Merge pull request #295 from dmcdougall/bump-version

Bump version and update changelog

CHANGES

@@ -4,6 +4,7 @@ Simulation, and Optimization.
 -----------------------------------------------------
 
 Version 0.51.0
+  * Add canned likelihood for scalar GPMSA use-case a la Higdon et al
   * Add a logit-transformed transition kernel for more efficient proposals
   * Adding jeffreys distribution as an available prior distribution
   * Adding likelihood value caching to ML sampler

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script. 
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.50.1], [[email protected]])
+AC_INIT([queso], [0.51.0], [[email protected]])
 PACKAGE_DESCRIPTION="The parallel C++ statistical library QUESO: Quantification of uncertainty for estimation, simulation and optimization"
 AC_SUBST([PACKAGE_DESCRIPTION])
 PACKAGE_URL="https://github.com/libqueso/queso"

manual/users/users.tex

@@ -78,7 +78,7 @@
 \newcommand{\D}{ {\bf D}}
 
 \newcommand{\myverb}[1]{ \indent{ \begin{verbatim} #1 \end{verbatim} } }
-\newcommand{\QUESOversion}{0.50.0}
+\newcommand{\QUESOversion}{0.51.0}
 
 \usepackage{color}
 \definecolor{dkgreen}{rgb}{0,0.6,0}

manual/users/users_2_installation.tex

@@ -177,16 +177,16 @@ \section{Configure QUESO Building Environment}\label{sec:Queso_configure}
 
 
 
-Therefore, the basic steps to configure QUESO using Boost, GSL (required), HDF5 and Trilinos (optional) for installation at `\verb+$HOME/LIBRARIES/QUESO-0.50.0+' are:
+Therefore, the basic steps to configure QUESO using Boost, GSL (required), HDF5 and Trilinos (optional) for installation at `\verb+$HOME/LIBRARIES/QUESO-0.51.0+' are:
 \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}]
-$  ./configure --prefix=$HOME/LIBRARIES/QUESO-0.50.0 \
+$  ./configure --prefix=$HOME/LIBRARIES/QUESO-0.51.0 \
   --with-boost=$HOME/LIBRARIES/boost-1.53.0 \
   --with-gsl=$HOME/LIBRARIES/gsl-1.15 \
   --with-hdf5=$HOME/LIBRARIES/hdf5-1.8.10 \
   --with-trilinos=$HOME/LIBRARIES/trilinos-11.2.4
   \end{lstlisting}
 
-Note: the directory `\verb+$HOME/LIBRARIES/QUESO-0.50.0+' does not need to exist in advance, since it will be created by the command \verb+make install+ described in Section \ref{sec:install_Queso_make}.
+Note: the directory `\verb+$HOME/LIBRARIES/QUESO-0.51.0+' does not need to exist in advance, since it will be created by the command \verb+make install+ described in Section \ref{sec:install_Queso_make}.
 
 
 \section{Compile, Check and Install \Queso{}}\label{sec:install_Queso_make}
@@ -266,7 +266,7 @@ \section{Summary of Installation Steps}\label{sec:summary}
 Supposing you have downloaded the file `queso-0.47.1.tar.gz' into \texttt{\$HOME/queso\_download/}.
 %
 In a BASH shell, the basic steps to configure QUESO using GRVY, Boost and GSL for installation at 
-`\verb+$HOME/LIBRARIES/QUESO-0.50.0+'  are:
+`\verb+$HOME/LIBRARIES/QUESO-0.51.0+'  are:
 
 \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}]
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
@@ -283,7 +283,7 @@ \section{Summary of Installation Steps}\label{sec:summary}
 $ cd $HOME/queso_download/               #enter source dir
 $ gunzip < queso-0.47.1.tar.gz  | tar xf -
 $ cd $HOME/queso_download/queso-0.47.1   #enter the build dir
-$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.50.0 \
+$ ./configure --prefix=$HOME/LIBRARIES/QUESO-0.51.0 \
   --with-boost=$HOME/LIBRARIES/boost-1.53.0 \
   --with-gsl=$HOME/LIBRARIES/gsl-1.15 \
   --with-hdf5=$HOME/LIBRARIES/hdf5-1.8.10 \
@@ -292,13 +292,13 @@ \section{Summary of Installation Steps}\label{sec:summary}
 $ make check
 $ make install 
 $ make docs
-$ ls $HOME/LIBRARIES/QUESO-0.50.0 #listing QUESO installation dir
+$ ls $HOME/LIBRARIES/QUESO-0.51.0 #listing QUESO installation dir
 >>  bin  include  lib  examples
 \end{lstlisting}
 
