Merge branch 'UQTk_3.1.5'

sandialabs · Nov 23, 2024 · d401ac2 · d401ac2
2 parents 5ef5a24 + 02823b8
commit d401ac2
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "dep/sundials"]
 	path = dep/sundials
-	url = https://github.com/LLNL/sundials.git
+	url = https://github.com/LLNL/sundials.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.1)
+cmake_minimum_required (VERSION 3.12)
 set (CMAKE_CXX_STANDARD 14)
 project (UQTk)
 

diff --git a/PyUQTk/CMakeLists.txt b/PyUQTk/CMakeLists.txt
@@ -1,5 +1,10 @@
 project (UQTk)
 
+# Enable support for modern IN_LIST operator
+if (POLICY CMP0057)
+  cmake_policy(SET CMP0057 NEW)
+endif()
+
 add_subdirectory (inference)
 add_subdirectory (plotting)
 add_subdirectory (sens)

diff --git a/PyUQTk/PyPCE/__init__.py b/PyUQTk/PyPCE/__init__.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/PyPCE/adaptation_tools.py b/PyUQTk/PyPCE/adaptation_tools.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/PyPCE/pce_tools.py b/PyUQTk/PyPCE/pce_tools.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/__init__.py b/PyUQTk/__init__.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/bcs/PyBCS.cpp b/PyUQTk/bcs/PyBCS.cpp
@@ -1,11 +1,11 @@
 //=====================================================================================
 //
-//                      The UQ Toolkit (UQTk) version 3.1.4
-//                          Copyright (2023) NTESS
+//                      The UQ Toolkit (UQTk) version 3.1.5
+//                          Copyright (2024) NTESS
 //                        https://www.sandia.gov/UQToolkit/
 //                        https://github.com/sandialabs/UQTk
 //
-//     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+//     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 //     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 //     retains certain rights in this software.
 //

diff --git a/PyUQTk/inference/__init__.py b/PyUQTk/inference/__init__.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/inference/bayes_evid.py b/PyUQTk/inference/bayes_evid.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/inference/evidence_solvers.py b/PyUQTk/inference/evidence_solvers.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/inference/mcmc.py b/PyUQTk/inference/mcmc.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/inference/postproc.py b/PyUQTk/inference/postproc.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/kle/CMakeLists.txt b/PyUQTk/kle/CMakeLists.txt
@@ -1,5 +1,4 @@
 # Using Pybind to build the python module
-
 find_package(pybind11 REQUIRED)
 
 include_directories(../../cpp/lib/array) #array directory

diff --git a/PyUQTk/kle/PyKle.cpp b/PyUQTk/kle/PyKle.cpp
@@ -1,11 +1,11 @@
 //=====================================================================================
 //
-//                      The UQ Toolkit (UQTk) version 3.1.4
-//                          Copyright (2023) NTESS
+//                      The UQ Toolkit (UQTk) version 3.1.5
+//                          Copyright (2024) NTESS
 //                        https://www.sandia.gov/UQToolkit/
 //                        https://github.com/sandialabs/UQTk
 //
-//     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+//     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 //     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 //     retains certain rights in this software.
 //

diff --git a/PyUQTk/mcmc/CMakeLists.txt b/PyUQTk/mcmc/CMakeLists.txt
@@ -73,8 +73,8 @@ if(BUILD_SUNDIALS)
 	SWIG_LINK_LIBRARIES(mcmc ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunlinsol/dense/libsundials_sunlinsoldense.a)
 	SWIG_LINK_LIBRARIES(mcmc ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunmatrix/dense/libsundials_sunmatrixdense.a)
 else()
-	SWIG_LINK_LIBRARIES(mcmc ${CMAKE_SUNDIALS_DIR}/lib/libsundials_cvode.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_nvecserial.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunlinsoldense.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunmatrixdense.a)
-endif()
+	SWIG_LINK_LIBRARIES(mcmc ${CMAKE_SUNDIALS_DIR}/lib/libsundials_core.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_cvode.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_nvecserial.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunlinsoldense.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunmatrixdense.a)
+	endif()
 
 INSTALL(TARGETS _mcmc DESTINATION PyUQTk/)
 INSTALL(FILES ${CMAKE_BINARY_DIR}/${outdir}PyUQTk/mcmc/mcmc.py DESTINATION PyUQTk)
diff --git a/PyUQTk/mcmc/mcmc.i b/PyUQTk/mcmc/mcmc.i
@@ -1,12 +1,12 @@
 %module(directors="1") mcmc
 //=====================================================================================
 //
-//                      The UQ Toolkit (UQTk) version 3.1.4
-//                          Copyright (2023) NTESS
+//                      The UQ Toolkit (UQTk) version 3.1.5
+//                          Copyright (2024) NTESS
 //                        https://www.sandia.gov/UQToolkit/
 //                        https://github.com/sandialabs/UQTk
 //
-//     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+//     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 //     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 //     retains certain rights in this software.
 //

diff --git a/PyUQTk/multirun/__init__.py b/PyUQTk/multirun/__init__.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/multirun/multirun.py b/PyUQTk/multirun/multirun.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/multirun/srun.x b/PyUQTk/multirun/srun.x
@@ -1,12 +1,12 @@
 #!/bin/bash
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/numpy.cmake b/PyUQTk/numpy.cmake
@@ -1,27 +1,20 @@
-IF (NUMPY_INCLUDE_DIR)
-  SET(NUMPY_FIND_QUIETLY TRUE)
-endif (NUMPY_INCLUDE_DIR)
+# Use modern Python detection (requires CMake 3.12+)
+find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
 
