Apply pre-commmit fixes

.gitlab/pnnl/incline.gitlab-ci.yml

@@ -45,4 +45,4 @@ failure:
     - .report-status
   rules:
     - when: on_failure
-
+

CMakeLists.txt

@@ -13,31 +13,42 @@ project(ReSolve VERSION "0.1.0")
 
 set(CMAKE_CXX_STANDARD 11)
 
-set(PACKAGE_NAME  "ReSolve")
+set(PACKAGE_NAME "ReSolve")
 set(PACKAGE_TARNAME "resolve")
 
 # Prohibit in-source build
 if("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}")
   message(FATAL_ERROR "In-source build prohibited.")
 endif()
 
-option(RESOLVE_TEST_WITH_BSUB "Use `jsrun` instead of `mpirun` commands when running tests" OFF)
-option(RESOLVE_USE_KLU  "Use KLU, AMD and COLAMD libraries from SuiteSparse" ON)
+option(RESOLVE_TEST_WITH_BSUB
+       "Use `jsrun` instead of `mpirun` commands when running tests" OFF
+)
+option(RESOLVE_USE_KLU "Use KLU, AMD and COLAMD libraries from SuiteSparse" ON)
 option(RESOLVE_USE_CUDA "Use CUDA language and SDK" OFF)
-option(RESOLVE_USE_HIP  "Use HIP language and ROCm library" OFF)
+option(RESOLVE_USE_HIP "Use HIP language and ROCm library" OFF)
 
-option(RESOLVE_USE_GPU  "Use GPU device for computations" OFF)
+option(RESOLVE_USE_GPU "Use GPU device for computations" OFF)
 mark_as_advanced(FORCE RESOLVE_USE_GPU)
 
 option(RESOLVE_USE_DOXYGEN "Use Doxygen to generate Re::Solve documentation" ON)
-set(RESOLVE_CTEST_OUTPUT_DIR ${PROJECT_BINARY_DIR} CACHE PATH "Directory where CTest outputs are saved")
+set(RESOLVE_CTEST_OUTPUT_DIR
+    ${PROJECT_BINARY_DIR}
+    CACHE PATH "Directory where CTest outputs are saved"
+)
 
 if(RESOLVE_USE_CUDA)
-  set(RESOLVE_USE_GPU ON CACHE BOOL "Using CUDA GPU!" FORCE)
+  set(RESOLVE_USE_GPU
+      ON
+      CACHE BOOL "Using CUDA GPU!" FORCE
+  )
 endif()
 
 if(RESOLVE_USE_HIP)
-  set(RESOLVE_USE_GPU ON CACHE BOOL "Using HIP GPU!" FORCE)
+  set(RESOLVE_USE_GPU
+      ON
+      CACHE BOOL "Using HIP GPU!" FORCE
+  )
 endif()
 
 # MacOS specific things
@@ -51,53 +62,56 @@ set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib)
 # Add CMake sources from `cmake` dir
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
-# Including clang-format cmake files to do automatic checking of formating
-# TODO: Set up clang-format
-#include(./cmake/clang-format)
+# Including clang-format cmake files to do automatic checking of formating TODO:
+# Set up clang-format include(./cmake/clang-format)
 
-if (RESOLVE_USE_DOXYGEN)
+if(RESOLVE_USE_DOXYGEN)
   find_package(Doxygen)
 endif()
 
