Merge branch 'v0.50.0-release'

Author: dmcdougall

.gitignore

@@ -4,6 +4,7 @@
 .libs
 *.gcda
 *.gcno
+*~
 
 Makefile.in
 Makefile
@@ -15,6 +16,7 @@ aclocal.m4
 aminclude.am
 autom4te.cache
 build-aux
+.license.stamp
 
 _configs.sed
 config.log
@@ -36,11 +38,20 @@ examples/exStatisticalInverseProblem_gsl
 examples/exTgaValidationCycle_gsl
 examples/gravity_gsl
 examples/tga2_gsl
+examples/gaussian_random_field
+examples/gaussian_random_field_genmesh
+examples/infinite_dim/inverse_options
+examples/infinite_dim/parallel_inverse_options
+examples/inverse_problem
+examples/operator
+examples/parallel_inverse_problem
 
 src/core/inc/queso.h
 src/libqueso.la
 src/queso_version
 
+inc/queso/*.h
+
 test/gsl_tests/get_min_max_vec
 test/gsl_tests/get_set_row_column
 test/gsl_tests/input
@@ -67,3 +78,19 @@ test/test_uqGslMatrixConstructorFatal
 test/test_uqGslVector
 test/test_uqGslVectorConstructorFatal
 test/test_uqTeuchosVector
+test/chain0
+test/outputData
+test/test_Environment/copy_env
+test/test_DistArrayCopy
+test/test_DistArrayCtor
+test/test_DistArrayEquals
+test/test_DistArrayMisc
+test/test_GslVectorSpaceCtor
+test/test_GslVectorSpaceMisc
+test/test_IntersectionSubsetContains
+test/test_inf_gaussian
+test/test_inf_options
+test/test_infinite/inf_options
+test/test_operator
+test/test_uqexception
+test/test_SequenceOfVectorsErase

.travis.yml

@@ -0,0 +1,8 @@
+language: cpp
+compiler:
+  - gcc
+  - clang
+before_script:
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq libgsl0-dev libmpich2-dev libboost-all-dev
+script: ./bootstrap && ./configure && make && make check

CHANGES

@@ -11,11 +11,21 @@ Version 0.47.1
 Version 0.47.0
   * 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 0.47.0 (In progress)
+Version 0.50.0 (In progress)
 
-  * Migrated library to github
+  * 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 (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

LICENSE

@@ -1,6 +1,6 @@
 //-----------------------------------------------------------------------bl-
 //--------------------------------------------------------------------------
-// 
+//
 // QUESO - a library to support the Quantification of Uncertainty
 // for Estimation, Simulation and Optimization
 //
@@ -17,7 +17,7 @@
 //
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
-// Foundation, Inc. 51 Franklin Street, Fifth Floor, 
+// Foundation, Inc. 51 Franklin Street, Fifth Floor,
 // Boston, MA  02110-1301  USA
 //
 //-----------------------------------------------------------------------el-

Makefile.am

@@ -3,7 +3,7 @@ ACLOCAL_AMFLAGS  = -I m4 -I m4/common
 EXTRA_DIST       = $(DX_CONFIG) QUESO_users_manual.pdf CHANGES AUTHORS COPYING LICENSE
 
 # Build in these directories:
-SUBDIRS          = src/contrib/ANN src examples test/gsl_tests test doxygen
+SUBDIRS          = inc/queso src/contrib/ANN src examples test/gsl_tests test doxygen
 
