Initial commit for vle-2.0 version

AZODYN/Authors.txt

+Authors
+-------
+- first name last name < yourmail @ your server >

AZODYN/CMakeCPack.cmake

+SET(CPACK_GENERATOR "ZIP")
+SET(CPACK_SOURCE_GENERATOR "ZIP")
+
+SET(CPACK_PACKAGE_NAME "${PROJECT_NAME}")
+SET(CPACK_PACKAGE_VENDOR "VLE Development Team")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Package Virtual Laboratory Environment")
+SET(CPACK_PACKAGE_CONTACT "Gauthier Quesnel <quesnel@users.sourceforge.net>")
+SET(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/Readme.txt")
+SET(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/License.txt")
+SET(CPACK_PACKAGE_VERSION_MAJOR "${MODEL_MAJOR}")
+SET(CPACK_PACKAGE_VERSION_MINOR "${MODEL_MINOR}")
+SET(CPACK_PACKAGE_VERSION_EXTRA "${MODEL_EXTRA}")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${VLE_NAME}")
+SET(CPACK_INCLUDE_TOPLEVEL_DIRECTORY 0)
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${VLE_NAME}")
+SET(CPACK_PACKAGE_FILE_NAME "${VLE_NAME}-${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}")
+SET(CPACK_SOURCE_IGNORE_FILES "\\\\.swp$;/\\\\.gitignore;/build/;/buildvle/;/plugins/;/lib/;/doc/html/;/output/;/\\\\.git/")
+
+INCLUDE(CPack)
+
+# vim:tw=0:ts=8:tw=0:sw=2:sts=2

