Merge branch 'v0.55.0-release'

Author: dmcdougall

.gitignore

@@ -214,3 +214,15 @@ test/test_SharedPtr
 test/output_test_serialEnv
 test/test_Environment/input_test_serialEnv
 test/test_serialEnv
+test/test_jeffreys_pdf
+test/test_gaussian_pdf_gradient
+test/test_log_normal_pdf_gradient
+test/test_beta_pdf_gradient
+test/output_test_intercomm0_gravity_1
+test/output_test_intercomm0_gravity_2
+test/test_intercomm0_gravity
+test/test_intercomm0/gravity_1proc.txt
+test/test_intercomm0/gravity_2proc.txt
+test/test_intercomm0/test_intercomm0_gravity_run.sh
+test/test_seq_of_vec_hdf5_write
+test/test_SequenceOfVectors/test_seq_of_vec_hdf5_write_run.sh

CHANGES

@@ -3,7 +3,13 @@ QUESO: Quantification of Uncertainty for Estimation,
 Simulation, and Optimization.
 -----------------------------------------------------
 
-Version 0.54.0
+Version 0.55.0 (in progress)
+  * Fix bug in JeffreysJointPdf
+  * Adding gradient support for Beta, Log Normal, and Gaussian PDFs
+  * Fix MLE/MAP bug when subEnvironments have more than one MPI process
+  * Add support for HDF5 output
+
+Version 0.54.0 (Oct 8, 2015)
   * Fix memory leak in test_GslVector
   * Make MPI optional
   * Optimise GSLMatrix::operator() and GslVector::operator[]
@@ -13,50 +19,45 @@ Version 0.54.0
   * Fix some compiler warnings
   * Fix HDF5 #include issues
 
-Version 0.53.0
+Version 0.53.0 (Jun 11, 2015)
   * Add linear interpolation surrogates
   * Refactor input options processing
   * Refactor existing queso errors and asserts
   * Add new error checking macros
   * Add basic scoped pointer wrappers
   * Better error message reporting for bad sample covariance matrices
 
-Version 0.52.0
+Version 0.52.0 (Apr 9, 2015)
   * Add canned Gaussian likelihoods
   * Fix bug in logit transform logic
 
-Version 0.51.0
+Version 0.51.0 (Nov 29, 2014)
   * 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
   * Adding Eric Wright to contributors list
 
-Version 0.50.0
+Version 0.50.0 (Nov 16, 2013)
   * Implemented MCMC sampling on function spaces
   * Added function space MCMC unit tests
   * Added serial and parallel function space MCMC examples
   * Replace exit() calls with a macro exception handler
 
-Version 0.47.1
+Version 0.47.1 (Sep 23, 2013)
   * created two simple statistical examples, simpleStatisticalForwardProblem and simpleStatisticalInverseProblem
   * included description of the new examples on QUESO user's manual, including how to run and to process the generated data
   * updated QUESO user's manual to include description of validationCycle example
   * updated links for how to obtain QUESO and contact information (github/git)
+  * fixed broken Makefile
 
-Version 0.47.0
+Version 0.47.0 (Sep 4, 2013)
   * removed example statisticalInverseProblem as it has a bug - it fails to recreate the problem described in the Normal test from Laine's MCMC tool: http://helios.fmi.fi/~lainema/mcmc/ex/normalex.html.
 
-Version 0.47.1 (23 Sep 2013)
-
-  * Update manual and fix broken Makefile
-
 Version 0.47.0 (4 Sep 2013)
-
   * Migrated library to github
 
 Version 0.46 (13 May 2013)
-
   * changed libGRVY linkage to be optional
   * added additional regression tests to 'make check'
   * added rng (random number generator) class to accommodate either GSL or BOOST rng's

Makefile.am

@@ -17,6 +17,10 @@ AUX_DIST = build-aux/install-sh    \
 pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = queso.pc queso-deps.pc
 
+# Support for queso-config in $(exec_prefix)/bin
+queso_configdir      = $(exec_prefix)/bin
+queso_config_SCRIPTS = src/apps/queso-config
+
 if CODE_COVERAGE_ENABLED
 
 lcov_dir=$(top_builddir)/docs/html/lcov

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.65)
-AC_INIT([queso], [0.54.0], [queso-users@googlegroups.com])
+AC_INIT([queso], [0.55.0], [queso-users@googlegroups.com])
 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"
@@ -68,8 +68,8 @@ AC_ARG_ENABLE(debug, [  --enable-debug=[no/yes] turn on debugging
                      [default=$debug_default]],, enable_debug=$debug_default)
 
 if test "x$enable_debug" = "xyes"; then
-   CFLAGS="$CFLAGS -DDEBUG"
-   CXXFLAGS="$CXXFLAGS -DDEBUG"
+   QUESO_CPPFLAGS="$CPPFLAGS -DDEBUG"
+   AC_SUBST(QUESO_CPPFLAGS)
    AC_MSG_RESULT(yes)
 else
    AC_MSG_RESULT(no)
@@ -241,6 +241,8 @@ AC_CONFIG_FILES([
   test/test_InputOptionsParser/test_options_default.txt
   test/test_optimizer/input_test_optimizer_options
   test/test_Environment/input_test_serialEnv
+  test/test_intercomm0/gravity_1proc.txt
+  test/test_intercomm0/gravity_2proc.txt
 ])
 
 AC_CONFIG_FILES([test/test_Regression/test_cobra_samples_diff.sh
@@ -270,6 +272,22 @@ AC_CONFIG_FILES([
   chmod +x test/test_SequenceOfVectors/test_unifiedPositionsOfMaximum.sh
 ])
 
+AC_CONFIG_FILES([
+  test/test_intercomm0/test_intercomm0_gravity_run.sh
+],
+[
+  chmod +x test/test_intercomm0/test_intercomm0_gravity_run.sh
+])
+
+AC_CONFIG_FILES([
+  test/test_SequenceOfVectors/test_seq_of_vec_hdf5_write_run.sh
+],
+[
+  chmod +x test/test_SequenceOfVectors/test_seq_of_vec_hdf5_write_run.sh
+])
+
+AC_CONFIG_FILES(src/apps/queso-config, [chmod +x src/apps/queso-config])
+
 dnl ----------------------------------------------
 dnl Collect files for licence header stamping here
 dnl ----------------------------------------------