Merge branch 'develop' into 'main'

tools v0.4.1

See merge request njoy/tools!11

.github/scripts/prep_valgrind_test.sh

@@ -0,0 +1,16 @@
+#! /bin/bash
+echo "
+check_return_code() {
+        if [ \$? -ne 0 ]; then
+                echo \"Memory leak detected. Test Failed...\"
+                exit 1
+        fi
+}
+
+" > test_valgrind.sh
+
+find . -iname "*.test" -type f | while IFS= read -r line; do
+	dirname=$(dirname "$line")
+	realname=$(basename "$line")
+	echo "cd ${dirname}; valgrind --leak-check=full --show-leak-kinds=all --errors-for-leak-kinds=all --error-exitcode=1 ./${realname}; check_return_code; cd -" >> test_valgrind.sh
+done

.github/workflows/ContinuousIntegration.yml

@@ -11,12 +11,15 @@ on:
   pull_request:
     branches: 'main'
 
+# ubuntu-22.04 is x64
+# macos-13 is intel
+# macos-14 is arm64 (M1)
 jobs:
   build:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ ubuntu-22.04, macos-12 ]
+        os: [ ubuntu-22.04, macos-13, macos-14 ]
         cxx: [ clang++, g++-12 ]
         build_type: [ Debug, Release ]
 
@@ -29,11 +32,24 @@ jobs:
     - name: mkdir bin
       run: mkdir bin
     - name: cmake
-      run: cmake -DPYTHON_EXECUTABLE=$(which python3) -D CMAKE_CXX_COMPILER=`which ${{matrix.cxx}}` -D CMAKE_BUILD_TYPE=${{matrix.build_type}} -D tools.tests=ON ..
+      run: cmake -DCMAKE_CXX_FLAGS="-gdwarf-4" -DPYTHON_EXECUTABLE=$(which python3) -D CMAKE_CXX_COMPILER=`which ${{matrix.cxx}}` -D CMAKE_BUILD_TYPE=${{matrix.build_type}} -D tools.tests=ON ..
       working-directory: ./bin
     - name: make
       run: make -j2
       working-directory: ./bin
     - name: ctest
       run: ctest -j2
       working-directory: ./bin
+
+    - name: Setup Valgrind on Ubuntu
+      if: ${{matrix.os == 'ubuntu-22.04'}}
+      run: |
+        sudo apt-get install valgrind;
+        bash .github/scripts/prep_valgrind_test.sh
+      working-directory: .
+
+    - name: Run tests with Valgrind
+      if: ${{matrix.os == 'ubuntu-22.04'}}
+      run: |
+        bash test_valgrind.sh
+      working-directory: .

CMakeLists.txt

@@ -2,15 +2,15 @@
 # Preamble
 ########################################################################
 
-cmake_minimum_required( VERSION 3.24 )
+cmake_minimum_required( VERSION 3.27 )
 
 set( subproject OFF )
 if( DEFINED PROJECT_NAME )
   set( subproject ON )
 endif()
 
 project( tools
-  VERSION 0.4.0
+  VERSION 0.4.1
   LANGUAGES CXX
 )
 
@@ -83,7 +83,7 @@ if( tools.python )
 
   target_link_libraries( tools.python PRIVATE tools )
   target_include_directories( tools.python PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/python/src )
-  target_compile_options( tools.python PRIVATE "-fvisibility=hidden" )
+  set_target_properties( tools.python PROPERTIES CXX_VISIBILITY_PRESET hidden)
   set_target_properties( tools.python PROPERTIES OUTPUT_NAME tools )
   set_target_properties( tools.python PROPERTIES COMPILE_DEFINITIONS "PYBIND11" )
   set_target_properties( tools.python PROPERTIES POSITION_INDEPENDENT_CODE ON )

ReleaseNotes.md

@@ -1,6 +1,13 @@
 # Release Notes—tools
 Given here are some release notes for tools.
 
