Merge pull request #89 from sbmlteam/add_testsbxml

Add testsbxml
sbmlteam · May 23, 2023 · d35818b · d35818b
2 parents 1f68e3b + 058570f
commit d35818b
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Showing 62 changed files with 2,131 additions and 1,416 deletions.
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-1.0.0
+2.0.0
diff --git a/deviser/bindings_files/templates/python/CMakeLists.txt b/deviser/bindings_files/templates/python/CMakeLists.txt
@@ -34,14 +34,23 @@ if (LIBSBML_REMOVE_WRAPPERS)
   endforeach()
 endif(LIBSBML_REMOVE_WRAPPERS)
 
+if(WITH_LIBSBML)
+    <verbatim>
+    set(SWIG_EXTRA_FLAGS -DSWIGEXPORT 
+    -DLIBSBML_CPP_NAMESPACE_BEGIN -DLIBSBML_CPP_NAMESPACE_END -DLIBSBML_CPP_NAMESPACE_QUALIFIER -DLIBSBML_CPP_NAMESPACE_USE
+    -DLIBNUML_CPP_NAMESPACE_BEGIN -DLIBNUML_CPP_NAMESPACE_END -DLIBNUML_CPP_NAMESPACE_QUALIFIER -DLIBNUML_CPP_NAMESPACE_USE
+    )
+    </verbatim>
+endif()
+if(WITH_LIBLX)
+    <verbatim>
+    set(SWIG_EXTRA_FLAGS -DSWIGEXPORT 
+    -DLIBLX_CPP_NAMESPACE_BEGIN -DLIBLX_CPP_NAMESPACE_END -DLIBLX_CPP_NAMESPACE_QUALIFIER -DLIBLX_CPP_NAMESPACE_USE
+    -DLIBNUML_CPP_NAMESPACE_BEGIN -DLIBNUML_CPP_NAMESPACE_END -DLIBNUML_CPP_NAMESPACE_QUALIFIER -DLIBNUML_CPP_NAMESPACE_USE
+    )
+    </verbatim>
+endif()
 
-<verbatim>
-
-set(SWIG_EXTRA_FLAGS -DSWIGEXPORT 
-   -DLIBSBML_CPP_NAMESPACE_BEGIN -DLIBSBML_CPP_NAMESPACE_END -DLIBSBML_CPP_NAMESPACE_QUALIFIER -DLIBSBML_CPP_NAMESPACE_USE
-   -DLIBNUML_CPP_NAMESPACE_BEGIN -DLIBNUML_CPP_NAMESPACE_END -DLIBNUML_CPP_NAMESPACE_QUALIFIER -DLIBNUML_CPP_NAMESPACE_USE
-   )
-</verbatim>
 if(NOT UNIX)
   set(SWIG_EXTRA_FLAGS ${SWIG_EXTRA_FLAGS} -DSWIGWIN -DSWIG_CSHARP_NO_WSTRING_HELPER )
 endif()
@@ -57,7 +66,7 @@ ADD_CUSTOM_COMMAND(
       -I${CMAKE_CURRENT_SOURCE_DIR}
 <library_dependencies/>
 <verbatim>
-         -I${LIBSBML_INCLUDE_DIR}/
+         -I${LINKED_INCLUDE_DIR}/
 </verbatim>
       -c++
       -python    
@@ -86,7 +95,7 @@ add_custom_target(binding_python_swig ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/li
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../swig)
 <verbatim>
-include_directories(${LIBSBML_INCLUDE_DIR})
+include_directories(${LINKED_INCLUDE_DIR})
 </verbatim>
 <include_library_dependencies/>
 include_directories(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../)

diff --git a/deviser/bindings_files/templates/swig/ListWrapper.h b/deviser/bindings_files/templates/swig/ListWrapper.h
@@ -2,9 +2,9 @@
 #define ListWrapper_h
 
 <verbatim>
-#include <sbml/util/List.h>
+#include <util/List.h>
+#include <common/extern.h>
 </verbatim>
-#include <sbml/common/extern.h>
 
 LIBSBML_CPP_NAMESPACE_USE
 

diff --git a/deviser/bindings_files/templates/swig/lib.h b/deviser/bindings_files/templates/swig/lib.h
@@ -1,6 +1,6 @@
 
-#include <sbml/common/libsbml-version.h>
-#include <sbml/common/SBMLOperationReturnValues.h>
+#include <common/libsbml-version.h>
+#include <common/SBMLOperationReturnValues.h>
 
