documentation work

doc/source/GettingStarted.txt

@@ -1,6 +1,6 @@
-\tableofcontents
+@tableofcontents
 
-/*! \page intro Introduction 
+/*! @page intro Introduction 
 
 PIO is a software interface layer designed to encapsolate the
 complexities of parallel IO and make it easier to replace the lower
@@ -9,12 +9,14 @@ href=http://www.unidata.ucar.edu/software/netcdf/docs/html_guide/index.html#user
 netcdf </a> and <a
 href=http://trac.mcs.anl.gov/projects/parallel-netcdf> pnetcdf </a>.
 
+@image html PIO_Library_Architecture1.jpg
+
 Basic description of how to optimize IO in a parallel environment:
 
-PIO calls are collective.  A MPI communicator is set in a call to \ref
+PIO calls are collective.  A MPI communicator is set in a call to @ref
 PIO_init and all tasks associated with that communicator must
 participate in all subsequent calls to PIO.  An application can make
-multiple calls to \ref PIO_init in order to support multiple MPI
+multiple calls to @ref PIO_init in order to support multiple MPI
 communicators.
 
 Begin by getting and unpacking the most recent release of PIO from
@@ -27,21 +29,21 @@ any remaining questions can be answered.
 
 ### Using PIO has three basic steps. ###
 
-1. Your program should call the \ref PIO_init function, and provide
+1. Your program should call the @ref PIO_init function, and provide
 the MPI communicator (and the rank within that communicator) of the
 calling task. This call initializes an IO system type structure that
 will be used in subsequent file and decomposition functions.
 
-2. You can open a file for reading or writing with a call to \ref
-PIO_createfile or \ref PIO_openfile. In this call you will specify the
+2. You can open a file for reading or writing with a call to @ref
+PIO_createfile or @ref PIO_openfile. In this call you will specify the
 file type: pio_iotype_netcdf, pio_iotype_pnetcdf, pio_iotype_netcdf4c
 or pio_iotype_netcdf4p; along with the file name and optionally the
 netcdf mode.
 
 3. Finally, you can read or write decomposed data to the output
 file. You must describe the mapping between the organization of data
 in the file and that same data in the application space.  This is done
-in a call to \ref PIO_initdecomp. In the simplest call to this
+in a call to @ref PIO_initdecomp. In the simplest call to this
 function, a one dimensional integer array is passed from each task,
 the values in the array represent the offset from the beginning of the
 array on file.

doc/source/base.txt

@@ -1,27 +1,11 @@
-/******************************************************************************
- *
- * 
- *
- * Copyright (C) 2009 
- *
- * Permission to use, copy, modify, and distribute this software and its
- * documentation under the terms of the GNU General Public License is hereby 
- * granted. No representations are made about the suitability of this software 
- * for any purpose. It is provided "as is" without express or implied warranty.
- * See the GNU General Public License for more details.
- *
- * Documents produced by Doxygen are derivative works derived from the
- * input used in their production; they are not affected by this license.
- *
- */ 
 /*! 
 
-\mainpage Parallel I/O Libraries (PIO)
+@mainpage Parallel I/O Libraries (PIO)
 
-\author Jim Edwards
-\author John M. Dennis
-\author Mariana Vertenstein
-\author Edward Hartnett
+@author Jim Edwards
+@author John M. Dennis
+@author Mariana Vertenstein
+@author Edward Hartnett
 
 The Parallel IO libraries (PIO) are high-level parallel I/O C and
 Fortran libraries for structured grid applications. PIO provides a
@@ -41,15 +25,15 @@ examples on how it can be used. Please watch the PIO GitHub site
 [https://github.com/NCAR/ParallelIO] for announcements and new
 releases.
 
- - \ref intro
- - \ref install
- - \ref mach_walkthrough
- - \ref decomp
- - \ref error
- - \ref test
- - \ref examp
- - \ref faq
- - \ref api
- - \ref c_api
- - \ref contributing_code
+ - @ref intro
+ - @ref install
+ - @ref mach_walkthrough
+ - @ref decomp
+ - @ref error
+ - @ref test
+ - @ref examp
+ - @ref faq
+ - @ref api
+ - @ref c_api
+ - @ref contributing_code
 */

doc/source/contributing_code.txt

@@ -1,4 +1,4 @@
-/*! \page contributing_code Guide for Contributors
+/*! @page contributing_code Guide for Contributors
 
 # Introduction #
 
@@ -118,34 +118,19 @@ all issues have been resolved.
 <ul>
 
 <li>Programmers begin work on a feature or fix by branching from
-develop.
+master.
 
-<li>When a branch is ready, it is submitted to code review.
+<li>When a branch is ready, it is submitted to code review via pull
+request. Travis CI testing is automatically run on the PR.
 
 <li>When code review is complete, and the changes are approved, the PR
-is merged into the develop branch.
+is merged into the master branch.
 
-<li>Mutliple merges into the develop branch may take place between
-test cycles. (???)
-
-<li>The develop branch is tested automatically by Jenkins.
-
-<li>The develop branch is tested periodically by CDash (every ~6
-hours).
-
-<li>After all jenkins and Cdash builds complete successfully, with all
-tests passing, and no warnings, the PR is merged into master by the
-integrator.
-
-<li>Multiple PRs may be merged to master between test cycles. (???)
+<li>The master branch is tested periodically by CDash (every ~6
+hours). Any test failures and the merge to master may be rolled back.
 
 <li>The branch is then deleted by whomever merged it to master.
 
-<li>The master branch is then tested on Jenkins.
-
-<li>The master branch is tested on CDash. Any test failures and the
-merge to master will be rolled back.
-
 </ul>
 
 ## Formatting Example ##
@@ -247,11 +232,4 @@ int PIOc_inq_attname(int ncid, int varid, int attnum, char *name)
 }
 </pre>
 
-## Further Information ##
-
-<p>For style issues not already covered in this document, see this <a
-href="https://www.kernel.org/doc/Documentation/CodingStyle">style
-guide</a>.
-
-_Last updated: 05-16-2016_
 */