Merge pull request #9 from lcgraham/master

Adding significant updates

Author: lcgraham

.gitignore

@@ -1,4 +1,3 @@
-hershel_bin/
 test.py
 test/
 bin/
@@ -15,10 +14,4 @@ ipython_log.py
 *.e.*
 test.sub
 text.txt
-bin/
-lonestar_landuse_bin/
-remote_bin/
-examples/subdomain_specific/
-polyadcirc/run_framework/subdomain.py
-polyadcirc/run_framework/fulldomain.py
 gh-pages/

doc/Makefile

@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
-BUILDDIR      = ../gh-pages
+BUILDDIR      = _build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)

doc/conf.py

@@ -18,14 +18,29 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
 
+
+
+
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.intersphinx']
+
+intersphinx_cache_limit = 10 #days to keep cached inventories
+intersphinx_mapping = {'python': ('https://docs.python.org/2.7', None),
+                'polyadcirc' : ('http://ut-chg.github.io/PolyADCIRC', None),
+                         'matplotlib':('http://matplotlib.sourceforge.net',
+                             None),
+                         'numpy':('http://docs.scipy.org/doc/numpy',None),
+                         'np':('http://docs.scipy.org/doc/numpy',None),
+                         'scipy':('http://docs.scipy.org/doc/scipy',None)
+                                                                               }
+
+todo_include_todos = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -40,17 +55,17 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'PolySim'
+project = u'PolyADCIRC'
 copyright = u'2013, Lindley Graham'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.0'
+version = '0.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = '0.3.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -96,7 +111,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -129,7 +144,7 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
@@ -169,7 +184,7 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PolySimdoc'
+htmlhelp_basename = 'PolyADCIRCdoc'
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -188,7 +203,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'PolySim.tex', u'PolySim Documentation',
+  ('index', 'PolyADCIRC.tex', u'PolyADCIRC Documentation',
    u'Lindley Graham', 'manual'),
 ]
 
@@ -218,7 +233,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'polysim', u'PolySim Documentation',
+    ('index', 'polyadcirc', u'PolyADCIRC Documentation',
      [u'Lindley Graham'], 1)
 ]
 
@@ -232,8 +247,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'PolySim', u'PolySim Documentation',
-   u'Lindley Graham', 'PolySim', 'One line description of project.',
+  ('index', 'PolyADCIRC', u'PolyADCIRC Documentation',
+   u'Lindley Graham', 'PolyADCIRC', 'Python batch ADCIRC interface.',
    'Miscellaneous'),
 ]
 

doc/index.rst

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 Welcome to PolyADCIRC's documentation!
-==========================================
+======================================
 
 Python-based framework for running batches of parallel `ADCIRC <adcirc.org>`_
 simulations with varying parameters (Manning's *n* and limited variable
@@ -13,25 +13,32 @@ modified verion of :program:`GridData` (Griddata_v1.32.F90).
 :program:`GridData` is a :program:`FORTRAN` program originally developed by
 Seizo Tanaka (ST3) and C.H.Lab., University of Notre Dame.
 
+This code also extends the :program:`PolyADCIRC` framework to interface with a slightly
+modifed version of :program:`Subdomain ADCIRC v.50`. :program:`Subdomain ADCIRC
+v.50` was developed by Alper Altuntas and Jason Simon under the direction of
+John Baugh; Department of Civil, Construction, and Enviromental Engineering
+North Carolina State University (NCSU), Raleigh, NC 27695.
+
 All code documented here is written for Linux with a bash shell. It can be
 modified for other shells. This code requires `GNU Parallel
 <http://www.gnu.org/software/parallel/>`_ to be installed in order to run
 properly.
 
-Useful scripts are contained in ``examples/``
-Python source code for this package is contained in ``polyadcirc/``
-
+.. note:: If you plan on making ANY changes to the repos make a NEW branch!
 
 Contents:
 
 .. toctree::
    :maxdepth: 2
 
    overview
-   Running on TACC <running_on_TACC>
+   Running on Lonestar <running_on_lonestar>
    submerged_wall
    Large Jobs <large_jobs>
    All about mapping landuse data to the mesh <landuse_stuff>
+   subdomain
+   references
+   modules
    todo_list
 
 .. todo:: Add pictures and comment examples.
@@ -43,6 +50,8 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
+
+==========
 Disclaimer
 ==========
 This code was originally developed for research purposes use at your own risk.