Merge pull request #22 from hsorby/usecase_1i

All review comments have been addressed and tests are passing. Closes #20.

CMakeLists.txt

@@ -16,7 +16,7 @@
 cmake_minimum_required(VERSION 3.2)
 
 set(PROJECT_NAME libCellML)
-project(${PROJECT_NAME} CXX)
+project(${PROJECT_NAME} VERSION 0.1.0 LANGUAGES CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 include(common)
@@ -33,7 +33,12 @@ endif()
 if(COVERAGE AND GCOV_FOUND)
   set( LIBCELLML_COVERAGE "${COVERAGE}" CACHE BOOL ${_PARAM_ANNOTATION} FORCE )
 elseif(COVERAGE)
-  message(WARNING "Coverage testing requested but gcov or it's requirements not found!")
+  if (CMAKE_COMPILER_IS_GCC)
+    message(WARNING "Coverage testing requested but gcov or its requirements not found!")
+  else()
+    message(WARNING "Coverage testing is not possible without a GNU C++ compiler!")
+  endif()
+  unset(COVERAGE CACHE)
 endif()
 
 # MEMCHECK ==> LIBCELLML_MEMCHECK
@@ -44,7 +49,12 @@ endif()
 if( MEMCHECK AND VALGRIND_FOUND )
   set( LIBCELLML_MEMCHECK "${MEMCHECK}" CACHE BOOL ${_PARAM_ANNOTATION} FORCE )
 elseif(MEMCHECK)
-  message(WARNING "Memcheck testing requested but valgrind or it's requirements not found!")
+  if (CMAKE_COMPILER_IS_GCC)
+    message(WARNING "Memcheck testing requested but valgrind or its requirements not found!")
+  else()
+    message(WARNING "Memcheck testing is not possible without a GNU C++ compiler!")
+  endif()
+  unset(MEMCHECK CACHE)
 endif()
 
 # UNIT_TESTS ==> LIBCELLML_UNIT_TESTS

docs/mainpage.dox

@@ -0,0 +1,8 @@
+
+///  @mainpage libCellML
+
+libCellML Code Documentation
+============================
+
+This is the documentation for the source code.
+

doxy.config

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =
+OUTPUT_DIRECTORY       = docs/build/html/code
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -152,7 +152,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        = /home/libcellml/buildslave/Documentation_Builder/libcellml/src/api src/api /home/libcellml/buildslave/Documentation_Builder/libcellml/src/ src
+STRIP_FROM_PATH        = /home/libcellml/buildslave/Documentation_Builder/libcellml/src/api src/api /home/libcellml/buildslave/Documentation_Builder/libcellml/src/ src docs
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -281,7 +281,7 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # Note that for custom extensions you also need to set FILE_PATTERNS otherwise
 # the files are not read by doxygen.
 
-EXTENSION_MAPPING      =
+EXTENSION_MAPPING      = dox=md
 
 # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
@@ -758,7 +758,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = $(DOXYGEN_INPUT_DIR) src
+INPUT                  = $(DOXYGEN_INPUT_DIR) src docs/mainpage.dox
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1023,7 +1023,7 @@ GENERATE_HTML          = YES
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = .
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).

src/CMakeLists.txt

@@ -12,19 +12,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.cmake_minimum_required (VERSION 3.1)
 
