Merge branch 'master' into baagaard/fix-setup-darwin

* master:
Added some more hints.
Update to spatialdata 1.9.5.
Update to 2.1.0.
Update copyright.
Update URL for issues (use git).
Update copyright.
Update m4 to current.
Remove --depth 1 from git clone commands.
Updated netCDF4 python. Fixed associated dependency.
Fixed spelling in documentation.
Updated mpich, openmpi, and cppunit packages.

Conflicts:
	Makefile.am

Author: baagaard-usgs

COPYING

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2014 University of California, Davis
+Copyright (c) 2010-2015 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

INSTALL

@@ -25,6 +25,8 @@ out the PyLith and PETSc source code from the Git repositories
 (requires git be installed); only use this option if you need the
 bleeding edge versions and are willing to rebuild frequently.
 
+If you encounter trouble during the installation, see the
+TROUBLESHOOTING section at the end of this file.
 
 ======================================================================
 System Requirements
@@ -62,7 +64,13 @@ IMPORTANT: We *STRONGLY* recommend that you run the configure script
   in a different directory from the PyLith Installer source code. We
   recommend creating a build directory (for example,
   $HOME/build/pylith) where you build any software with a subdirectory
-  for PyLith.
+  for PyLith. 
+
+IMPORTANT: We also *STRONGLY* recommend that you install PyLith and
+  its dependencies to its own directory (for example
+  --prefix=$HOME/pylith). This makes it easier to start over should
+  you encounter an error, in addition to managing multiple versions or
+  different builds.
 
 WARNING: If you need to reconfigure the installer, then you should
   remove all of your build and install files *BEFORE* running
@@ -122,14 +130,14 @@ STEP 1 - Download and unpack the installer
 
 Download the installer.
 
-  http://www.geodynamics.org/cig/software/pylith/pylith-installer-2.0.3-0.tgz
+  http://www.geodynamics.org/cig/software/pylith/pylith-installer-2.1.0-0.tgz
 
 Untar the source code for the installer:
 
   mkdir -p $HOME/src/pylith
   cd $HOME/src/pylith
-  mv $HOME/Downloads/pylith-installer-2.0.3-0.tgz
-  tar -zxf pylith-installer-2.0.3-0.tgz
+  mv $HOME/Downloads/pylith-installer-2.1.0-0.tgz
+  tar -zxf pylith-installer-2.1.0-0.tgz
 
 
 ----------------------------------------------------------------------
@@ -152,7 +160,7 @@ need to be built.
 
 Run configure with --help to see all of the command line arguments.
 
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure --help
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure --help
 
 -------
 DEFAULT
@@ -164,7 +172,7 @@ DEFAULT
     * MPI
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --with-make-threads=2 \
     --prefix=$HOME/pylith
 
@@ -178,7 +186,7 @@ WITHOUT FORTRAN
     * MPI
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --with-fortran=no \
     --with-make-threads=2 \
     --petsc_options="--download-chaco=1 --download-c-blas-lapack=1" \
@@ -202,7 +210,7 @@ DESKTOP-LINUX-MINIMAL
     * cppunit
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --disable-cppunit \
     --disable-numpy \
     --disable-proj4 \
@@ -222,7 +230,7 @@ DESKTOP-LINUX-OPENMPI
     * C, C++, Fortran compilers
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --enable-python \
     --enable-mpi=openmpi \
     --with-make-threads=2 \
@@ -258,7 +266,7 @@ DESKTOP-DARWIN
   With Fortran support:
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --enable-gcc=fortran \
     --enable-python \
     --enable-mpi=openmpi \
@@ -288,7 +296,7 @@ CLUSTER
     * MPI
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --enable-python \
     --with-make-threads=2 \
     --prefix=$HOME/pylith
@@ -314,7 +322,7 @@ DEVELOPER
     * Mercurial
 
   mkdir -p $HOME/build/pylith
-  $HOME/src/pylith/pylith-installer-2.0.3-0/configure \
+  $HOME/src/pylith/pylith-installer-2.1.0-0/configure \
     --with-pylith-git=master \
     --with-make-threads=2 \
     --prefix=$HOME/pylith
@@ -400,6 +408,27 @@ automatically every time you open a shell.
 TROUBLESHOOTING
 ======================================================================
 
+----------------------------------------------------------------------
+Hints
+----------------------------------------------------------------------
+
+1. Did you forget STEP 3?
+
+   If you added the PyLith environment variables to your shell setup
+   (.bashrc), check to make sure the PyLith directory is listed before
+   other directories in your PATH, LD_LIBRARY_PATH (for Linux),
+   DYLD_LIBRARY_PATH (for Darwin), and PYTHONPATH.
+
+2. If you run into an error and change something (compiler,
+   environment variable, etc), you should reconfigure and rebuild.
+
+  a. Remove the build and install directories ($HOME/build/pylith and
+    $HOME/pylith).
+
+    rm -r $HOME/build/pylith and $HOME/pylith
+
+  b. Try again starting at STEP 2.
+
 ----------------------------------------------------------------------
 numpy fails to build due to a blas/lapack problem
 ----------------------------------------------------------------------
@@ -511,4 +540,4 @@ make: *** [load.o] Error 1
 A fix is to insert the line
 
 #include <config.h>
-above the "#include <stdlib.h>" statement near the beginning of ncgen3/genlib.h.
+above the "#include <stdlib.h>" statement near the beginning of ncgen3/genlib.h.