Merge branch 'baagaard/add-release-2.2.0'

* baagaard/add-release-2.2.0: (21 commits)
  Update release checklist to include DOI info.
  Add DOI to README.
  Add software citation w/DOI to manual and code.
  Add DOI to PyLith version info.
  Fix bug in destroying submatrices (use MatDestroySubMatrices()).
  Updated contrib configuration.
  Set version number for cover thumbnail.
  Added list of new features in v2.2.0 to manual.
  Fix link in README.
  Added link to CHANGES in README.
  Update release checklist.
  Updated CHANGES and release notes.
  Fix some formatting typos in manual (Lyx conversion).
  Update release checklist.
  Create macro for PyLith version number.
  Updated manual for v2.2.0. Still need to add list of new features.
  Fixed typo in travis config.
  Add Linux w/clang compiler to build matrix.
  Update copyright.
  Remove obsolete playpen directory.
  ...

Author: baagaard-usgs

.gitmodules

@@ -7,6 +7,3 @@
 [submodule "templates/friction/m4"]
 	path = templates/friction/m4
 	url = git://github.com/geodynamics/autoconf_cig.git
-[submodule "playpen/memcheck/m4"]
-	path = playpen/memcheck/m4
-	url = git://github.com/geodynamics/autoconf_cig.git

.travis.yml

@@ -4,10 +4,15 @@ sudo: false
 
 language: cpp
 
+# :TODO: @brad Add osx build (need homebrew packages)..
 matrix:
   include:
     - os: linux
       env: LD_LIBRARY_PATH="${DEPS_DIR}/lib:${TARGET_DIR}/lib:${LD_LIBRARY_PATH}"
+      compiler: gcc
+    - os: linux
+      env: LD_LIBRARY_PATH="${DEPS_DIR}/lib:${TARGET_DIR}/lib:${LD_LIBRARY_PATH}"
+      compiler: clang
 
 # Limit number of commits in cloning
 git:

CHANGES

@@ -1,14 +1,51 @@
-See
-https://github.com/geodynamics/pylith/commits/master
+See https://github.com/geodynamics/pylith/commits/master
 for the complete log of changes made to PyLith.
 
+======================================================================
+MIGRATING FROM VERSION 2.1 TO 2.2
+======================================================================
+
+No changes are needed to parameter or other input files. The default
+format for pylithinfo output is now JSON.
+
+----------------------------------------------------------------------
+Version 2.2.0
+----------------------------------------------------------------------
+
+* Added a browser-based parameter viewer for interactive viewing of
+  all PyLith parameters and version information. See Section 4.10
+  PyLith Parameter Viewer of the PyLith user manual.
+
+* Converted the user manual from Lyx to LaTeX and added syntax
+  highlighting of parameter and spatial database files. Fixed several
+  typos.
+
+* Fixed bug that sometimes resulted in an inconsistent fault
+  orientation when running in parallel. The bug appears to have been
+  introduced in v2.0.
+
+* Fixed two bugs in output of solution at points that sometimes
+  happened in parallel simulations. The errors include:
+
+    - The order of the station names does not match the order of the
+      points. The point data is written in parallel by process order,
+      so the points for process 0 are written first, then those for
+      process 1, etc. This often results in reordering of the
+      points. The station names were written in the original order.
+    
+    - The output values for some points are incorrect. The wrong cells
+      were being used in the interpolation.
+
+* Updated PETSc to v3.7.5.
+
 ======================================================================
 MIGRATING FROM VERSION 2.0 TO 2.1
 ======================================================================
 
 The points file for OutputSolnPoints must now contain station names as
 the first column.
 
+
 ----------------------------------------------------------------------
 Version 2.1.4
 ----------------------------------------------------------------------

COPYING

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2016 University of California, Davis
+Copyright (c) 2010-2017 University of California, Davis
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

Makefile.am

@@ -9,7 +9,7 @@
 # This code was developed as part of the Computational Infrastructure
 # for Geodynamics (http://geodynamics.org).
 #
-# Copyright (c) 2010-2016 University of California, Davis
+# Copyright (c) 2010-2017 University of California, Davis
 #
 # See COPYING for license information.
 #

README.md

@@ -1,8 +1,9 @@
 # PyLith
 
 [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/geodynamics/pylith/blob/master/COPYING)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXX)
 
-* Branch build status
+## Build status
 * Master: [![Build Status](https://travis-ci.org/geodynamics/pylith.svg?branch=master)](https://travis-ci.org/geodynamics/pylith)
 * Maint: [![Build Status](https://travis-ci.org/geodynamics/pylith.svg?branch=maint)](https://travis-ci.org/geodynamics/pylith)
 * Next: [![Build Status](https://travis-ci.org/geodynamics/pylith.svg?branch=next)](https://travis-ci.org/geodynamics/pylith)
@@ -42,6 +43,10 @@ and volcanoes.
 * Templates for adding your own bulk rheologies, fault constitutive models, and interfacing with a custom seismic velocity model.
 * User-friendly computation of static 3-D Green's functions
 
+## Release Notes
+
+See [CHANGES](CHANGES) for a complete list of changes for each release.
+
 ## Authors
 
 * Brad Aagaard, Earthquake Science Center, USGS, USA

applications/Makefile.am

@@ -9,7 +9,7 @@
 # This code was developed as part of the Computational Infrastructure
 # for Geodynamics (http://geodynamics.org).
 #
-# Copyright (c) 2010-2016 University of California, Davis
+# Copyright (c) 2010-2017 University of California, Davis
 #
 # See COPYING for license information.
 #

applications/pylith.in

@@ -10,7 +10,7 @@
 # This code was developed as part of the Computational Infrastructure
 # for Geodynamics (http://geodynamics.org).
 #
-# Copyright (c) 2010-2016 University of California, Davis
+# Copyright (c) 2010-2017 University of California, Davis
 #
 # See COPYING for license information.
 #

applications/utilities/Makefile.am

@@ -9,7 +9,7 @@
 # This code was developed as part of the Computational Infrastructure
 # for Geodynamics (http://geodynamics.org).
 #
-# Copyright (c) 2010-2016 University of California, Davis
+# Copyright (c) 2010-2017 University of California, Davis
 #
 # See COPYING for license information.
 #

applications/utilities/powerlaw_gendb.py

@@ -9,7 +9,7 @@
 # This code was developed as part of the Computational Infrastructure
 # for Geodynamics (http://geodynamics.org).
 #
-# Copyright (c) 2010-2016 University of California, Davis
+# Copyright (c) 2010-2017 University of California, Davis
 #
 # See COPYING for license information.
 #