merge upstream changes

Author: dezed-ukaea

.github/workflows/docs.yaml

@@ -0,0 +1,27 @@
+name: Pages
+on:
+  push:
+    branches:
+    - main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: "3.9"
+        architecture: "x64"
+    - name: Checkout
+      uses: actions/checkout@main
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+    - name: build docs
+      uses: mattnotmitt/[email protected]
+      with:
+        doxyfile-path: 'Doxyfile'
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/doxygen/html

.github/workflows/fdp_cpp_api.yaml

@@ -42,10 +42,10 @@ jobs:
       - name: Install Dependencies
         run: |
           sudo apt update
-          sudo apt install -y lcov libjsoncpp-dev curl libcurl4-openssl-dev libyaml-cpp-dev libhdf5-dev
+          sudo apt install -y lcov libjsoncpp-dev curl libcurl4-openssl-dev libyaml-cpp-dev gcovr
       - name: Configure Library
         run: |
-          cmake -Bbuild -DFDPAPI_BUILD_TESTS=ON
+          cmake -Bbuild -DFDPAPI_BUILD_TESTS=ON -DFDPAPI_CODE_COVERAGE=ON -DCMAKE_BUILD_TYPE=Debug
       - name: Fetch cache
         uses: actions/[email protected]
         with:
@@ -60,21 +60,19 @@ jobs:
           wget -nv https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip
           unzip -q build-wrapper-linux-x86.zip          
           echo "${PWD}/build-wrapper-linux-x86" >> $GITHUB_PATH
-      - name: Compile FDP-Cpp-API
-        run: build-wrapper-linux-x86-64 --out-dir bw-outputs cmake --build build
-        env:
-          CIBuild: 1
-          BUILD_TESTS: True
-      - name: Run Unit Tests
+      - name: Build and Run Unit Tests
         run: |
-         cmake --build build --target test
+         build-wrapper-linux-x86-64 --out-dir bw-outputs cmake --build build --target coverage
          if [ $? -eq 0 ]; then
            echo "Unit tests completed successfully"
            exit 0
          else
            echo "Unit tests failed"
            exit 1
          fi
+        env:
+          CIBuild: 1
+          BUILD_TESTS: True 
       - name: SonarCloud Scan
         run: |
           sonar-scanner -Dsonar.host.url=https://sonarcloud.io -Dsonar.login=$SONAR_TOKEN -X
@@ -91,7 +89,6 @@ jobs:
       - name: Install Dependencies
         run: |
           brew install cmake
-          brew install hdf5
           brew install curl
       - name: Configure Library
         run: |
@@ -107,20 +104,8 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: ilammy/msvc-dev-cmd@v1
-      - name: Install Dependencies
-        run: |
-          choco install wget
-          wget -O hdf5.zip https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/windows/hdf5-1.12.1-Std-win10_64-vs14.zip
-          tar -xf hdf5.zip
-          cd hdf
-          msiexec /i HDF5-1.12.1-win64.msi /quiet /qn /norestart /log log.log INSTALL_ROOT="$Env:RUNNER_TEMP\HDF5_ROOT" | Out-Null
-          gc log.log
       - name: Configure Library
         run: |
           cmake -Bbuild -DFDPAPI_BUILD_TESTS=ON
-        env: 
-          HDF5_ROOT: ${{ runner.temp }}\HDF5_ROOT
       - name: Compile FDP-Cpp-API
         run: cmake --build build --config=Release
-        env: 
-          HDF5_ROOT: ${{ runner.temp }}\HDF5_ROOT

.gitignore

@@ -4,4 +4,5 @@ build/
 .bash_profile
 test/data_store/
 data_store/
-.fair
+.fair
+venv/

CMakeLists.txt

@@ -16,6 +16,12 @@ ELSE()
     set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Release")
 ENDIF()
 
+IF( FDPAPI_CODE_COVERAGE )
+    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -O0 --coverage")
+    message("CXX Flags: ${CMAKE_CXX_FLAGS}")
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O0")
+ENDIF()
+
 # Define Project
 PROJECT( fdpapi
     VERSION 0.1.0
@@ -26,20 +32,6 @@ PROJECT( fdpapi
 
 set( FDPAPI fdpapi )
 