-if ( DOXYGEN_FOUND )
-  set( DOXYGEN_OUTPUT_DIRECTORY ./sphinx/_build/doxygen )
-  set( DOXYGEN_COLLABORATION_GRAPH YES )
-  set( DOXYGEN_EXTRACT_ALL YES )
-  set( DOXYGEN_CLASS_DIAGRAMS YES )
-  set( DOXYGEN_HIDE_UNDOC_RELATIONS NO )
-  set( DOXYGEN_HAVE_DOT YES )
-  set( DOXYGEN_CLASS_GRAPH YES )
-  set( DOXYGEN_CALL_GRAPH YES )
-  set( DOXYGEN_CALLER_GRAPH YES )
-  set( DOXYGEN_COLLABORATION_GRAPH YES )
-  set( DOXYGEN_BUILTIN_STL_SUPPORT YES )
-  set( DOXYGEN_EXTRACT_PRIVATE YES )
-  set( DOXYGEN_EXTRACT_PACKAGE YES )
-  set( DOXYGEN_EXTRACT_STATIC YES )
-  set( DOXYGEN_EXTRACT_LOCALMETHODS YES )
-  set( DOXYGEN_UML_LOOK YES )
-  set( DOXYGEN_UML_LIMIT_NUM_FIELDS 50 )
-  set( DOXYGEN_TEMPLATE_RELATIONS YES )
-  set( DOXYGEN_DOT_GRAPH_MAX_NODES 100 )
-  set( DOXYGEN_MAX_DOT_GRAPH_DEPTH 0 )
-  set( DOXYGEN_DOT_TRANSPARENT YES )
+if(DOXYGEN_FOUND)
+  set(DOXYGEN_OUTPUT_DIRECTORY ./sphinx/_build/doxygen)
+  set(DOXYGEN_COLLABORATION_GRAPH YES)
+  set(DOXYGEN_EXTRACT_ALL YES)
+  set(DOXYGEN_CLASS_DIAGRAMS YES)
+  set(DOXYGEN_HIDE_UNDOC_RELATIONS NO)
+  set(DOXYGEN_HAVE_DOT YES)
+  set(DOXYGEN_CLASS_GRAPH YES)
+  set(DOXYGEN_CALL_GRAPH YES)
+  set(DOXYGEN_CALLER_GRAPH YES)
+  set(DOXYGEN_COLLABORATION_GRAPH YES)
+  set(DOXYGEN_BUILTIN_STL_SUPPORT YES)
+  set(DOXYGEN_EXTRACT_PRIVATE YES)
+  set(DOXYGEN_EXTRACT_PACKAGE YES)
+  set(DOXYGEN_EXTRACT_STATIC YES)
+  set(DOXYGEN_EXTRACT_LOCALMETHODS YES)
+  set(DOXYGEN_UML_LOOK YES)
+  set(DOXYGEN_UML_LIMIT_NUM_FIELDS 50)
+  set(DOXYGEN_TEMPLATE_RELATIONS YES)
+  set(DOXYGEN_DOT_GRAPH_MAX_NODES 100)
+  set(DOXYGEN_MAX_DOT_GRAPH_DEPTH 0)
+  set(DOXYGEN_DOT_TRANSPARENT YES)
   set(DOXYGEN_DISABLE_INDEX NO)
   set(DOXYGEN_FULL_SIDEBAR NO)
   set(DOXYGEN_GENERATE_TREEVIEW YES)
-  set(DOXYGEN_HTML_EXTRA_STYLESHEET "./docs/doxygen/doxygen-awesome-css/doxygen-awesome.css")
+  set(DOXYGEN_HTML_EXTRA_STYLESHEET
+      "./docs/doxygen/doxygen-awesome-css/doxygen-awesome.css"
+  )
   set(DOXYGEN_HTML_COLORSTYLE LIGHT)
-  doxygen_add_docs( doxygen ${RPP_PROJECT_SOURCE_DIR} )
+  doxygen_add_docs(doxygen ${RPP_PROJECT_SOURCE_DIR})
 
 else()
-  message( "Doxygen need to be installed to generate the doxygen documentation" )
+  message("Doxygen need to be installed to generate the doxygen documentation")
 endif()
 
-
-if (RESOLVE_USE_KLU)
+if(RESOLVE_USE_KLU)
   include(FindKLU)
   if(NOT KLU_LIBRARY)
     message(STATUS "Cannot find KLU, disabling SuiteSparse module ...")
-    set(RESOLVE_USE_KLU OFF CACHE BOOL "Build without SuiteSparse AMD module." FORCE)
+    set(RESOLVE_USE_KLU
+        OFF
+        CACHE BOOL "Build without SuiteSparse AMD module." FORCE
+    )
   endif()
 else()
   message(STATUS "Not using SuiteSparse KLU")
@@ -116,7 +130,10 @@ if(RESOLVE_USE_CUDA)
   endif()
 
   if(NOT DEFINED CMAKE_CUDA_ARCHITECTURES)
-    set(CMAKE_CUDA_ARCHITECTURES 60 CACHE STRING "Selects CUDA architectures")
+    set(CMAKE_CUDA_ARCHITECTURES
+        60
+        CACHE STRING "Selects CUDA architectures"
+    )
   endif()
 
   set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --expt-extended-lambda")
@@ -134,16 +151,14 @@ else()
   message(STATUS "Not using HIP")
 endif(RESOLVE_USE_HIP)
 