+## tools v0.4.1
+Bug fixes:
+  - iterator guards were added to the disco parser to avoid valgrind errors in ENDFtk.
+  - the stride_view iterator was missing the reference type, which is required to create vectors using these stride view iterators in C++17.
+
+A few updates were made in the CMake files for Windows compilation issues. The GitHub CI was also updated: macos-14 (arm64 architecture) was added in addition to macos-13 (intel architecture).
+
 ## [tools v0.4.0](https://github.com/njoy/tools/pull/44)
 New features:
   - added a partial implementation of the C++23 ranges standard: chunk_view, chunk_by_view, stride_view and repeat_view (LLVM implementations for these views were used as models for our C++17 based implementations)

cmake/dependencies.cmake

@@ -1,4 +1,4 @@
-cmake_minimum_required( VERSION 3.24 )
+cmake_minimum_required( VERSION 3.27 )
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/.cmake)
 include( shacl_FetchContent )
 #######################################################################

src/tools/Log.hpp

@@ -16,19 +16,19 @@ namespace tools {
  */
 class Log {
 
-  static auto initialize_logger() {
+  static std::shared_ptr<spdlog::logger> initialize_logger() {
 
-    auto instance = spdlog::stdout_color_st( "njoy" );
+    std::shared_ptr<spdlog::logger> instance = spdlog::stdout_color_st( "njoy" );
     instance->set_pattern( "[%^%l%$] %v" );
     #ifndef NDEBUG
     instance->set_level( spdlog::level::debug );
     #endif
     return instance;
   }
 
-  static auto& logger() {
+  static std::shared_ptr<spdlog::logger>& logger() {
 
-    static auto instance = initialize_logger();
+    static std::shared_ptr<spdlog::logger> instance = initialize_logger();
     return instance;
   }
 

src/tools/disco/BaseField/test/BaseField.test.cpp

@@ -18,14 +18,10 @@ class TestBaseField : protected BaseField {
 
 SCENARIO( "BaseField" ) {
 
-  std::string string = " a\t\n\r\n\f";
-  string += char{ std::char_traits<char>::eof() };
+  std::string string = "+abc";
   auto iter = string.begin();
   unsigned int position = 0;
 
-  string = "+abc";
-  position = 0;
-  iter = string.begin();
   TestBaseField::skipPlusSign( iter, position );
   CHECK( iter == string.begin() + 1 );
   CHECK( position == 1 );

src/tools/disco/BaseFixedWidthField/test/BaseFixedWidthField.test.cpp

@@ -20,14 +20,10 @@ class TestBaseFixedWidthField : protected BaseFixedWidthField< Width > {
 
 SCENARIO( "BaseFixedWidthField" ) {
 
-  std::string string = " a\t\n\r\n\f";
-  string += char{ std::char_traits<char>::eof() };
+  std::string string = "+abc";
   auto iter = string.begin();
   unsigned int position = 0;
 
-  string = "+abc";
-  position = 0;
-  iter = string.begin();
   TestBaseFixedWidthField< 6 >::skipPlusSign( iter, position );
   CHECK( iter == string.begin() + 1 );
   CHECK( position == 1 );

src/tools/disco/Character.hpp

@@ -38,13 +38,17 @@ class Character : public BaseFixedWidthField< Width > {
    *  @param[in,out] iter       an iterator to a character in a range
    */
   template < typename Representation, typename Iterator >
-  static Representation read( Iterator& iter, const Iterator& ) {
+  static Representation read( Iterator& iter, const Iterator& end ) {
 
     Representation value;
+    if ( iter >= end ) {
+
+      return value;
+    }
     value.reserve( Width );
 
     unsigned int position = 0;
-    while( position < Width && ! ( isNewLine( iter ) || isEndOfFile( iter ) ) ) {
+    while( position < Width && ! isNewLine( iter ) ) {
 
       ++position;
       value.push_back( *iter++ );

src/tools/disco/Column.hpp

@@ -37,10 +37,10 @@ class Column : public BaseFixedWidthField< Width > {
    *  @param[in,out] iter   an iterator to a character in a range
    */
   template < typename Iterator >
-  static void read( Iterator& iter, const Iterator& ) {
+  static void read( Iterator& iter, const Iterator& end ) {
 
     unsigned int position = 0;
-    while( position < Width && ! ( isNewLine( iter ) || isEndOfFile( iter ) ) ) {
+    while( position < Width && ! ( isNewLine( iter ) || iter >= end ) ) {
 