 % 
 % \paragraph*{Note:} According to  Section \ref{sec:Queso_tree}, \texttt{\$HOME/queso\_download/} is the source tree, \\ \verb+$HOME/queso_download/queso-0.47.1+ is the build tree, and \newline
-% \verb+$HOME/LIBRARIES/QUESO-0.50.0+ is the installation tree.
+% \verb+$HOME/LIBRARIES/QUESO-0.51.0+ is the installation tree.
 % 
 
 
@@ -361,7 +361,7 @@ \section{The Installed Directory Structure} \label{sc-installed-dir-structure}
  \item \verb+bin+: contains the executable \verb+queso_version+, which provides information about the installed library. The code bellow presents a sample output:
 
 \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}]
-kemelli@margarida:~/LIBRARIES/QUESO-0.50.0/bin$ ./queso_version 
+kemelli@margarida:~/LIBRARIES/QUESO-0.51.0/bin$ ./queso_version 
 ---------------------------------------------------------------
 QUESO Library: Version = 0.47.1 (47.1)
 
@@ -381,13 +381,13 @@ \section{The Installed Directory Structure} \label{sc-installed-dir-structure}
 GLPK DIR     = 
 HDF5 DIR     = 
 ---------------------------------------------------------------
-kemelli@margarida:~/LIBRARIES/QUESO-0.50.0/bin$ 
+kemelli@margarida:~/LIBRARIES/QUESO-0.51.0/bin$ 
 \end{lstlisting}
 
- \item \verb+lib+: contains the static and dynamic versions of the library. The full to path to this directory, e.g., \verb+$HOME/LIBRARIES/QUESO-0.50.0/lib+ should be added to the user's \verb+LD_LIBRARY_PATH+ environmental variable in order to use QUESO library with his/her application code:
+ \item \verb+lib+: contains the static and dynamic versions of the library. The full to path to this directory, e.g., \verb+$HOME/LIBRARIES/QUESO-0.51.0/lib+ should be added to the user's \verb+LD_LIBRARY_PATH+ environmental variable in order to use QUESO library with his/her application code:
 \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}]
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
- $HOME/LIBRARIES/QUESO-0.50.0/lib
+ $HOME/LIBRARIES/QUESO-0.51.0/lib
 \end{lstlisting}
 
 
@@ -410,13 +410,13 @@ \section{Create your Application with the Installed QUESO} \label{sc-use-queso}
 your \verb+.bashrc+ (supposing you have a BASH-shell):
 \begin{lstlisting}[{basicstyle=\footnotesize\ttfamily}]
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
- $HOME/LIBRARIES/QUESO-0.50.0/lib
+ $HOME/LIBRARIES/QUESO-0.51.0/lib
 \end{lstlisting}
 
 % or into your \verb+.cshrc+ file (supposing you have a C-shell):
 % \begin{lstlisting}[label={},caption={}]
 % setenv LD_LIBRARY_PATH \$LD_LIBRARY_PATH:
-%        $HOME/LIBRARIES/QUESO-0.50.0/lib
+%        $HOME/LIBRARIES/QUESO-0.51.0/lib
 % \end{lstlisting}
 
 
@@ -426,7 +426,7 @@ \section{Create your Application with the Installed QUESO} \label{sc-use-queso}
 library through a Makefile such as the one displayed as follows:
 
 \begin{lstlisting}[basicstyle={\footnotesize\ttfamily},deletekeywords={export,rm}]
-QUESO_DIR = $HOME/LIBRARIES/QUESO-0.50.0/
+QUESO_DIR = $HOME/LIBRARIES/QUESO-0.51.0/
 BOOST_DIR = $HOME/LIBRARIES/boost-1.53.0/
 GSL_DIR = $HOME/LIBRARIES/gsl-1.15/
 GRVY_DIR = $HOME/LIBRARIES/grvy-0.32.0

manual/users/users_5a_example_sip.tex

@@ -98,7 +98,7 @@ \subsection{Running the Example}\label{sec:sip-run}
 
 To run the executable provided (available after QUESO installation), enter the following commands:
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/
 $ cd examples/simpleStatisticalInverseProblem
 $ rm outputData/*
 $ ./exSimpleStatisticalInverseProblem_gsl example.inp    
@@ -178,12 +178,12 @@ \subsection{Create your own Makefile}\label{sec:sip-makefile}
 
 Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are:
 \begin{lstlisting}
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/simpleStatisticalInverseProblem/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/simpleStatisticalInverseProblem/
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
   $HOME/LIBRARIES/gsl-1.15/lib/:\
   $HOME/LIBRARIES/boost-1.53.0/lib/:\
   $HOME/LIBRARIES/hdf5-1.8.10/lib:\
-  $HOME/LIBRARIES/QUESO-0.50.0/lib 
+  $HOME/LIBRARIES/QUESO-0.51.0/lib 
 $ make -f Makefile_example_margarida 
 $ ./simple_sip_example example.inp
 \end{lstlisting}

manual/users/users_5b_example_sfp.tex

@@ -50,7 +50,7 @@ \subsection{Running the Example}\label{sec:sfp-run}
 
 To run the executable provided (available after QUESO installation), enter the following commands:
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/
 $ cd examples/simpleStatisticalForwardProblem
 $ rm outputData/*
 $ ./exSimpleStatisticalForwardProblem_gsl example.inp    
@@ -117,12 +117,12 @@ \subsection{Create your own Makefile}\label{sec:sfp-makefile}
 
 Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are:
 \begin{lstlisting}
-$ cd HOME/LIBRARIES/QUESO-0.50.0/examples/simpleStatisticalForwardProblem 
+$ cd HOME/LIBRARIES/QUESO-0.51.0/examples/simpleStatisticalForwardProblem 
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
   $HOME/LIBRARIES/gsl-1.15/lib/:\
   $HOME/LIBRARIES/boost-1.53.0/lib/:\
   $HOME/LIBRARIES/hdf5-1.8.10/lib:\
-  $HOME/LIBRARIES/QUESO-0.50.0/lib 
+  $HOME/LIBRARIES/QUESO-0.51.0/lib 
 $ make -f Makefile_sfp_example_margarida 
 $ ./simple_sfp_example simple_sfp_example.inp
 \end{lstlisting}

manual/users/users_5c_example_gravity.tex

@@ -198,14 +198,14 @@ \subsection{Running the Example}\label{sec:gravity-run}
 
 To run the executable provided (available after QUESO installation), enter the following commands:
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/gravity
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/gravity
 $ rm outputData/*
 $ ./gravity_gsl gravity_inv_fwd.inp
 \end{lstlisting}
 
 The console output of the program is:
 \begin{lstlisting}[caption={Console output of program \texttt{gravity\_gsl}}, label={code:console_output},language={bash}]
-kemelli@violeta:~/LIBRARIES/QUESO-0.50.0/examples/gravity$ ./gravity_gsl gravity_inv_fwd.inp 
+kemelli@violeta:~/LIBRARIES/QUESO-0.51.0/examples/gravity$ ./gravity_gsl gravity_inv_fwd.inp 
 ---------------------------------------------------------------------
 QUESO Library: Version = 0.47.1 (47.1)
 
@@ -251,7 +251,7 @@ \subsection{Running the Example}\label{sec:gravity-run}
 
 Ending run at Mon Apr 29 17:27:33 2013
 Total run time = 1 seconds
-kemelli@violeta:~/LIBRARIES/QUESO-0.50.0/examples/gravity$ 
+kemelli@violeta:~/LIBRARIES/QUESO-0.51.0/examples/gravity$ 
 \end{lstlisting}
 
 
@@ -334,7 +334,7 @@ \subsection{Running the Gravity Example with Several Processors}
 
 
 \begin{lstlisting}[caption={}, label={},language={bash}]
-cd $HOME/LIBRARIES/QUESO-0.50.0/examples/gravity/
+cd $HOME/LIBRARIES/QUESO-0.51.0/examples/gravity/
 mpirun -np 8 ./gravity_gsl gravity_inv_fwd.inp
 \end{lstlisting}
 

manual/users/users_5e_example_ml_modal.tex

@@ -9,7 +9,7 @@ \section{\texttt{modal}}\label{sec:example_modal}
 Choosing between a one-mode or a two-mode target distribution is done at execution level, as presented in the following code line:
 
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/
 $ cd examples/modal
 $ rm outputData/*
 $ ./modal_gsl example.inp <num_of_nodes>
@@ -57,7 +57,7 @@ \subsubsection{Running the One-Mode Example}
 