 #include <sbml/SBMLTypes.h>
 
@@ -18,16 +18,16 @@
 #include <sbml/math/L3Parser.h>
 #include <sbml/math/L3ParserSettings.h>
 
-#include <sbml/xml/XMLAttributes.h>
-#include <sbml/xml/XMLNamespaces.h>
-#include <sbml/xml/XMLConstructorException.h>
-#include <sbml/xml/XMLToken.h>
-#include <sbml/xml/XMLNode.h>
-#include <sbml/xml/XMLTriple.h>
-#include <sbml/xml/XMLInputStream.h>
-#include <sbml/xml/XMLOutputStream.h>
-#include <sbml/xml/XMLError.h>
-#include <sbml/xml/XMLErrorLog.h>
+#include <xml/XMLAttributes.h>
+#include <xml/XMLNamespaces.h>
+#include <xml/XMLConstructorException.h>
+#include <xml/XMLToken.h>
+#include <xml/XMLNode.h>
+#include <xml/XMLTriple.h>
+#include <xml/XMLInputStream.h>
+#include <xml/XMLOutputStream.h>
+#include <xml/XMLError.h>
+#include <xml/XMLErrorLog.h>
 </verbatim>
 
 <dependencies>

diff --git a/deviser/bindings_files/templates/swig/lib.i b/deviser/bindings_files/templates/swig/lib.i
@@ -30,12 +30,12 @@ LIBSBML_CPP_NAMESPACE_USE
 #include "local.cpp"
 %}
 
-%import  sbml/common/libsbml-namespace.h
-%import  sbml/common/extern.h
-%import  sbml/common/sbmlfwd.h
+%import  common/libsbml-namespace.h
+%import  common/extern.h
+%import  common/sbmlfwd.h
 <verbatim>
-%import  sbml/common/extern.h
-%import  sbml/xml/XMLExtern.h
+%import  common/extern.h
+%import  xml/XMLExtern.h
 </verbatim>
 
 /**
@@ -296,25 +296,25 @@ typedef std::vector<XMLError*> XmlErrorStdVector;
 %template(SBMLErrorStdVector) std::vector<SBMLError>;
 typedef std::vector<SBMLError> SBMLErrorStdVector;
 
-%include sbml/common/libsbml-version.h
-%include sbml/common/SBMLOperationReturnValues.h
+%include common/libsbml-version.h
+%include common/SBMLOperationReturnValues.h
 <verbatim>
-%include sbml/common/libsbml-version.h
-%include sbml/common/operationReturnValues.h
+%include common/libsbml-version.h
+%include common/operationReturnValues.h
 
 %include sbml/SyntaxChecker.h
 %include sbml/ExpectedAttributes.h
 
-%include sbml/xml/XMLAttributes.h
-%include sbml/xml/XMLConstructorException.h
-%include sbml/xml/XMLNamespaces.h
-%include sbml/xml/XMLToken.h
-%include sbml/xml/XMLNode.h
-%include sbml/xml/XMLTriple.h
-%include sbml/xml/XMLOutputStream.h
-%include sbml/xml/XMLInputStream.h
-%include sbml/xml/XMLError.h
-%include sbml/xml/XMLErrorLog.h
+%include xml/XMLAttributes.h
+%include xml/XMLConstructorException.h
+%include xml/XMLNamespaces.h
+%include xml/XMLToken.h
+%include xml/XMLNode.h
+%include xml/XMLTriple.h
+%include xml/XMLOutputStream.h
+%include xml/XMLInputStream.h
+%include xml/XMLError.h
+%include xml/XMLErrorLog.h
 
 %include ASTNodes.i
 </verbatim> 

diff --git a/deviser/cmake_files/templates/code/CMakeLists.txt b/deviser/cmake_files/templates/code/CMakeLists.txt
@@ -4,154 +4,14 @@
 # 
 ###############################################################################
 
-
-include(CheckLibraryExists)
-check_library_exists(m sqrt "" HAVE_LIBM)
-
-# generate configuration for this system
-configure_file(
-  ${CMAKE_CURRENT_SOURCE_DIR}/common/libsbml-config-common.h.cmake
-  "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-config-common.h"
-  )
-
-# Replace: @PACKAGE_VERSION@ and @LIBSBML_VERSION_NUMERIC@
-configure_file (
-  "${CMAKE_CURRENT_SOURCE_DIR}/common/libsbml-version.h.cmake"
-  "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-version.h"
-  )
-
-configure_file (
-  "${CMAKE_CURRENT_SOURCE_DIR}/common/libsbml-namespace.h.cmake"
-  "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-namespace.h"
-  )
 
