merging c+11 changes with master branch

.github/workflows/main-testing.yml

@@ -0,0 +1,88 @@
+name: main-validation
+
+on:
+  push:
+    branches: [ master, issue37]
+  pull_request:
+    branches: [ master ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally
+    # well on Windows or Mac.  You can convert this to a matrix build if you need
+    # cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, macos-latest, windows-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: seanmiddleditch/gha-setup-ninja@v3
+
+    - name: Build on windows and run check
+      if: matrix.os == 'windows-latest'
+      run: |
+        mkdir build
+        cd build
+        cmake -G "Ninja" ..
+        ninja
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libgcc_s_seh-1.dll ${{github.workspace}}/build/.
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libstdc++-6.dll ${{github.workspace}}/build/.
+        # cp C:/ProgramData/chocolatey/lib/mingw/tools/install/mingw64/bin/libwinpthread-1.dll ${{github.workspace}}/build/.
+        ./NFsim.exe -h
+
+    - name: Configure CMake
+      if: matrix.os != 'windows-latest'
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+    - name: Build unix
+      if: matrix.os != 'windows-latest'
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+          ${{ runner.os }}-
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r validate/requirements.txt
+    - name: Validation
+      run: python validate/validate.py validate/.
+    - name: Prepare unix bundle
+      if: matrix.os != 'windows-latest'
+      run: |
+        cd 
+        mkdir ${{github.workspace}}/bundle_${{ matrix.os }}
+        cp ${{github.workspace}}/build/NFsim ${{github.workspace}}/bundle_${{ matrix.os }}/.
+    - name: Prepare windows bundle
+      if: matrix.os == 'windows-latest'
+      run: |
+        cd 
+        mkdir ${{github.workspace}}/bundle_${{ matrix.os }}
+        cp ${{github.workspace}}/build/NFsim.exe ${{github.workspace}}/bundle_${{ matrix.os }}/.        
+        cp ${{github.workspace}}/build/*.dll ${{github.workspace}}/bundle_${{ matrix.os }}/.
+    - name: Archive compiled NFsim
+      uses: actions/upload-artifact@v3
+      with:
+        name: NFsim_bin_${{ matrix.os }}
+        path: ${{github.workspace}}/bundle_${{ matrix.os }}

.gitignore

@@ -0,0 +1,13 @@
+build
+.vscode
+build_test_files
+validate/basicModels/*.*dat
+validate/basicModels/*.net
+validate/basicModels/*.xml
+validate/basicModels/*.tsv
+validate/basicModels/*.json
+test/Issue37/test2.nfevent.json
+test/Issue37/test.nfevent.json
+test/Issue37/out.gdat
+test/Issue37/issue37_test2.species
+test/Issue37/issue37_test2.gdat