AZODYN/CMakeLists.txt

+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+PROJECT(AZODYN CXX C)
+set (CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake ${CMAKE_MODULE_PATH})
+ENABLE_TESTING()
+
+SET(MODEL_MAJOR 0)
+SET(MODEL_MINOR 1)
+SET(MODEL_PATCH 0)
+SET(MODEL_NAME "${PROJECT_NAME}-${MODEL_MAJOR}.${MODEL_MINOR}.${MODEL_PATCH}")
+SET(VLE_NAME "${PROJECT_NAME}-${MODEL_MAJOR}.${MODEL_MINOR}")
+
+##
+## Options for compilation of package
+##
+
+option(WITH_TEST "will build the test [default: ON]" ON)
+option(WITH_DOC "will compile doc and install it [default: OFF]" OFF)
+option(WITH_WARNINGS "will compile with g++ warnings [default: ON]" ON)
+option(WITH_GVLE "use the GVLE [default: on]" ON)
+
+##
+## Flags
+##
+
+if (CMAKE_BUILD_TYPE STREQUAL "")
+  SET(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Choose the type of build" FORCE)
+endif ()
+
+if (CMAKE_COMPILER_IS_GNUCC AND CMAKE_COMPILER_IS_GNUCXX)
+  if (NOT WITH_WARNINGS)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w")
+  else (NOT WITH_WARNINGS)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -Wextra")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
+  endif (NOT WITH_WARNINGS)
+  if ("${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR
+      "${CMAKE_BUILD_TYPE}" STREQUAL "RelWithDebInfo")
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -ggdb3")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ggdb3")
+  endif ()
+endif ()
+
+##
+## Modules
+##
+
+include(CheckIncludeFileCXX)
+include(CheckIncludeFile)
+include(CheckLibraryExists)
+include(CMakeDetermineCCompiler)
+include(CheckCXXCompilerFlag)
+
+CHECK_CXX_COMPILER_FLAG("-std=c++14" COMPILER_SUPPORTS_CXX14)
+CHECK_CXX_COMPILER_FLAG("-std=c++1y" COMPILER_SUPPORTS_CXX1Y)
+
+if (COMPILER_SUPPORTS_CXX14)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+elseif(COMPILER_SUPPORTS_CXX1Y)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++1y")
+else()
+  message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++14/1y support.
+                 Please use a different C++ compiler.")
+endif()
+
+##
+## cmake policy
+##
+if (COMMAND CMAKE_POLICY)
+  cmake_policy(SET CMP0020 NEW)#for qt link
+endif (COMMAND CMAKE_POLICY)
+
+##
+## Check VLE and package dependencies
+##
+
+set(VLE_DEBUG 0)
+set(VLE_ABI_VERSION 2.0)
+find_package(VLE REQUIRED)
+set (VleUtils_DIR "${VLE_SHARE_DIR}/cmake")
+set (CMAKE_MODULE_PATH ${VLE_SHARE_DIR}/cmake ${CMAKE_MODULE_PATH})
+find_package(VleUtils REQUIRED)
+VleCheckDependencies()
+
+##
+## Check GVLE and package dependencies
+##
+
+if (WITH_GVLE)
+  set(GVLE_DEBUG 0)
+  find_package(GVLE)
+  if (GVLE_FOUND)
+    set (HAVE_GVLE 1 CACHE INTERNAL "" FORCE)
+  else ()
+    message (WARNING "GVLE not found!")
+  endif ()
+endif ()
+
+##
+## Find Qt
+##
+
+if (HAVE_GVLE)
+  set(QMAKE_QUERY_LIBPATH qmake -query QT_INSTALL_LIBS)
+  execute_process(COMMAND ${QMAKE_QUERY_LIBPATH} OUTPUT_VARIABLE
+    CMAKE_PREFIX_PATH)
+  find_package(Qt5 COMPONENTS Widgets Gui Xml)
+  if (NOT Qt5_FOUND)
+    message(FATAL_ERROR "Qt5 is required")
+  endif (NOT Qt5_FOUND)
+  if (NOT Qt5Widgets_FOUND)
+    message(FATAL_ERROR "Qt5Widgets is required")
+  endif (NOT Qt5Widgets_FOUND)
+  if (NOT Qt5Gui_FOUND)
+    message(FATAL_ERROR "Qt5Gui is required")
+  endif (NOT Qt5Gui_FOUND)
+  if (NOT Qt5Xml_FOUND)
+    message(FATAL_ERROR "Qt5Xml is required")
+  endif (NOT Qt5Xml_FOUND)
+endif ()
+
+##
+## Generate the doxygen
+##
+
+if (WITH_DOC)
+ FIND_PACKAGE(Doxygen)
+ if (DOXYGEN)
+  SET(DOXYGEN_SOURCE_DIR "${PROJECT_SOURCE_DIR}/src")
+  SET(DOXYGEN_OUTPUT_MODELING_DIR "${PROJECT_BINARY_DIR}/doxygen/modeling")
+  SET(DOXYGEN_OUTPUT_SOURCE_DIR "${PROJECT_BINARY_DIR}/doxygen/sources")
+  CONFIGURE_FILE("cmake/doxygen-modeling.conf.in"
+    "${PROJECT_BINARY_DIR}/doxygen-modeling.conf")
+  CONFIGURE_FILE("cmake/doxygen-sources.conf.in"
+    "${PROJECT_BINARY_DIR}/doxygen-sources.conf")
+  FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/doxygen")
+  FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/doxygen/modeling")
+  FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/doxygen/sources")
+
+  ADD_CUSTOM_COMMAND(
+    OUTPUT "${PROJECT_BINARY_DIR}/doxygen/modeling/index.html"
+    DEPENDS "${PROJECT_BINARY_DIR}/doxygen-modeling.conf"
+    COMMAND "${DOXYGEN}"
+    ARGS "${PROJECT_BINARY_DIR}/doxygen-modeling.conf")
+
+  ADD_CUSTOM_COMMAND(
+    OUTPUT "${PROJECT_BINARY_DIR}/doxygen/sources/index.html"
+    DEPENDS "${PROJECT_BINARY_DIR}/doxygen-sources.conf"
+    COMMAND "${DOXYGEN}"
+    ARGS "${PROJECT_BINARY_DIR}/doxygen-sources.conf")
+
+  ADD_CUSTOM_TARGET(doc_modeling ALL DEPENDS
+    "${PROJECT_BINARY_DIR}/doxygen-modeling.conf"
+    "${PROJECT_BINARY_DIR}/doxygen/modeling/index.html" VERBATIM)
+  ADD_CUSTOM_TARGET(doc_sources ALL DEPENDS
+    "${PROJECT_BINARY_DIR}/doxygen-sources.conf"
+    "${PROJECT_BINARY_DIR}/doxygen/sources/index.html" VERBATIM)
+
+  INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/doxygen/modeling/html" DESTINATION
+    "doc/html/modeling")
+  INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/doxygen/sources/html" DESTINATION
+    "doc/html/sources")
+ endif (DOXYGEN)
+endif ()
+
+##
+## Subdirectory
+##
+
+if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/data")
+  add_subdirectory(data)
+endif ()
+if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/metadata")
+  add_subdirectory(metadata)
+endif ()
+if (WITH_DOC)
+  if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/doc")
+    add_subdirectory(doc)
+  endif ()
+endif ()
+if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/exp")
+  add_subdirectory(exp)
+endif ()
+if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src")
+  add_subdirectory(src)
+endif ()
+if (WITH_TEST)
+  if (IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/test")
+    add_subdirectory(test)
+  endif ()
+endif ()
+
+##
+## CPack configuration
+##
+
+INSTALL(FILES Authors.txt Description.txt License.txt News.txt Readme.txt
+  DESTINATION .)
+
+INCLUDE(CMakeCPack.cmake)