-
 # The binary dir is already a global include directory
 configure_file(
   ${CMAKE_SOURCE_DIR}/resolve/resolve_defs.hpp.in
-  ${CMAKE_BINARY_DIR}/resolve/resolve_defs.hpp)
-install(
-  FILES ${CMAKE_BINARY_DIR}/resolve/resolve_defs.hpp
-  DESTINATION include/resolve
-  )
-
+  ${CMAKE_BINARY_DIR}/resolve/resolve_defs.hpp
+)
+install(FILES ${CMAKE_BINARY_DIR}/resolve/resolve_defs.hpp
+        DESTINATION include/resolve
+)
 
 # Enable testing
 enable_testing()
@@ -155,31 +170,38 @@ add_subdirectory(resolve)
 include(CMakePackageConfigHelpers)
 
 # Creates a version file for the package
-write_basic_package_version_file(ReSolveConfigVersion.cmake
-                                 VERSION ${CMAKE_PROJECT_VERSION}
-                                 COMPATIBILITY AnyNewerVersion)
+write_basic_package_version_file(
+  ReSolveConfigVersion.cmake
+  VERSION ${CMAKE_PROJECT_VERSION}
+  COMPATIBILITY AnyNewerVersion
+)
 
 # Generate install rules for targets
-install(EXPORT ReSolveTargets
-        FILE ReSolveTargets.cmake
-        NAMESPACE ReSolve::
-        DESTINATION share/resolve/cmake
+install(
+  EXPORT ReSolveTargets
+  FILE ReSolveTargets.cmake
+  NAMESPACE ReSolve::
+  DESTINATION share/resolve/cmake
 )
 
-
 # Creates a config file
-configure_package_config_file(./cmake/ReSolveConfig.cmake.in
-                              ${CMAKE_CURRENT_BINARY_DIR}/ReSolveConfig.cmake
-                              INSTALL_DESTINATION share/resolve/cmake)
+configure_package_config_file(
+  ./cmake/ReSolveConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/ReSolveConfig.cmake
+  INSTALL_DESTINATION share/resolve/cmake
+)
 
 # Generates install rules for cmake config files
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ReSolveConfig.cmake"
-        "${CMAKE_CURRENT_BINARY_DIR}/ReSolveConfigVersion.cmake"
-        DESTINATION share/resolve/cmake)
-
+              "${CMAKE_CURRENT_BINARY_DIR}/ReSolveConfigVersion.cmake"
+        DESTINATION share/resolve/cmake
+)
+
 # Add usage examples
 add_subdirectory(examples)
 
 # Add tests
-set(RESOLVE_CTEST_OUTPUT_DIR ${PROJECT_BINARY_DIR} CACHE PATH "Directory where CTest outputs are saved")
+set(RESOLVE_CTEST_OUTPUT_DIR
+    ${PROJECT_BINARY_DIR}
+    CACHE PATH "Directory where CTest outputs are saved"
+)
 add_subdirectory(tests)

CONTRIBUTING.md

@@ -185,5 +185,3 @@ class Matrix   // No, class is outside ReSolve namespace
 {
   // matrix code
 };
-
-

LICENSE

@@ -54,4 +54,4 @@ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-******************************************************************************
+******************************************************************************

README.md

@@ -111,4 +111,3 @@ contributions to ReSolve must be made under the smae licensing terms.
 **Please Note** If you are using ReSolve with any third party libraries linked
 in (e.g., KLU), be sure to review the respective license of the package as that
 license may have more restrictive terms than the ReSolve license.
-

buildsystem/ascent-env.sh

@@ -2,4 +2,3 @@
 module load gcc/10.2
 # Load spack deps
 source ./buildsystem/spack/ascent/modules/dependencies.sh
-