-# To set the variables PYTHON_EXECUTABLE
-FIND_PACKAGE(PythonInterp QUIET REQUIRED)
-FIND_PACKAGE(PythonLibs QUIET REQUIRED)
+# Check if NumPy was found
+if (Python3_NumPy_FOUND)
+    # Extract NumPy include directory and version
+    set(NUMPY_INCLUDE_DIR ${Python3_NumPy_INCLUDE_DIRS})
+    set(NUMPY_VERSION ${Python3_NumPy_VERSION})
 
-# Look for the include path
-# WARNING: The variable PYTHON_EXECUTABLE is defined by the script FindPythonInterp.cmake
-EXECUTE_PROCESS(COMMAND "${PYTHON_EXECUTABLE}" -c "import numpy; print (numpy.get_include()); print (numpy.version.version)"
-                 OUTPUT_VARIABLE NUMPY_OUTPUT
-                 ERROR_VARIABLE NUMPY_ERROR)
-
-IF(NOT NUMPY_ERROR)
-  STRING(REPLACE "\n" ";" NUMPY_OUTPUT ${NUMPY_OUTPUT})
-  LIST(GET NUMPY_OUTPUT 0 NUMPY_INCLUDE_DIR)
-  LIST(GET NUMPY_OUTPUT 1 NUMPY_VERSION)
-ENDIF(NOT NUMPY_ERROR)
+    # Debugging output
+    message(STATUS "Found NumPy:")
+    message(STATUS "  Include Directory: ${NUMPY_INCLUDE_DIR}")
+    message(STATUS "  Version: ${NUMPY_VERSION}")
+else()
+    # Handle error if NumPy is not found
+    message(FATAL_ERROR "NumPy not found. Please ensure NumPy is installed in your Python3 environment.")
+endif()
 
-INCLUDE(FindPackageHandleStandardArgs)
-
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(NumPy DEFAULT_MSG NUMPY_VERSION NUMPY_INCLUDE_DIR)
-
-MARK_AS_ADVANCED(NUMPY_INCLUDE_DIR)
-
-INCLUDE_DIRECTORIES(${NUMPY_INCLUDE_DIR})
+# Include NumPy headers
+include_directories(${NUMPY_INCLUDE_DIR})
diff --git a/PyUQTk/numpy/numpy.i b/PyUQTk/numpy/numpy.i
@@ -1,12 +1,12 @@
 /* -*- C -*-  (not really, but good for syntax highlighting) */
 //=====================================================================================
 //
-//                      The UQ Toolkit (UQTk) version 3.1.4
-//                          Copyright (2023) NTESS
+//                      The UQ Toolkit (UQTk) version 3.1.5
+//                          Copyright (2024) NTESS
 //                        https://www.sandia.gov/UQToolkit/
 //                        https://github.com/sandialabs/UQTk
 //
-//     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+//     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 //     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 //     retains certain rights in this software.
 //

diff --git a/PyUQTk/pce/CMakeLists.txt b/PyUQTk/pce/CMakeLists.txt
@@ -1,5 +1,4 @@
 # Using Pybind to build the python module for PCE
-
 find_package(pybind11 REQUIRED)
 
 #include source files
@@ -26,9 +25,9 @@ pybind11_add_module(_pce pypce.cpp)
 
 
 if(BUILD_SUNDIALS)
-	TARGET_LINK_LIBRARIES(_pce PUBLIC uqtk depuqtk blas lapack gfortran ${PROJECT_BINARY_DIR}/../dep/sundials/src/cvode/libsundials_cvode.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/nvector/serial/libsundials_nvecserial.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunlinsol/dense/libsundials_sunlinsoldense.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunmatrix/dense/libsundials_sunmatrixdense.a)
+	TARGET_LINK_LIBRARIES(_pce PUBLIC uqtk depuqtk blas lapack gfortran ${PROJECT_BINARY_DIR}/../dep/sundials/src/sundials/libsundials_core.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/cvode/libsundials_cvode.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/nvector/serial/libsundials_nvecserial.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunlinsol/dense/libsundials_sunlinsoldense.a ${PROJECT_BINARY_DIR}/../dep/sundials/src/sunmatrix/dense/libsundials_sunmatrixdense.a)
 else()
-	TARGET_LINK_LIBRARIES(_pce PUBLIC uqtk depuqtk blas lapack gfortran ${CMAKE_SUNDIALS_DIR}/lib/libsundials_cvode.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_nvecserial.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunlinsoldense.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunmatrixdense.a)
+	TARGET_LINK_LIBRARIES(_pce PUBLIC uqtk depuqtk blas lapack gfortran ${CMAKE_SUNDIALS_DIR}/lib/libsundials_core.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_nvecserial.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_cvode.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunlinsoldense.a ${CMAKE_SUNDIALS_DIR}/lib/libsundials_sunmatrixdense.a)
 endif()
 
 #SET(copy_FILES

diff --git a/PyUQTk/plotting/__init__.py b/PyUQTk/plotting/__init__.py
@@ -1,11 +1,11 @@
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/plotting/fits.py b/PyUQTk/plotting/fits.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #

diff --git a/PyUQTk/plotting/inout.py b/PyUQTk/plotting/inout.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 #=====================================================================================
 #
-#                      The UQ Toolkit (UQTk) version 3.1.4
-#                          Copyright (2023) NTESS
+#                      The UQ Toolkit (UQTk) version 3.1.5
+#                          Copyright (2024) NTESS
 #                        https://www.sandia.gov/UQToolkit/
 #                        https://github.com/sandialabs/UQTk
 #
-#     Copyright 2023 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+#     Copyright 2024 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 #     Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
 #     retains certain rights in this software.
 #