       ++position;
       ++iter;

src/tools/disco/FreeFormatCharacter.hpp

@@ -35,10 +35,6 @@ class FreeFormatCharacter : public BaseField {
     iter = std::find_if( iter, end,
                          [] ( auto&& value )
                             { return ! std::isspace( value ); }  );
-    if ( isEndOfFile( iter ) ) {
-
-      throw std::runtime_error( "Cannot read valid string: end of file encountered" );
-    }
 
     auto temp = std::find_if( iter, end,
                               [] ( auto&& value )

src/tools/disco/FreeFormatInteger.hpp

@@ -41,10 +41,6 @@ class FreeFormatInteger : public BaseField {
     iter = std::find_if( iter, end,
                          [] ( auto&& value )
                             { return ! std::isspace( value ); }  );
-    if ( isEndOfFile( iter ) ) {
-
-      throw std::runtime_error( "Cannot read valid integer: end of file encountered" );
-    }
 
     // we are using fast_float::from_chars instead of std::from_chars since
     // not all standard c++ libraries implement the floating point version of

src/tools/disco/FreeFormatInteger/test/FreeFormatInteger.test.cpp

@@ -103,13 +103,6 @@ SCENARIO( "Integer" ) {
       end = string.end();
       CHECK( 123 == FreeFormatInteger::read< int >( iter, end ) );
       CHECK( iter == end - 1 );
-
-      string = "    +123";
-      string += char{ std::char_traits<char>::eof() };
-      iter = string.begin();
-      end = string.end();
-      CHECK( 123 == FreeFormatInteger::read< int >( iter, end ) );
-      CHECK( iter == end - 1 );
     } // THEN
   } // GIVEN
 

src/tools/disco/FreeFormatReal.hpp

@@ -41,10 +41,6 @@ class FreeFormatReal : public BaseField {
     iter = std::find_if( iter, end,
                          [] ( auto&& value )
                             { return ! std::isspace( value ); }  );
-    if ( isEndOfFile( iter ) ) {
-
-      throw std::runtime_error( "Cannot read valid real value: end of file encountered" );
-    }
 
     // we are using fast_float::from_chars_advanced instead of std::from_chars
     // since not all standard c++ libraries implement the floating point version

src/tools/disco/FreeFormatReal/test/FreeFormatReal.test.cpp

@@ -213,13 +213,6 @@ SCENARIO( "Integer" ) {
       end = string.end();
       CHECK_THAT( 123, WithinRel( FreeFormatReal::read< double >( iter, end ) ) );
       CHECK( iter == end - 1 );
-
-      string = "    +123";
-      string += char{ std::char_traits<char>::eof() };
-      iter = string.begin();
-      end = string.end();
-      CHECK_THAT( 123, WithinRel( FreeFormatReal::read< double >( iter, end ) ) );
-      CHECK( iter == end - 1 );
     } // THEN
   } // GIVEN
 

src/tools/disco/Integer.hpp

@@ -41,14 +41,14 @@ class Integer : public BaseFixedWidthField< Width > {
    *  @param[in,out] iter       an iterator to a character in a range
    */
   template < typename Representation, typename Iterator >
-  static Representation read( Iterator& iter, const Iterator& ) {
+  static Representation read( Iterator& iter, const Iterator& end ) {
 
     unsigned int position = 0;
-    const auto end = iter + Width;
+    const auto final = iter + Width;
     Representation value = 0;
 
     skipSpaces( iter, position );
-    if ( isNewLine( iter ) || isEndOfFile( iter ) || Width == position ) {
+    if ( isNewLine( iter ) || Width == position || iter >= end ) {
 
       return value;
     }
@@ -62,7 +62,7 @@ class Integer : public BaseFixedWidthField< Width > {
     // we are using fast_float::from_chars instead of std::from_chars since
     // not all standard c++ libraries implement the floating point version of
     // std::from_chars
-    auto result = fast_float::from_chars( &*iter, &*end, value );
+    auto result = fast_float::from_chars( &*iter, &*final, value );
     if ( result.ec == std::errc() ) {
 
       auto advance = result.ptr - &*iter;
@@ -77,7 +77,7 @@ class Integer : public BaseFixedWidthField< Width > {
     skipSpaces( iter, position );
     if ( Width != position ) {
 
