Merge 2ce11ec into ba911c1

sandialabs · Oct 11, 2024 · 7e9b9a3 · 7e9b9a3
2 parents ba911c1 + 2ce11ec
commit 7e9b9a3
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Showing 33 changed files with 31,518 additions and 252 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -43,31 +43,78 @@ jobs:
     # For linux, we will perform developer checks, so we need boost
     - name: Set up dependencies
       if: runner.os == 'Linux'
-      run: sudo apt-get update && sudo apt-get install -y build-essential libboost-all-dev
+      run: sudo apt-get update && sudo apt-get install -y build-essential libboost-all-dev gfortran
 
     - name: Create build directory
       run: mkdir build
 
     - name: Configure CMake on Windows
       if: runner.os == 'Windows'
-      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=OFF -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON
+      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=OFF -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DSpecUtils_C_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=install_prefix
 
     # On linux we will perform developer checks and compile as debug to catch asserts
     - name: Configure CMake on Linux
       if: runner.os == 'Linux'
-      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=ON -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON
+      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=ON -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=OFF -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DSpecUtils_C_BINDINGS=ON -DSpecUtils_FORTRAN_SWIG=ON -DCMAKE_INSTALL_PREFIX=install_prefix
 
     - name: Configure CMake on macOS
       if: runner.os == 'macOS'
-      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON
+      run: cmake -S ${{ github.workspace }} -B build -DSpecUtils_BUILD_UNIT_TESTS=ON -DSpecUtils_BUILD_REGRESSION_TEST=ON -DSpecUtils_ENABLE_EQUALITY_CHECKS=ON -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DSpecUtils_C_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=install_prefix
 
     - name: Build macOS and Windows
       if: runner.os != 'Linux'
       run: cmake --build build --config Release
 
     - name: Build Linux
       if: runner.os == 'Linux'
-      run: cmake --build build --config Debug
+      run: cmake --build build --config Release -j $(nproc)
 
     - name: Run tests
-      run: ctest --test-dir build -C Release
+      run: ctest --rerun-failed --output-on-failure --test-dir build -C Release
+
+    - name: Package Lib
+      if: runner.os == 'boost' && runner.os == 'Windows'
+      run: |
+        cmake -S ${{ github.workspace }} -B build_static_lib_shared_runtime -DSpecUtils_BUILD_UNIT_TESTS=OFF -DSpecUtils_BUILD_REGRESSION_TEST=OFF -DSpecUtils_ENABLE_EQUALITY_CHECKS=OFF -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DCMAKE_INSTALL_PREFIX=install_prefix_static_lib_shared_runtime -DSpecUtils_USE_MSVC_MultiThreadDLL=ON -DSpecUtils_SHARED_LIB=OFF
+        cmake --build build_static_lib_shared_runtime --config Release --target package
+        #
+        cmake -S ${{ github.workspace }} -B build_shared_lib_shared_runtime -DSpecUtils_BUILD_UNIT_TESTS=OFF -DSpecUtils_BUILD_REGRESSION_TEST=OFF -DSpecUtils_ENABLE_EQUALITY_CHECKS=OFF -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DCMAKE_INSTALL_PREFIX=install_prefix_build_shared_lib_shared_runtime -DSpecUtils_USE_MSVC_MultiThreadDLL=ON -DSpecUtils_SHARED_LIB=ON
+        cmake --build build_shared_lib_shared_runtime --config Release --target package
+        #
+        cmake -S ${{ github.workspace }} -B build_shared_lib_static_runtime -DSpecUtils_BUILD_UNIT_TESTS=OFF -DSpecUtils_BUILD_REGRESSION_TEST=OFF -DSpecUtils_ENABLE_EQUALITY_CHECKS=OFF -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DCMAKE_INSTALL_PREFIX=install_prefix_build_shared_lib_static_runtime -DSpecUtils_USE_MSVC_MultiThreadDLL=OFF -DSpecUtils_SHARED_LIB=ON
+        cmake --build build_shared_lib_static_runtime --config Release --target package
+        #
+        cmake -S ${{ github.workspace }} -B build_static_lib_static_runtime -DSpecUtils_BUILD_UNIT_TESTS=OFF -DSpecUtils_BUILD_REGRESSION_TEST=OFF -DSpecUtils_ENABLE_EQUALITY_CHECKS=OFF -DPERFORM_DEVELOPER_CHECKS=OFF -DSpecUtils_ENABLE_D3_CHART=ON -DSpecUtils_D3_SUPPORT_FILE_STATIC=ON -DSpecUtils_ENABLE_URI_SPECTRA=ON -DCMAKE_BUILD_TYPE=Release -DSpecUtils_FLT_PARSE_METHOD=${{ matrix.num-parse-method }} -DSpecUtils_FETCH_FAST_FLOAT=ON -DCMAKE_INSTALL_PREFIX=install_prefix_build_static_lib_static_runtime -DSpecUtils_USE_MSVC_MultiThreadDLL=OFF -DSpecUtils_SHARED_LIB=OFF
+        cmake --build build_static_lib_static_runtime --config Release --target package
+
+# Update the bleeding-edge tag to be current commit
+    - name: Run latest-tag
+      uses: EndBug/[email protected]
+      if: runner.os == 'Windows'
+      with:
+        ref: bleeding-edge
+        description: Latest successful automated build
+
+    - name: Upload windows build to GitHub Artifact
+      uses: actions/upload-artifact@v4
+      if: runner.os == 'Windows'
+      with: 
+        name: SpecUtils_${{ runner.os }}_latest
+        path: '.\build_*\*.zip'
+
+    - name: Create Release
+      uses: ncipollo/[email protected]
+      if: runner.os == 'Windows'
+      with:
+        artifacts: '.\build_*\*.zip'
+        draft: false
+        prerelease: true
+        body: "An automated, and untested build of the latest code pushed to the repository."
+        allowUpdates: true
+        generateReleaseNotes: false
+        name: "Bleeding Edge Build"
+        removeArtifacts: true
+        replacesArtifacts: true
+        tag: 'bleeding-edge'
+        commit: ${{ github.sha }}
+        makeLatest: true
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -10,6 +10,8 @@ endif()
 