AZODYN/Description.txt

+Package: AZODYN
+Version: 0.1.0
+Depends:
+Build-Depends: vle.discrete-time
+Conflicts:
+Maintainer: Ronan Trépos <ronan.trepos@inra.fr>
+Description: Still in progress
+ .
+Tags: record crop model
+Url: http://recordb.toulouse.inra.fr/distributions/2.0
+Size: 0
+MD5sum: xxxx

AZODYN/License.txt

+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+- Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+- The name of the author may not be used to endorse or promote products derived
+  from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+OF SUCH DAMAGE.

AZODYN/News.txt

+Changes from previous versions of the examples
+==============================================
+
+Initial version 0.1.0
+---------------------
+
+- initial packaging.

AZODYN/R/azodyn_simus.R

+###
+#example fo simulations of AZODYN using vle.recursive R API
+##
+
+library(rvle)
+source(paste(sep="", Sys.getenv("VLE_HOME"),
+             "/pkgs-2.0/vle.recursive/R/vle.recursive.R"))
+
+# init the zheat simulator
+f = vle.recursive.init(pkg="AZODYN", file="AzodynWheat.vpz")
+
+# show the content
+vle.recursive.showEmbedded(f)
+
+# build an experiment plan of 3 simulations zith different sowing density,
+# and different max root depth
+simData = data.frame(cPlant.densite_semis = c(200,215,230),
+                     cPlant.ProfRacmax = c(1000,1300,1600));
+
+# config the simulator with the simulations
+simData = vle.recursive.parseSim(file_sim=simData, rvle_handle=f);
+
+# get available simulqtion outputs
+out_vars = vle.recursive.getAvailOutputs(f)
+
+# configure selected outputs
+vle.recursive.configOutputs(f, 
+  output_vars = c(LAI=out_vars$LAI, MSpot=out_vars$MSpot),
+  integration='all')
+
+# simulate
+res = vle.recursive.simulate(rvle_handle=f)
+
+# plot
+vle.recursive.plot(res, output_vars = c("LAI","MSpot"))
+

AZODYN/Readme.txt

+Requirements
+============
+
+vle      2.0  http://www.vle-project.org
+boost    1.49 http://www.boost.org
+cmake    2.8  http://www.cmake.org
+
+
+Installation
+============
+
+$ vle --package=MyProject configure
+$ vle --package=MyProject build

