and functions, as visible in the
			MOOSE Python module, into a Markdown text file. THIS IS CURRENTLY
            BROKEN.
    - py/create_rest_doc.py: This Python script compiles all the inline 
            documentation for MOOSE classes and functions, as visible in the
            MOOSE Python module, into a reST text file.
    - py/index.rst: This is the index file for use when building the Python
            docs using sphinx.
    - py/moose_builtins.rst: This is for sphinx to process the pymoose builtin 
            doc strings (using autodoc extension)
    - py/moose_classes.rst: This is generated by running py/create_rest_doc.py
            and has the extracted inline documentation of MOOSE classes and
            their fields.
	- build: Shell script to do the necessary compilation and conversions.

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N.B.: This text file has Windows-style line endings (CR/LF) for easy
viewing in Windows. We will try to keep the other text files here
Windows-compatible (e.g.: *.markdown files), but we may slip.
If you have difficulty viewing them in Notepad, try the inbuilt Wordpad
editor, or better still, download a good text editor like Notepad++ or Geany.
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