-# The version number.
-set(LIBCELLML_VERSION_MAJOR 0)
-set(LIBCELLML_VERSION_MINOR 1)
-set(LIBCELLML_VERSION_PATCH 0)
-
-foreach(VERSION_PART LIBCELLML_VERSION_MAJOR LIBCELLML_VERSION_MINOR LIBCELLML_VERSION_PATCH)
+foreach(VERSION_PART libCellML_VERSION_MAJOR libCellML_VERSION_MINOR libCellML_VERSION_PATCH)
   string(LENGTH ${${VERSION_PART}} VERSION_PART_LENGTH)
   if(VERSION_PART_LENGTH EQUAL 1)
     set(${VERSION_PART}_PAD 0)
   endif()
 endforeach()
-set(LIBCELLML_LIBRARY_VERSION 0x${LIBCELLML_VERSION_MAJOR_PAD}${LIBCELLML_VERSION_MAJOR}${LIBCELLML_VERSION_MINOR_PAD}${LIBCELLML_VERSION_MINOR}${LIBCELLML_VERSION_PATCH_PAD}${LIBCELLML_VERSION_PATCH})
-set(LIBCELLML_LIBRARY_VERSION_STRING "${LIBCELLML_VERSION_MAJOR}.${LIBCELLML_VERSION_MINOR}.${LIBCELLML_VERSION_PATCH}")
+set(LIBCELLML_LIBRARY_VERSION 0x${libCellML_VERSION_MAJOR_PAD}${libCellML_VERSION_MAJOR}${libCellML_VERSION_MINOR_PAD}${libCellML_VERSION_MINOR}${libCellML_VERSION_PATCH_PAD}${libCellML_VERSION_PATCH})
+set(LIBCELLML_LIBRARY_VERSION_STRING "${libCellML_VERSION_MAJOR}.${libCellML_VERSION_MINOR}.${libCellML_VERSION_PATCH}")
 
 set(CELLML_EXPORT_H "${CMAKE_CURRENT_BINARY_DIR}/api/libcellml/libcellml_export.h")
 set(LIBCELLML_CONFIG_H "${CMAKE_CURRENT_BINARY_DIR}/libcellml_config.h")
@@ -35,10 +30,14 @@ configure_file(
 
 set(SOURCE_FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/version.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/model.cpp
 )
 
 set(API_HEADER_FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/version.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/model.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/entity.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/enumerations.h
   ${CELLML_EXPORT_H}
 )
 
@@ -52,18 +51,25 @@ add_compiler_export_flags()
 add_library(cellml
   ${SOURCE_FILES}
   ${HEADER_FILES}
+  ${MODULE_HEADER_FILES}
   ${API_HEADER_FILES}
 )
 
 target_include_directories(cellml
   PUBLIC
   $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/api>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/api>
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/module>
   $<INSTALL_INTERFACE:include/>
+  $<INSTALL_INTERFACE:include/libcellml/module>
   PRIVATE
   ${CMAKE_CURRENT_BINARY_DIR}
 )
 
+set_target_properties(cellml PROPERTIES
+  CXX_STANDARD 11
+  CXX_STANDARD_REQUIRED ON)
+
 if(LIBCELLML_TREAT_WARNINGS_AS_ERRORS)
   target_warnings_as_errors(cellml)
 endif()
@@ -95,5 +101,10 @@ install(FILES
   DESTINATION include/libcellml
 )
 
+install(FILES
+  ${MODULE_HEADER_FILES}
+  DESTINATION include/libcellml/module
+)
+
 install(EXPORT libcellml-targets DESTINATION lib/cmake)
 

src/api/libcellml/entity.h

@@ -0,0 +1,45 @@
+/*
+Copyright 2015 University of Auckland
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.Some license of other
+*/
+
+#ifndef LIBCELLML_LIBCELLML_ENTITY_H_
+#define LIBCELLML_LIBCELLML_ENTITY_H_
+
+#include "libcellml/enumerations.h"
+
+namespace libcellml {
+
+/**
+ * @brief The Entity class.
+ * Base class for all serialisable libCellML classes.
+ */
+class Entity
+{
+protected:
+    /**
+     * @brief Pure virtual serialise method.
+     * Pure virtual serialise method for serialising a CellML object to a std::string.
+     * @param format The format to serialise the object to.
+     * @return std::string representation of the object.
+     */
+    virtual std::string serialise(libcellml::CELLML_FORMATS format) const = 0;
+
+};
+
+}
+
+#endif /* LIBCELLML_LIBCELLML_ENTITY_H_ */
+
+