AZODYN/cmake/FindVLE.cmake

+# FindVLE.cmake
+# =============
+#
+# Try to find VLE
+#
+# Copyright 2012-2016 INRA
+# Gauthier Quesnel <quesnel@users.sourceforge.net>
+# Ronan Trépos <ronan.trepos@toulouse.inra.fr>
+#
+# Distributed under the OS-approved BSD License (the "License");
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#
+# Once done this will define:
+#
+#  VLE_FOUND             - The system has VLE
+#  VLE_INCLUDE_DIRS      - The VLE include directory
+#  VLE_LIBRARY_DIRS      - Directories containing libraries to link
+#  VLE_LIBRARIES         - Link these to use shared libraries of VLE
+#  VLE_SHARE_DIR         - Base directory for VLE shared files
+#
+# CMake variables used by this module:
+#  VLE_ABI_VERSION       - gives the VLE version to search for (e.g 1.1, 1.2)
+#                          (REQUIRED)
+#  VLE_DEBUG             - If true, prints debug traces
+#                          (default OFF)
+#  VLE_USING_CMAKE       - If true, on windows, use cmake for finding VLE,
+#                          else use pkgconfig
+#                          (default ON)
+#  VLE_BASEPATH_LOCAL    - cmake variable for base path of vle
+#                          (default NOT_DEFINED)
+#
+# Environment variables used by this module:
+#
+#  VLE_BASEPATH          - environment variable for base path of vle
+#
+#=============================================================================
+#
+# Usage
+# -----
+#
+# set(VLE_ABI_VERSION 2.0)
+# find_package(VLE REQUIRED)
+#
+#=============================================================================
+
+#
+# Check VLE_ABI_VERSION
+#
+
+if (NOT DEFINED VLE_ABI_VERSION)
+  message (FATAL_ERROR "Cmake variable VLE_ABI_VERSION is not set")
+endif ()
+
+
+#
+# Set default behavior of find vle
+#
+
+if (WIN32)
+  if (DEFINED VLE_USING_CMAKE)
+     set (_find_vle_using_cmake ${VLE_USING_CMAKE})
+  else (DEFINED VLE_USING_CMAKE)
+     set (_find_vle_using_cmake 1)
+  endif (DEFINED VLE_USING_CMAKE)
+else (WIN32)
+  set (_find_vle_using_cmake 0)
+endif (WIN32)
+
+if (DEFINED VLE_DEBUG)
+  set (_vle_debug  ${VLE_DEBUG})
+else ()
+  set (_vle_debug 0)
+endif ()
+
+
+#
+# Find VLE
+#
+
+if (${_find_vle_using_cmake})
+
+  find_path(_vle_base_include vle-${VLE_ABI_VERSION}/vle/vle.hpp PATHS
+    $ENV{VLE_BASEPATH}/include
+    ${VLE_BASEPATH_LOCAL}/include
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;Path]/include"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;]/include"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\Wow6432Node\\VLE ${VLE_ABI_VERSION}.0;]/include"
+	NO_DEFAULT_PATH)
+
+  find_path(_vle_base_bin vle.exe PATHS
+    $ENV{VLE_BASEPATH}/bin
+    ${VLE_BASEPATH_LOCAL}/bin
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;Path]/bin"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;]/bin"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\Wow6432Node\\VLE ${VLE_ABI_VERSION}.0;]/bin"
+	NO_DEFAULT_PATH)
+
+  find_path(_vle_base_lib libvle-${VLE_ABI_VERSION}.a PATHS
+    $ENV{VLE_BASEPATH}/lib
+    ${VLE_BASEPATH_LOCAL}/lib
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;Path]/lib"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\VLE ${VLE_ABI_VERSION}.0;]/lib"
+    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\VLE Development Team\\Wow6432Node\\VLE ${VLE_ABI_VERSION}.0;]/lib"
+	NO_DEFAULT_PATH)
+
+  if (${_vle_debug})
+    message (" vle_debug _vle_base_include ${_vle_base_include}")
+    message (" vle_debug _vle_base_bin ${_vle_base_bin}")
+    message (" vle_debug _vle_base_lib ${_vle_base_lib}")
+  endif ()
+
+  if(NOT _vle_base_include OR NOT _vle_base_bin OR NOT _vle_base_lib)
+     message (FATAL_ERROR "Missing vle dependencies")
+  endif ()
+
+  set(VLE_INCLUDE_DIRS
+    ${_vle_base_include}/vle-${VLE_ABI_VERSION}; ${_vle_base_include};
+    ${_vle_base_include}/libxml2)
+
+  set(VLE_LIBRARY_DIRS
+    ${_vle_base_bin};${_vle_base_lib})
+
+  set (VLE_LIBRARIES
+    vle-${VLE_ABI_VERSION} xml2 intl)
+
+  set (VLE_SHARE_DIR "${_vle_base_include}/../share/vle-${VLE_ABI_VERSION}")
+
+else (${_find_vle_using_cmake})
+  find_package(PkgConfig REQUIRED)
+  PKG_CHECK_MODULES(VLE vle-${VLE_ABI_VERSION})
+  # select only the directory of vle, containing the pkgs directory
+  # to build VLE_SHARE_DIR
+  find_path(vle_lib_dir vle PATHS
+            ${VLE_INCLUDE_DIRS} NO_DEFAULT_PATH)
+  set (VLE_SHARE_DIR "${vle_lib_dir}/../../share/vle-${VLE_ABI_VERSION}")
+endif (${_find_vle_using_cmake})
+
+
+# handle the QUIETLY and REQUIRED arguments and set VLE_FOUND to TRUE if all
+# listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(VLE REQUIRED_VARS VLE_INCLUDE_DIRS
+                        VLE_LIBRARIES VLE_SHARE_DIR)
+
+if (${_vle_debug})
+  message (" vle_debug VLE_INCLUDE_DIRS ${VLE_INCLUDE_DIRS}")
+  message (" vle_debug VLE_LIBRARY_DIRS ${VLE_LIBRARY_DIRS}")
+  message (" vle_debug VLE_LIBRARIES ${VLE_LIBRARIES}")
+  message (" vle_debug VLE_SHARE_DIR ${VLE_SHARE_DIR}")
+endif ()
+
+#mark_as_advanced(VLE_INCLUDE_DIRS VLE_LIBRARIES VLE_LIBRARY_DIRS)

AZODYN/data/CMakeLists.txt

+install(DIRECTORY . DESTINATION data FILES_MATCHING PATTERN "*.dat")
+install(DIRECTORY . DESTINATION data FILES_MATCHING PATTERN "*.csv")
+install(DIRECTORY . DESTINATION data FILES_MATCHING PATTERN "*.txt")
+