-# Use HDF5 Static Libraries on Windows
-if ( WIN32 )
-    SET (HDF5_USE_STATIC_LIBRARIES TRUE)
-ENDIF()
-
-# Find HDF5 Package
-find_package(HDF5 COMPONENTS C CXX)
-
-# If the HDF5 Package is not found stop
-if (NOT HDF5_FOUND)
-    message( FATAL_ERROR "HDF5 Library Not Found, 
-        Please install it and ensure the Environment Variable HDF5_ROOT is set")
-ENDIF()
-
 # Set Output Directories to avoid issues on multi release compilers
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
@@ -90,49 +82,16 @@ ENDIF()
 
 # Compile Code Coverage if Specified with Tests
 IF( FDPAPI_CODE_COVERAGE AND FDPAPI_BUILD_TESTS )
-    MESSAGE( STATUS "[Coverage]")
-    SET( COVERAGE_COMPILER_FLAGS "--coverage -fprofile-arcs -ftest-coverage" )
-	SET( CMAKE_CXX_FLAGS "-std=gnu++17 -O0 -Wall -Wextra -Werror ${COVERAGE_COMPILER_FLAGS} ${CMAKE_CXX_FLAGS}" )
-    SET( CMAKE_C_FLAGS "-O0 -Wall -Wextra ${COVERAGE_COMPILER_FLAGS} ${CMAKE_C_FLAGS}" )
-    MESSAGE( "\t CMAKE_CXX_FLAGS: ${CMAKE_CXX_FLAGS}" )
-    MESSAGE( "\t CMAKE_C_FLAGS: ${CMAKE_C_FLAGS}" )
-    
-
-	find_program( LCOV_PATH  NAMES lcov lcov.bat lcov.exe lcov.perl)
-	find_program( GCOV_PATH gcov )
-	
-	set(LCOV_EXCLUDES "build/*" "/usr*")
-	
-	add_custom_target(coverage
-	
-        # Cleanup lcov
-        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -directory . -b ${PROJECT_SOURCE_DIR} --zerocounters
-	
-	    # Create baseline to make sure untouched files show up in the report
-		COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -c -i -d . -b ${PROJECT_SOURCE_DIR} -o ${FDPAPI}.base
-	
-	    # Run executables
-		COMMAND ${CMAKE_BINARY_DIR}/test/${FDPAPI}-tests ${COV_TEST_FLAGS}
-	
-	    # Capturing lcov counters and generating report
-		COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} --directory . -b ${PROJECT_SOURCE_DIR} --capture --output-file ${FDPAPI}.capture
-	
-	    # add baseline counters
-		COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -a ${FDPAPI}.base -a ${FDPAPI}.capture --output-file ${FDPAPI}.total
-	
-	    # filter collected data to final coverage report and merge outputs
-		COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} --remove ${FDPAPI}.total ${LCOV_EXCLUDES} --output-file ${FDPAPI}.info
-	
-        # Set output files as GENERATED (will be removed on 'make clean')
-        BYPRODUCTS
-            ${FDPAPI}.base
-            ${FDPAPI}.capture
-            ${FDPAPI}.total
-            ${FDPAPI}.info
-            ${FDPAPI}  # report directory
-
-        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
-        VERBATIM # Protect arguments to commands
-        COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
-	)
+    if(CMAKE_COMPILER_IS_GNUCXX)
+        LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake_modules")
+        include(CodeCoverage)
+        APPEND_COVERAGE_COMPILER_FLAGS()
+
+        #set(COVERAGE_EXCLUDES 'build/*' 'usr/*')
+        #set(Coverage_BASE_DIRECTORY ${CMAKE_SOURCE_DIR})
+        setup_target_for_coverage_gcovr_sonar(NAME coverage
+                              EXECUTABLE bin/${FDPAPI}-tests
+                              DEPENDENCIES ${FDPAPI}-tests
+                              BASE_DIRECTORY ${CMAKE_SOURCE_DIR})
+    endif()
 ENDIF()