 # Doxygen support
 
@@ -45,54 +45,61 @@ endif
 
 # Files to be deleted by 'make maintainer-clean'
 
-MAINTAINERCLEANFILES =     \
-	aclocal.m4             \
-	autom4te.cache/*       \
-	$(AUX_DIST)            \
-	config.log             \
-	config.status          \
-	config.sub             \
-	configure              \
-	config.h	       \
-	config.h.in	       \
-        config_queso.h         \
-        config_queso.h.tmp.in  \
-        config_queso.h.tmp.in~ \
-	Makefile.in            \
-	src/Makefile.in       \
-	src/contrib/ANN/Makefile.in \
-	src/contrib/ANN/lib/Makefile.in \
-	src/contrib/ANN/test/Makefile.in \
-	src/core/Makefile.in \
-	src/core/src/Makefile.in \
-	src/core/inc/Makefile.in \
-	src/misc/Makefile.in \
-	src/misc/src/Makefile.in \
-	src/misc/inc/Makefile.in \
-	src/basic/Makefile.in \
-	src/basic/src/Makefile.in \
-	src/basic/inc/Makefile.in \
-	src/stats/Makefile.in \
-	src/stats/src/Makefile.in \
-	src/stats/inc/Makefile.in \
-	src/gp/Makefile.in \
-	src/gp/src/Makefile.in \
-	src/gp/inc/Makefile.in \
-	examples/Makefile.in \
-	examples/markovChain1/Makefile.in \
-	examples/markovChain1/src/Makefile.in \
-	examples/monteCarlo/Makefile.in \
-	examples/monteCarlo/src/Makefile.in \
-	examples/pyramid/Makefile.in \
-	examples/pyramid/src/Makefile.in \
-	examples/pyramid/src/physics_1/Makefile.in \
-	examples/pyramid/src/physics_1_2/Makefile.in \
-	examples/pyramid/src/physics_2/Makefile.in \
-	examples/tga/Makefile.in \
-	examples/tga/src/Makefile.in \
-	examples/simpleStatisticalInverseProblem/src/Makefile.in \
-	examples/simpleStatisticalForwardProblem/src/Makefile.in \
-	doxygen/Makefile.in
+MAINTAINERCLEANFILES =
+MAINTAINERCLEANFILES += aclocal.m4
+MAINTAINERCLEANFILES += autom4te.cache/*
+MAINTAINERCLEANFILES += $(AUX_DIST)
+MAINTAINERCLEANFILES += config.log
+MAINTAINERCLEANFILES += config.status
+MAINTAINERCLEANFILES += config.sub
+MAINTAINERCLEANFILES += configure
+MAINTAINERCLEANFILES += config.h
+MAINTAINERCLEANFILES += config.h.in
+MAINTAINERCLEANFILES += config_queso.h
+MAINTAINERCLEANFILES += config_queso.h.tmp.in
+MAINTAINERCLEANFILES += config_queso.h.tmp.in~
+MAINTAINERCLEANFILES += Makefile.in
+MAINTAINERCLEANFILES += src/Makefile.in
+MAINTAINERCLEANFILES += src/contrib/ANN/Makefile.in
+MAINTAINERCLEANFILES += src/contrib/ANN/lib/Makefile.in
+MAINTAINERCLEANFILES += src/contrib/ANN/test/Makefile.in
+MAINTAINERCLEANFILES += src/core/Makefile.in
+MAINTAINERCLEANFILES += src/core/src/Makefile.in
+MAINTAINERCLEANFILES += src/core/inc/Makefile.in
+MAINTAINERCLEANFILES += src/misc/Makefile.in
+MAINTAINERCLEANFILES += src/misc/src/Makefile.in
+MAINTAINERCLEANFILES += src/misc/inc/Makefile.in
+MAINTAINERCLEANFILES += src/basic/Makefile.in
+MAINTAINERCLEANFILES += src/basic/src/Makefile.in
+MAINTAINERCLEANFILES += src/basic/inc/Makefile.in
+MAINTAINERCLEANFILES += src/stats/Makefile.in
+MAINTAINERCLEANFILES += src/stats/src/Makefile.in
+MAINTAINERCLEANFILES += src/stats/inc/Makefile.in
+MAINTAINERCLEANFILES += src/gp/Makefile.in
+MAINTAINERCLEANFILES += src/gp/src/Makefile.in
+MAINTAINERCLEANFILES += src/gp/inc/Makefile.in
+MAINTAINERCLEANFILES += inc/queso/Makefile.in
+MAINTAINERCLEANFILES += test/Makefile.in
+MAINTAINERCLEANFILES += test/gsl_tests/Makefile.in
+MAINTAINERCLEANFILES += test/t01_valid_cycle/Makefile.in
+MAINTAINERCLEANFILES += test/t02_sip_sfp/Makefile.in
+MAINTAINERCLEANFILES += test/t03_sequence/Makefile.in
+MAINTAINERCLEANFILES += test/t04_bimodal/Makefile.in
+MAINTAINERCLEANFILES += examples/Makefile.in
+MAINTAINERCLEANFILES += examples/markovChain1/Makefile.in
+MAINTAINERCLEANFILES += examples/markovChain1/src/Makefile.in
+MAINTAINERCLEANFILES += examples/monteCarlo/Makefile.in
+MAINTAINERCLEANFILES += examples/monteCarlo/src/Makefile.in
+MAINTAINERCLEANFILES += examples/pyramid/Makefile.in
+MAINTAINERCLEANFILES += examples/pyramid/src/Makefile.in
+MAINTAINERCLEANFILES += examples/pyramid/src/physics_1/Makefile.in
+MAINTAINERCLEANFILES += examples/pyramid/src/physics_1_2/Makefile.in
+MAINTAINERCLEANFILES += examples/pyramid/src/physics_2/Makefile.in
+MAINTAINERCLEANFILES += examples/tga/Makefile.in
+MAINTAINERCLEANFILES += examples/tga/src/Makefile.in
+MAINTAINERCLEANFILES += examples/simpleStatisticalInverseProblem/src/Makefile.in
+MAINTAINERCLEANFILES += examples/simpleStatisticalForwardProblem/src/Makefile.in
+MAINTAINERCLEANFILES += doxygen/Makefile.in
 