 project( SpecUtils VERSION 1.0.0 )
 
+enable_testing()
+
 option( SpecUtils_ENABLE_D3_CHART "Enables exporting of the D3 chart format" ON )
 option( SpecUtils_D3_SUPPORT_FILE_STATIC "Compiles the JS and CSS files into memory, rather than reading files on disk; disable to allow changing JS/CSS without having to recompile" ON )
 option( SpecUtils_ENABLE_URI_SPECTRA "Enables encoding/decoding spectra to URIs (for, ex, QR-codes) - requires linking to zlib" OFF )
@@ -21,6 +23,7 @@ option( SpecUtils_BUILD_REGRESSION_TEST "Creates executable to perform interacti
 option( SpecUtils_BUILD_EXAMPLE "Builds example SpecUtil applications" OFF )
 option( SpecUtils_PYTHON_BINDINGS "Creates python bindings to the c++ code" OFF )
 option( SpecUtils_JAVA_SWIG "Creates swig/java bindings to the c++ code" OFF )
+option( SpecUtils_FORTRAN_SWIG "Creates swig/FORTRAN bindings to the c++ code" OFF )
 option( SpecUtils_C_BINDINGS "Creates C bindings to the c++ code" OFF )
 option( SpecUtils_INJA_TEMPLATES "Creates inja template interface" OFF )
 option( SpecUtils_USE_SIMD "Use SIMD operations; i386/x64 only right now, and very alpha, and extremely minimally used" OFF )
@@ -82,7 +85,7 @@ endif()
 
 
 # If we are building this on Windows, not as a sub-project, lets enable selecting C++ runtime
-if( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
+if( MSVC )
   get_directory_property(hasParent PARENT_DIRECTORY)
   if(NOT hasParent)
     option(${PROJECT_NAME}_USE_MSVC_MultiThreadDLL "Use dynamically-link runtime library." OFF)
@@ -96,7 +99,7 @@ if( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
     endif()
     message(STATUS "Using CMAKE_MSVC_RUNTIME_LIBRARY ${CMAKE_MSVC_RUNTIME_LIBRARY}")
   endif(NOT hasParent)
-endif( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
+endif( MSVC )
 
 
 if( SpecUtils_BUILD_EXAMPLE )
@@ -330,7 +333,7 @@ if( SpecUtils_USE_FAST_FLOAT )
       FetchContent_GetProperties( fast_float )
       FetchContent_MakeAvailable( fast_float )
 
-      target_include_directories( SpecUtils PUBLIC ${fast_float_SOURCE_DIR} )
+      target_include_directories( SpecUtils PRIVATE ${fast_float_SOURCE_DIR} )
     endif( SpecUtils_FETCH_FAST_FLOAT )
   endif( NOT FAST_FLOAT_FILE_PATH )
 endif( SpecUtils_USE_FAST_FLOAT )
@@ -417,6 +420,9 @@ if( SpecUtils_JAVA_SWIG )
   target_link_libraries( SpecUtils PUBLIC ${JAVA_LIBRARIES} )
 endif( SpecUtils_JAVA_SWIG )
 