CMakeLists.txt

@@ -0,0 +1,69 @@
+cmake_minimum_required(VERSION 2.8.9)
+
+project(NFsim)
+
+#find_package(XMLRPC REQUIRED abyss-server c++2)
+
+
+#if (NOT XMLRPC_FOUND) 
+#  message (FATAL_ERROR "XMLRPC-C not found") 
+#endif (NOT XMLRPC_FOUND) 
+
+set(CMAKE_BUILD_TYPE Release)
+
+set(SUB_DIRS
+    src/nauty24 
+    src/NFutil 
+    src/NFutil/MTrand 
+    src/NFtest/transcription 
+    src/NFtest/tlbr 
+    src/NFtest/simple_system 
+    src/NFtest/agentcell/cell 
+    src/NFtest/agentcell 
+    src/NFscheduler 
+    src/NFreactions/transformations 
+    src/NFreactions/reactions 
+    src/NFreactions/reactantLists 
+    src/NFreactions/mappings 
+    src/NFreactions 
+    src/NFoutput 
+    src/NFinput 
+    src/NFinput/TinyXML 
+    src/NFinput/json 
+    src/NFfunction/muParser 
+    src/NFfunction 
+    src/NFcore 
+    src/NFcore/reactionSelector 
+    src/NFcore/moleculeLists 
+)
+add_definitions("-Wno-deprecated-declarations")
+
+
+IF(CMAKE_SYSTEM_NAME  MATCHES "Windows")
+   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+#   SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+#   SET(BUILD_SHARED_LIBRARIES OFF)
+#   SET(CMAKE_EXE_LINKER_FLAGS "-static")
+ELSE(CMAKE_SYSTEM_NAME  MATCHES "Windows")
+   set_source_files_properties( src/NFreactions/reactions/DORreaction.cpp PROPERTIES  COMPILE_FLAGS  -std=c++11 )
+   set_source_files_properties( src/NFcore/molecule.cpp                   PROPERTIES  COMPILE_FLAGS  -std=c++11 ) 
+   set_source_files_properties( src/NFcore/templateMolecule.cpp           PROPERTIES  COMPILE_FLAGS  -std=c++11 ) 
+   set_source_files_properties( src/NFinput/NFinput.cpp                   PROPERTIES  COMPILE_FLAGS  -std=c++11 ) 
+ENDIF(CMAKE_SYSTEM_NAME  MATCHES "Windows")
+
+
+#include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${XMLRPC_INCLUDE_DIRS} ${SUB_DIRS})
+include_directories(${CMAKE_CURRENT_SOURCE_DIR} include ${SUB_DIRS})
+
+
+file(GLOB_RECURSE src_files  "${CMAKE_CURRENT_SOURCE_DIR}/src/*cpp")
+file(GLOB_RECURSE c_src_files  "${CMAKE_CURRENT_SOURCE_DIR}/src/*c")
+
+
+set(SRC_FILES 
+    ${src_files} 
+    ${c_src_files} 
+)
+
+
+add_executable(${PROJECT_NAME} ${SRC_FILES} )

CMakeLists.x86.txt

@@ -0,0 +1,58 @@
+cmake_minimum_required(VERSION 2.8.9)
+
+project(NFsim)
+
+#find_package(XMLRPC REQUIRED abyss-server c++2)
+
+SET(CMAKE_C_COMPILER   C:/cygwin/bin/gcc.exe)
+SET(CMAKE_CXX_COMPILER C:/cygwin/bin/g++.exe)
+
+
+#if (NOT XMLRPC_FOUND) 
+#  message (FATAL_ERROR "XMLRPC-C not found") 
+#endif (NOT XMLRPC_FOUND) 
+
+set(CMAKE_BUILD_TYPE Release)
+
+set(SUB_DIRS
+    src/nauty24 
+    src/NFutil 
+    src/NFutil/MTrand 
+    src/NFtest/transcription 
+    src/NFtest/tlbr 
+    src/NFtest/simple_system 
+    src/NFtest/agentcell/cell 
+    src/NFtest/agentcell 
+    src/NFscheduler 
+    src/NFreactions/transformations 
+    src/NFreactions/reactions 
+    src/NFreactions/reactantLists 
+    src/NFreactions/mappings 
+    src/NFreactions 
+    src/NFoutput 
+    src/NFinput 
+    src/NFinput/TinyXML 
+    src/NFinput/json 
+    src/NFfunction/muParser 
+    src/NFfunction 
+    src/NFcore 
+    src/NFcore/reactionSelector 
+    src/NFcore/moleculeLists 
+)
+add_definitions("-Wno-deprecated-declarations")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11    -DTIXML_USE_STL  ")
+
+include_directories(${CMAKE_CURRENT_SOURCE_DIR} include ${SUB_DIRS})
+
+
+file(GLOB_RECURSE src_files  "${CMAKE_CURRENT_SOURCE_DIR}/src/*cpp")
+file(GLOB_RECURSE c_src_files  "${CMAKE_CURRENT_SOURCE_DIR}/src/*c")
+
+
+set(SRC_FILES 
+    ${src_files} 
+    ${c_src_files} 
+)
+
+
+add_executable(${PROJECT_NAME} ${SRC_FILES} )