 MOSTLYCLEANFILES = $(DX_CLEANFILES)
 
@@ -104,39 +111,52 @@ MOSTLYCLEANFILES = $(DX_CLEANFILES)
 
 # Additional files to be deleted by 'make distclean'
 
-DISTCLEANFILES = _configs.sed \
-	test/t01_valid_cycle/outputData/file_cal_fp_qoi2.m \
-	test/t01_valid_cycle/outputData/file_cal_fp_qoi2_sub0.m \
-	test/t01_valid_cycle/outputData/file_val_ip_raw2_sub0.m \
-	test/t01_valid_cycle/outputData/file_cal_ip_raw2_sub0.m \
-	test/t01_valid_cycle/outputData/file_cal_ip_raw2.m \
-	test/t01_valid_cycle/outputData/file_val_fp_qoi2_sub0.m \
-	test/t01_valid_cycle/outputData/screen_sub0.txt \
-	test/t01_valid_cycle/outputData/file_val_fp_qoi2.m \
-	test/t01_valid_cycle/outputData/file_val_ip_raw2.m \
-	test/t01_valid_cycle/outputData/tgaValOutput_sub0.m \
-	test/t01_valid_cycle/outputData/tgaCalOutput_sub0.m \
-	test/t04_bimodal/outputData/display_sub0.txt \
-	test/t04_bimodal/outputData/sipOutput_ml_sub0.m \
-	test/t04_bimodal/outputData/filtChain_ml.m \
-	test/t04_bimodal/outputData/rawChain_ml.m \
-	test/gsl_tests/outputData/display_sub0.txt \
-	test/gslvector_out_sub0.m \
-	test/t02_sip_sfp/outputData/sfpOutput_sub0.m \
-	test/t02_sip_sfp/outputData/ip_raw_chain_sub0.m \
-	test/t02_sip_sfp/outputData/fp_p_seq.m \
-	test/t02_sip_sfp/outputData/display_sub0.txt \
-	test/t02_sip_sfp/outputData/nada1 \
-	test/t02_sip_sfp/outputData/sipOutput_sub0.m \
-	test/t02_sip_sfp/outputData/nada0 \
-	test/t02_sip_sfp/outputData/ip_raw_chain.m \
-	test/t02_sip_sfp/outputData/fp_q_seq.m \
-	test/t02_sip_sfp/outputData/ip_filt_chain_sub0.m \
-	test/t02_sip_sfp/outputData/fp_q_seq_sub0.m \
-	test/t02_sip_sfp/outputData/ip_filt_chain.m \
-	test/t02_sip_sfp/outputData/fp_p_seq_sub0.m \
-	aminclude.am \
-	config_queso.h
+DISTCLEANFILES =
+DISTCLEANFILES += _configs.sed
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_fp_qoi2.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_fp_qoi2_sub0.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2_sub0.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2_sub0.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_cal_ip_raw2.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_fp_qoi2_sub0.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/screen_sub0.txt
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_fp_qoi2.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/file_val_ip_raw2.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/tgaValOutput_sub0.m
+DISTCLEANFILES += test/t01_valid_cycle/outputData/tgaCalOutput_sub0.m
+DISTCLEANFILES += test/t04_bimodal/outputData/display_sub0.txt
+DISTCLEANFILES += test/t04_bimodal/outputData/sipOutput_ml_sub0.m
+DISTCLEANFILES += test/t04_bimodal/outputData/filtChain_ml.m
+DISTCLEANFILES += test/t04_bimodal/outputData/rawChain_ml.m
+DISTCLEANFILES += test/gsl_tests/outputData/display_sub0.txt
+DISTCLEANFILES += test/gslvector_out_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/sfpOutput_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_p_seq.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/display_sub0.txt
+DISTCLEANFILES += test/t02_sip_sfp/outputData/nada1
+DISTCLEANFILES += test/t02_sip_sfp/outputData/sipOutput_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/nada0
+DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_raw_chain.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_q_seq.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_q_seq_sub0.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/ip_filt_chain.m
+DISTCLEANFILES += test/t02_sip_sfp/outputData/fp_p_seq_sub0.m
+DISTCLEANFILES += test/outputData/*
+DISTCLEANFILES += aminclude.am
+DISTCLEANFILES += config_queso.h
+
+CLEANFILES =
+if GIT_CLONE
+CLEANFILES += src/.license.stamp
+CLEANFILES += test/.license.stamp
+CLEANFILES += test/gsl_tests/.license.stamp
+CLEANFILES += test/t01_valid_cycle/.license.stamp
+CLEANFILES += test/t02_sip_sfp/.license.stamp
+CLEANFILES += test/t03_sequence/.license.stamp
+CLEANFILES += test/t04_bimodal/.license.stamp
+endif
 
 # Required for AX_AM_MACROS
 #@INC_AMINCLUDE@