-
-###############################################################################
-#
-# mark header files for installation
-#
-foreach(dir annotation common compress conversion extension math units util validator xml  )
-
-  file(GLOB header_files "${CMAKE_CURRENT_SOURCE_DIR}/${dir}/*.h")
-  install(FILES ${header_files} DESTINATION include/sbml/${dir})
-
-endforeach(dir)
-
-file(GLOB files "${CMAKE_CURRENT_SOURCE_DIR}/*.h")
-install(FILES ${files} DESTINATION include/sbml)
-
-# install generated headers
-install(FILES 
-       "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-version.h"
-       "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-config-common.h"
-       "${CMAKE_CURRENT_BINARY_DIR}/common/libsbml-namespace.h"
-        DESTINATION include/sbml/common)
-
-###############################################################################
-#
-# specify include directories
-#
-include_directories(BEFORE ${CMAKE_CURRENT_SOURCE_DIR})
-<verbatim>
-include_directories(BEFORE ${LIBSBML_INCLUDE_DIR})
-</verbatim>
-<include_dependency_directories/>
-include_directories(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/..)
-include_directories(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/..)
-
-if (EXTRA_DEFS)
-add_definitions(${EXTRA_DEFS})
-endif()
-
 ###############################################################################
 #
-# Find all sources
-#
-
-foreach (directory common sbml )
-
-  set(dir ${directory})
-
-  if ("${directory}" STREQUAL "sbml")
-    set(dir ".")
-  endif()
-
-
-  file(GLOB temp
-      ${dir}/*.cpp
-      ${dir}/*.c
-      ${dir}/*.h)
-
-  # create source group for IDEs
-  source_group(${directory} FILES ${temp})
-
-  # add to libsbml sources
-  set(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${temp})
-
-endforeach()
-
-###############################################################################
-#
-# this is a directory level operation!
-#
-if (MSVC)
-if (WITH_STATIC_RUNTIME)
-  foreach(flag_var
-    CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-    CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
-    CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-    CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-
-    if(${flag_var} MATCHES "/MD")
-      string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
-    endif(${flag_var} MATCHES "/MD")
-
-
-  endforeach(flag_var)
-  add_definitions( -D_MT)
-endif(WITH_STATIC_RUNTIME)
-endif(MSVC)
-
-###############################################################################
-#
-# Build library
-#
-
-if (NOT LIBSBML_SKIP_SHARED_LIBRARY)
-
-add_library (${LIBSBML_LIBRARY} SHARED ${LIBSBML_SOURCES} )
-
-if (LIBSBML_SHARED_VERSION)
-  set_target_properties(${LIBSBML_LIBRARY} PROPERTIES COMPILE_DEFINITIONS "LIBSBML_EXPORTS=1")
-  set_target_properties(${LIBSBML_LIBRARY} PROPERTIES
-                      SOVERSION ${LIBSBML_VERSION_MAJOR}
-                      VERSION ${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH})
-endif()
-
-<sbml>
-target_link_libraries(${LIBREPLACE_LIBRARY} ${LIBSBML_LIBRARY} OTHER_LIBS ${EXTRA_LIBS})
-</sbml>
+# Build test files and add tests
+# 
+if(WITH_CHECK)
 
-INSTALL(TARGETS ${LIBSBML_LIBRARY}
-  RUNTIME DESTINATION bin
-  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  )
+  add_subdirectory(test)
 
 endif()
 
-add_library (${LIBSBML_LIBRARY}-static STATIC ${LIBSBML_SOURCES} )
-if (WIN32 AND NOT CYGWIN)
-  # don't decorate static library 
-  set_target_properties(${LIBSBML_LIBRARY}-static PROPERTIES COMPILE_DEFINITIONS "LIBSBML_STATIC=1")
-endif(WIN32 AND NOT CYGWIN)
-
-<sbml>
-target_link_libraries(${LIBREPLACE_LIBRARY}-static ${LIBSBML_LIBRARY} OTHER_LIBS ${EXTRA_LIBS})
-</sbml>
-
-INSTALL(TARGETS ${LIBSBML_LIBRARY}-static
-  RUNTIME DESTINATION bin
-  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  )