-      if ( ! isNewLine( iter ) && ! isEndOfFile( iter ) ) {
+      if ( ! isNewLine( iter ) ) {
 
         throw std::runtime_error( "cannot parse invalid integer number 3" );
       }

src/tools/disco/Integer/test/Integer.test.cpp

@@ -84,13 +84,6 @@ SCENARIO( "Integer" ) {
       end = string.end();
       CHECK( 123 == Integer< 10 >::read< int >( begin, end ) );
       CHECK( begin == end - 1 );
-
-      string = "    +123";
-      string += char{ std::char_traits<char>::eof() };
-      begin = string.begin();
-      end = string.end();
-      CHECK( 123 == Integer< 10 >::read< int >( begin, end ) );
-      CHECK( begin == end - 1 );
     } // THEN
   } // GIVEN
 

src/tools/disco/Real.hpp

@@ -33,14 +33,14 @@ class Real : public BaseFixedWidthField< Width > {
    *  @param[in,out] iter       an iterator to a character in a range
    */
   template < typename Representation, typename Iterator >
-  static Representation read( Iterator& iter, const Iterator& ) {
+  static Representation read( Iterator& iter, const Iterator& end ) {
 
     unsigned int position = 0;
-    const auto end = iter + Width;
+    const auto final = iter + Width;
     Representation value = 0.0;
 
     skipSpaces( iter, position );
-    if ( isNewLine( iter ) || isEndOfFile( iter ) || Width == position ) {
+    if ( isNewLine( iter ) || Width == position || iter >= end ) {
 
       return value;
     }
@@ -56,7 +56,7 @@ class Real : public BaseFixedWidthField< Width > {
     // of std::from_chars and because this allows us to read fortran formatted
     // floats
     fast_float::parse_options options{ fast_float::chars_format::fortran };
-    auto result = fast_float::from_chars_advanced( &*iter, &*end, value, options );
+    auto result = fast_float::from_chars_advanced( &*iter, &*final, value, options );
     if ( result.ec == std::errc() ) {
 
       auto advance = result.ptr - &*iter;
@@ -71,7 +71,7 @@ class Real : public BaseFixedWidthField< Width > {
     skipSpaces( iter, position );
     if ( Width != position ) {
 
-      if ( ! isNewLine( iter ) && ! isEndOfFile( iter ) ) {
+      if ( ! isNewLine( iter ) ) {
 
         throw std::runtime_error( "cannot parse invalid real number 3" );
       }

src/tools/disco/Real/test/Real.test.cpp

@@ -218,13 +218,6 @@ SCENARIO( "Real" ) {
       end = string.end();
       CHECK_THAT( 123, WithinRel( Real< 10 >::read< double >( begin, end ) ) );
       CHECK( begin == end - 1 );
-
-      string = "    +123";
-      string += char{ std::char_traits<char>::eof() };
-      begin = string.begin();
-      end = string.end();
-      CHECK_THAT( 123, WithinRel( Real< 10 >::read< double >( begin, end ) ) );
-      CHECK( begin == end - 1 );
     } // THEN
   } // GIVEN
 

src/tools/disco/Record.hpp

@@ -22,7 +22,7 @@ struct Record<> {
   template< typename Iterator >
   static void read( Iterator& iter, const Iterator& end ) {
 
-    while ( iter != end && ! ( isNewLine( iter )|| isEndOfFile( iter ) ) ) {
+    while ( iter != end && ! ( isNewLine( iter ) ) ) {
 
       ++iter;
     }

src/tools/disco/functions.hpp

@@ -69,15 +69,6 @@ bool isWhiteSpace( const Iterator& iter ) {
   return std::isspace( *iter );
 }
 
-/**
- *  @brief Return whether or not a character is the end of file character
- */
-template < typename Iterator >
-constexpr bool isEndOfFile( const Iterator& iter ) {
-
-  return std::char_traits< char >::eof() == *iter;
-}
-
 } // disco namespace
 } // tools namespace
 } // njoy namespace