 To run the executable provided considering a \underline{one-mode} distribution, enter the following commands:
 \begin{lstlisting}[label={},caption={Running the example with a one-mode distribution.}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/
 $ cd examples/modal
 $ rm outputData/*
 $ ./modal_gsl example.inp 1      #one mode!
@@ -113,7 +113,7 @@ \subsubsection{Running the Two-Mode Example}
 
 To run the executable provided considering a \underline{two-modes} distribution, enter the following commands:
 \begin{lstlisting}[label={},caption={Running the example with a two-mode distribution.}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/
 $ cd examples/modal
 $ rm outputData/*
 $ ./modal_gsl example.inp 2         # two modes!
@@ -194,12 +194,12 @@ \subsection{Create your own Makefile}\label{sec:modal-makefile}
 
 Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are:
 \begin{lstlisting}
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/modal/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/modal/
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
   $HOME/LIBRARIES/gsl-1.15/lib/:\
   $HOME/LIBRARIES/boost-1.53.0/lib/:\
   $HOME/LIBRARIES/hdf5-1.8.10/lib:\
-  $HOME/LIBRARIES/QUESO-0.50.0/lib 
+  $HOME/LIBRARIES/QUESO-0.51.0/lib 
 $ make -f Makefile_modal_violeta 
 $ ./modal_gsl example.inp <num_modes>
 \end{lstlisting}
@@ -318,4 +318,4 @@ \subsubsection{Autocorrelation Plots}
 \vspace{-10pt}
 \caption{Autocorrelation plots for $\theta_1$, $\theta_2$ and $\theta_3=\sigma^2$. Two-mode distribution.}
 \label{fig:modal_autocorr_2modes}
-\end{figure}
+\end{figure}

manual/users/users_5f_example_ml_bimodal.tex

@@ -35,7 +35,7 @@ \subsection{Running the Example}\label{sec:bimodal-run}
 
 To run the executable provided (available after QUESO installation), and generate figures for the chains, PDFs, CDFs, etc., enter the following commands:
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/bimodal
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/bimodal
 $ rm outputData/*
 $ ./bimodal_gsl bimodal_1chain.inp    
 $ matlab
@@ -113,12 +113,12 @@ \subsection{Create your own Makefile}\label{sec:bimodal-makefile}
 
 Thus, to compile, build and execute the code, the user just needs to run the following commands in the same directory where the files are:
 \begin{lstlisting}
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/bimodal/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/bimodal/
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
   $HOME/LIBRARIES/gsl-1.15/lib/:\
   $HOME/LIBRARIES/boost-1.53.0/lib/:\
   $HOME/LIBRARIES/hdf5-1.8.10/lib:\
-  $HOME/LIBRARIES/QUESO-0.50.0/lib 
+  $HOME/LIBRARIES/QUESO-0.51.0/lib 
 $ make -f Makefile_bimodal_violeta 
 $ ./bimodal_gsl example.inp
 \end{lstlisting}

manual/users/users_5g_example_ml_hysteretic.tex

@@ -118,7 +118,7 @@ \subsection{Running the Example}\label{sec:hysteretic-run}
 
 To run the executable provided (available after QUESO installation), and generate figures for the chains, KDEs, CDFs, autocorrelation and scatter plots, enter the following commands:
 \begin{lstlisting}[label={},caption={}]
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/example
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/example
 $ rm outputData/*
 $ ./example_gsl example_1chain.inp    
 $ matlab
@@ -178,12 +178,12 @@ \subsection{Create your own Makefile}\label{sec:hysteretic-makefile}
 
 Thus to compile, build and execute the code,  commands similar to the following should be entered:
 \begin{lstlisting}
-$ cd $HOME/LIBRARIES/QUESO-0.50.0/examples/hysteretic/
+$ cd $HOME/LIBRARIES/QUESO-0.51.0/examples/hysteretic/
 $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\
   $HOME/LIBRARIES/gsl-1.15/lib/:\
   $HOME/LIBRARIES/boost-1.53.0/lib/:\
   $HOME/LIBRARIES/hdf5-1.8.10/lib:\
-  $HOME/LIBRARIES/QUESO-0.50.0/lib 
+  $HOME/LIBRARIES/QUESO-0.51.0/lib 
 $ make -f Makefile_hysteretic_violeta 
 $ ./hysteretic_gsl example.inp
 \end{lstlisting}