+if( SpecUtils_FORTRAN_SWIG )
+  add_subdirectory(bindings/swig/fortran)
+endif( SpecUtils_FORTRAN_SWIG )
 
 if( MINGW )
   target_link_libraries( SpecUtils PUBLIC -static-libgcc -static libshlwapi.a libpthread.a libstdc++.a libwinpthread.a libmsvcrt.a )
@@ -427,8 +433,8 @@ elseif( WIN32 )
   target_link_libraries( SpecUtils PUBLIC "Shlwapi.lib" )
 endif( MINGW )
 
-target_include_directories( SpecUtils PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}
-                            PRIVATE ${THIRD_PARTY_DIR} ${Python3_INCLUDE_DIRS} )
+target_include_directories( SpecUtils PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}> 
+                            PRIVATE ${THIRD_PARTY_DIR} ${PYTHON_INCLUDE_DIRS} )
 
 if( SpecUtils_BUILD_REGRESSION_TEST )
   if( NOT SpecUtils_ENABLE_EQUALITY_CHECKS )
@@ -450,9 +456,74 @@ if( SpecUtils_BUILD_FUZZING_TESTS )
   add_subdirectory( fuzz_test )
 endif( SpecUtils_BUILD_FUZZING_TESTS )
 
+set_property( TARGET SpecUtils PROPERTY POSITION_INDEPENDENT_CODE ON )
+
+# Specify installation rules
+include(GNUInstallDirs)
+
+
+# Install the library
+install(TARGETS SpecUtils
+    EXPORT SpecUtilsTargets
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
+
+set( SpecUtils_config_OUT ${CMAKE_CURRENT_BINARY_DIR}/SpecUtils_config.h )
 configure_file(
     ${CMAKE_CURRENT_SOURCE_DIR}/SpecUtils/SpecUtils_config.h.in
-    ${CMAKE_CURRENT_BINARY_DIR}/SpecUtils_config.h
+    ${SpecUtils_config_OUT}
 )
+LIST(APPEND headers ${SpecUtils_config_OUT})
+# Install the headers
+install(FILES ${headers} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/SpecUtils)
 
+# Create and install the CMake package configuration files
+include(CMakePackageConfigHelpers)
+
+write_basic_package_version_file(
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfigVersion.cmake"
+    VERSION ${PROJECT_VERSION}
+    COMPATIBILITY AnyNewerVersion
+)
+
+configure_package_config_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/SpecUtilsConfig.cmake.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfig.cmake"
+    INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)
+
+install(FILES
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfig.cmake"
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfigVersion.cmake"
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)
+
+install(EXPORT SpecUtilsTargets
+    FILE SpecUtilsTargets.cmake
+    NAMESPACE SpecUtils::
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)
+
+set(CPACK_PACKAGE_NAME "SpecUtils")
+
+
+if( SpecUtils_SHARED_LIB )
+  set( SpecUtils_PACKAGE_POSTFIX "SharedLib" )
+else( SpecUtils_SHARED_LIB )
+  set( SpecUtils_PACKAGE_POSTFIX "StaticLib" )
+endif( SpecUtils_SHARED_LIB )
+
+if( DEFINED ${PROJECT_NAME}_USE_MSVC_MultiThreadDLL )
+  if( ${PROJECT_NAME}_USE_MSVC_MultiThreadDLL )
+    set( SpecUtils_PACKAGE_POSTFIX "${SpecUtils_PACKAGE_POSTFIX}-SharedRuntime" )
+  else()
+    set( SpecUtils_PACKAGE_POSTFIX "${SpecUtils_PACKAGE_POSTFIX}-StaticRuntime" )
+  endif()
+endif()
 
+set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CMAKE_SYSTEM_NAME}-${CMAKE_CXX_COMPILER_ID}-${CMAKE_CXX_COMPILER_VERSION}-${SpecUtils_PACKAGE_POSTFIX}")
+set(CPACK_GENERATOR "ZIP")
+include(CPack)
diff --git a/SpecUtils/EnergyCalibration.h b/SpecUtils/EnergyCalibration.h
@@ -41,6 +41,9 @@
  */
 namespace SpecUtils
 {
+
+  using DevPair = std::pair<float,float>;             
+  using DeviationPairs = std::vector<DevPair>; 
   /** The energy (or FWHM) calibration type that the calibration coefficients
    should be interpreted as.
    

diff --git a/SpecUtils/ParseUtils.h b/SpecUtils/ParseUtils.h
@@ -31,6 +31,8 @@
 #include <istream>
 #include <ostream>
 
+#include "SpecUtils/StringAlgo.h"
+
 /** Some functions and definitions that help to parse and write spectrum files,
  but maybe dont fit in other sections of code.
  */
@@ -290,6 +292,7 @@ Integral float_to_integral( float d )
     static constexpr Integral max_int_val = std::numeric_limits<Integral>::max();
     return std::signbit(d) ? min_int_val : max_int_val;
   }//float_to_integral
+
 }//namespace SpecUtils
 
 #endif //SpecUtils_ParseUtils_h