src/api/libcellml/enumerations.h

@@ -0,0 +1,37 @@
+/*
+Copyright 2015 University of Auckland
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.Some license of other
+*/
+
+#ifndef LIBCELLML_LIBCELLML_ENUMERATIONS_H_
+#define LIBCELLML_LIBCELLML_ENUMERATIONS_H_
+
+/** @file */
+
+namespace libcellml {
+
+/**
+ * @brief The CELLML_FORMATS enum.
+ * Enum describing the formats that are available for
+ * serialisation.
+ */
+enum CELLML_FORMATS
+{
+     CELLML_FORMAT_XML = 0 /**< XML format for CellML files. */
+};
+
+}
+
+#endif /* LIBCELLML_LIBCELLML_ENUMERATIONS_H_ */
+

src/api/libcellml/model.h

@@ -0,0 +1,72 @@
+/*
+Copyright 2015 University of Auckland
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.Some license of other
+*/
+
+#ifndef LIBCELLML_LIBCELLML_MODEL_H_
+#define LIBCELLML_LIBCELLML_MODEL_H_
+
+#include <string>
+#include <memory>
+
+#include "libcellml/libcellml_export.h"
+#include "libcellml/entity.h"
+
+//! Everything in libCellML is in this namespace.
+namespace libcellml {
+
+/**
+ * @brief The Model class.
+ * The Model class is for representing a CellML Model.
+ */
+class LIBCELLML_EXPORT Model: public Entity
+{
+public:
+    /**
+     * @brief Model Constructor.
+     * Default Model constructor.
+     */
+    Model();
+    /**
+     * @brief Model Destructor.
+     * Default Model destructor.
+     */
+    ~Model();
+
+    Model(Model&& rhs); /**< move constructor */
+    Model& operator=(Model&& rhs); /**< move assignment */
+
+    /**
+     * @brief serialise the Model.
+     * This method serialises the Model to a std:string representation in the
+     * desired format.
+     * @sa deserialise
+     * @param format The format to serialise the Model to.
+     * @return std::string representation of the Model in the given format.
+     */
+    std::string serialise(libcellml::CELLML_FORMATS format) const;
+
+private:
+
+    Model(const Model&) = delete; /**< non-copyable */
+    Model& operator=(const Model&) = delete; /**< non-copyable */
+
+    struct ModelImpl; /**< Forward declaration for pImpl idiom. */
+    std::unique_ptr<ModelImpl> mPimpl; /**< Private member to implementation pointer */
+};
+
+}
+
+#endif /* LIBCELLML_LIBCELLML_MODEL_H_ */
+

src/api/libcellml/module/libcellml

@@ -0,0 +1,24 @@
+
+/*
+Copyright 2015 University of Auckland
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.Some license of other
+*/
+
+#ifndef LIBCELLML_LIBCELLML_MODULE_LIBCELLML_H_
+#define LIBCELLML_LIBCELLML_MODULE_LIBCELLML_H_
+
+#include <libcellml/version.h>
+#include <libcellml/model.h>
+
+#endif  // LIBCELLML_LIBCELLML_MODULE_LIBCELLML_H_

src/configure/libcellml_config.h.in

@@ -21,9 +21,9 @@ limitations under the License.Some license of other
 
 namespace libcellml {
 
-#define LIBCELLML_VERSION_MAJOR @LIBCELLML_VERSION_MAJOR@
-#define LIBCELLML_VERSION_MINOR @LIBCELLML_VERSION_MINOR@
-#define LIBCELLML_VERSION_PATCH @LIBCELLML_VERSION_PATCH@
+#define LIBCELLML_VERSION_MAJOR @libCellML_VERSION_MAJOR@
+#define LIBCELLML_VERSION_MINOR @libCellML_VERSION_MINOR@
+#define LIBCELLML_VERSION_PATCH @libCellML_VERSION_PATCH@
 
 static unsigned int LIBCELLML_LIBRARY_VERSION=@LIBCELLML_LIBRARY_VERSION@;
 static const std::string LIBCELLML_LIBRARY_VERSION_STRING="@LIBCELLML_LIBRARY_VERSION_STRING@";