From 8d1ec298f9ccaf109a1fbfa933b0484eb031f558 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 20 Jan 2018 12:59:23 +0530
Subject: [PATCH] introduction folder is aded in doc. git are converted to pdf
in pdf #232. Using `libertine` font in pdf doc.
---
docs/source/conf.py | 33 +++++++++++------
docs/source/index.rst | 21 +----------
.../introduction/index_introduction.rst | 7 ++++
docs/source/introduction/introduction.rst | 35 +++++++++++++++++++
4 files changed, 65 insertions(+), 31 deletions(-)
create mode 100644 docs/source/introduction/index_introduction.rst
create mode 100644 docs/source/introduction/introduction.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 03dd973c..53522447 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -197,20 +197,29 @@ htmlhelp_basename = 'MOOSE'
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+'papersize': 'a4paper',
# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+'pointsize': '11pt',
# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+'preamble': r'''
+\usepackage{libertine}
+\usepackage{mathpazo}
+\usepackage{epstopdf}
+% Convert GIF to PNG in pdf.
+\epstopdfDeclareGraphicsRule{.gif}{png}{.png}{convert gif:#1 png:\OutputFile}
+\AppendGraphicsExtensions{.gif}
+ '''
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'MOOSE.tex', u'MOOSE Documentation',
- u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda storz', 'manual'),
+ ('index', 'MOOSE.tex', u'MOOSE User Manual',
+ r'Upinder Bhalla, Niraj Dudani, Subhasis Ray \\Aditya Gilra,Harsha Rani, Aviral Goel \\ Dilawar Singh, Malav Shah, Dhruva Gowda Storz'
+ , 'manual'
+ ),
]
# The name of an image file (relative to this directory) to place at the top of
@@ -219,13 +228,13 @@ latex_logo = 'images/moose_logo.png'
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
-#latex_use_parts = False
+latex_use_parts = True
# If true, show page references after internal links.
latex_show_pagerefs = True
# If true, show URL addresses after external links.
-#latex_show_urls = False
+latex_show_urls = True
# Documents to append as an appendix to all manuals.
#latex_appendices = []
@@ -239,12 +248,12 @@ latex_domain_indices = True
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'moose', u'MOOSE Documentation',
- [u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda storz'], 1)
+ ('index', 'moose', u'MOOSE User Manual',
+ [u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda Storz'], 1)
]
# If true, show URL addresses after external links.
-#man_show_urls = False
+man_show_urls = True
# -- Options for Texinfo output ------------------------------------------------
@@ -254,7 +263,9 @@ man_pages = [
# dir menu entry, description, category)
texinfo_documents = [
('index', 'MOOSE', u'MOOSE Documentation',
- u' Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda storz', 'MOOSE', 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
+ u'Upinder Bhalla, Niraj Dudani, Subhasis Ray, Aditya Gilra,Harsha Rani, Aviral Goel, Dilawar Singh, Malav Shah, Dhruva Gowda Storz'
+ , 'MOOSE'
+ , 'MOOSE is the Multiscale Object-Oriented Simulation Environment.',
'Science'),
]
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 62dfb486..55a9f2f5 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -2,29 +2,10 @@
sphinx-quickstart on Tue Jan 31 14:57:39 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-
-MOOSE
-=====
-
-What is MOOSE and what is it good for?
---------------------------------------
-MOOSE is the **Multiscale Object-Oriented Simulation Environment**. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
-
-.. figure:: images/Gallery_Moose_Multiscale.png
- :scale: 75%
- :alt: **multiple scales in moose**
-
- *Multiple scales can be modelled and simulated in MOOSE*
-
-MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
-
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
-
-MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
-
.. toctree::
:maxdepth: 2
+ /introduction/index_introduction
/install/index_install
/user/py/quickstart/index_qs
/user/py/cookbook/index_ckbk
diff --git a/docs/source/introduction/index_introduction.rst b/docs/source/introduction/index_introduction.rst
new file mode 100644
index 00000000..79dae614
--- /dev/null
+++ b/docs/source/introduction/index_introduction.rst
@@ -0,0 +1,7 @@
+Introduction
+============
+
+.. toctree::
+ :maxdepth: 1
+
+ introduction
diff --git a/docs/source/introduction/introduction.rst b/docs/source/introduction/introduction.rst
new file mode 100644
index 00000000..961f87f8
--- /dev/null
+++ b/docs/source/introduction/introduction.rst
@@ -0,0 +1,35 @@
+What is MOOSE and what is it good for?
+-------------------------------------
+
+MOOSE is the **Multiscale Object-Oriented Simulation Environment**. It is
+designed to simulate neural systems ranging from subcellular components and
+biochemical reactions to complex models of single neurons, circuits, and large
+networks. MOOSE can operate at many levels of detail, from stochastic chemical
+computations, to multicompartment single-neuron models, to spiking neuron
+network models.
+
+.. figure:: images/Gallery_Moose_Multiscale.png
+ :scale: 75%
+ :alt: **multiple scales in moose**
+
+ *Multiple scales can be modelled and simulated in MOOSE*
+
+MOOSE is multiscale: It can do all these calculations together. One of its major
+uses is to make biologically detailed models that combine electrical and
+chemical signaling.
+
+MOOSE is object-oriented. Biological concepts are mapped into classes, and a
+model is built by creating instances of these classes and connecting them by
+messages. MOOSE also has numerical classes whose job is to take over difficult
+computations in a certain domain, and do them fast. There are such solver
+classes for stochastic and deterministic chemistry, for diffusion, and for
+multicompartment neuronal models.
+
+MOOSE is a simulation environment, not just a numerical engine: It provides data
+representations and solvers (of course!), but also a scripting interface with
+Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for
+many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p
+formats, HDF5 and NSDF for data writing.
+
+.. toctree::
+ :maxdepth: 1
--
GitLab