buildsystem/incline-env.sh

@@ -12,4 +12,3 @@ unset GPU_DEVICE_ORDINAL
 
 # Load spack generated modules
 source ./buildsystem/spack/incline/modules/dependencies.sh
-

buildsystem/init-mirror.sh

@@ -15,4 +15,3 @@ res=$?
 chmod -R ugo+wrx $SPACK_MIRROR &
 
 exit $res
-

buildsystem/spack/ascent/env.sh

@@ -21,4 +21,3 @@ export SPACK_PYTHON=$(which python)
 export tempdir=$SPACK_CACHE
 export TMP=$SPACK_CACHE
 export TMPDIR=$SPACK_CACHE
-

buildsystem/spack/ascent/spack.yaml

@@ -65,4 +65,3 @@ spack:
       modules: [gcc/10.2]
       operating_system: rhel8
       target: ppc64le
-

buildsystem/spack/deception/spack.yaml

@@ -57,4 +57,4 @@ spack:
         fc: /share/apps/gcc/9.1.0/bin/gfortran
       operating_system: centos7
       target: x86_64
-      modules: [gcc/9.1.0]
+      modules: [gcc/9.1.0]

buildsystem/spack/incline/env.sh

@@ -24,4 +24,3 @@ export SPACK_PYTHON=$(which python3)
 export tempdir=$SPACK_CACHE
 export TMP=$SPACK_CACHE
 export TMPDIR=$SPACK_CACHE
-

cmake/FindKLU.cmake

@@ -1,4 +1,3 @@
-
 #[[
 
 Looks for `klu` library and header directory.
@@ -12,29 +11,29 @@ Users may set the following variables:
 
 ]]
 
-
-find_library(KLU_LIBRARY
-  NAMES
-  klu
-  PATHS
-  ${KLU_DIR} $ENV{KLU_DIR} ${HIOP_KLU_DIR}
-  ENV LD_LIBRARY_PATH ENV DYLD_LIBRARY_PATH
-  PATH_SUFFIXES
-  lib64 lib)
+find_library(
+  KLU_LIBRARY
+  NAMES klu
+  PATHS ${KLU_DIR}
+        $ENV{KLU_DIR}
+        ${HIOP_KLU_DIR}
+        ENV
+        LD_LIBRARY_PATH
+        ENV
+        DYLD_LIBRARY_PATH
+  PATH_SUFFIXES lib64 lib
+)
 
 if(KLU_LIBRARY)
   get_filename_component(KLU_LIBRARY_DIR ${KLU_LIBRARY} DIRECTORY)
 endif()
 
-find_path(KLU_INCLUDE_DIR
-  NAMES
-  klu.h
-  PATHS
-  ${KLU_DIR} $ENV{KLU_DIR} ${HIOP_KLU_DIR} ${KLU_LIBRARY_DIR}/..
-  PATH_SUFFIXES
-  include
-  include/suitesparse
-  include/klu)
+find_path(
+  KLU_INCLUDE_DIR
+  NAMES klu.h
+  PATHS ${KLU_DIR} $ENV{KLU_DIR} ${HIOP_KLU_DIR} ${KLU_LIBRARY_DIR}/..
+  PATH_SUFFIXES include include/suitesparse include/klu
+)
 
 if(KLU_LIBRARY)
   message(STATUS "Found klu include: ${KLU_INCLUDE_DIR}")
@@ -51,4 +50,3 @@ endif()
 
 set(KLU_INCLUDE_DIR CACHE PATH "Path to klu.h")
 set(KLU_LIBRARY CACHE PATH "Path to klu library")
-

cmake/ReSolveFindCudaLibraries.cmake

@@ -1,15 +1,13 @@
-# Exports target `resolve_cuda` which finds all cuda libraries needed by resolve.
-
+# Exports target `resolve_cuda` which finds all cuda libraries needed by
+# resolve.
 
 add_library(resolve_cuda INTERFACE)
 
 find_package(CUDAToolkit REQUIRED)
 
-target_link_libraries(resolve_cuda INTERFACE
-  CUDA::cusolver 
-  CUDA::cublas
-  CUDA::cusparse
-  CUDA::cudart
-  )
+target_link_libraries(
+  resolve_cuda INTERFACE CUDA::cusolver CUDA::cublas CUDA::cusparse
+                         CUDA::cudart
+)
 
 install(TARGETS resolve_cuda EXPORT ReSolveTargets)