--- imach/CMakeLists.txt	2015/09/03 07:53:42	1.4
+++ imach/CMakeLists.txt	2022/09/16 13:42:47	1.45
@@ -6,16 +6,30 @@
 #      FORCE)
 #  endif()
 # SET (CMAKE_CONFIGURATION_TYPES "Debug;RelWithDebinfo" CACHE STRING "" FORCE)
+set(PACKAGE_NAME "imach")
 SET(IMACH_VERSION_MAJOR 0)
-SET(IMACH_VERSION_MINOR 98q5)
+SET(IMACH_VERSION_MINOR 99r41)
 SET(IMACH_VERSION_PATCH 0)
 SET(IMACH_VERSION_NOTE "")
 SET(IMACH_VERSION ${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR})
+SET(@APPNAME@ imach-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR})
+SET(@NOTINNOREG@ )
+SET(@NOREG@ )
+SET(@IMACHSETUPVERSION@ imach-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR}-icl-setup)
+SET(@APPCOMPILATIONMODE@ icl)
+SET(@VERSION@ ${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR})
+SET(@GNUPLOTVERSION@ 5.1)
+SET(@INFOBEFOREFILE@ README.txt)
+SET(@LICENSEFILE@ Copying)
+SET(@PACKAGE@ imach)
+SET(@DICTLANG@ en)
+SET(@VERMAJOR@ )
+SET(@COPYRIGHT@ "Copyright (C)  2002-2015 EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121) 2013-2016- Intel Software 2015-2018 2000-2022 INED")
 #SET(IMACH_VERSION ${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR}.${IMACH_VERSION_PATCH})
 #MATH(EXPR IMACH_VERSION_NUMBER "100000*${IMACH_VERSION_MAJOR} + 100*${IMACH_VERSION_MINOR} + ${IMACH_VERSION_PATCH}")
 
 # #PROJECT(IMaCh${IMACH_VERSION_MAJOR})
-PROJECT (IMaCh)
+PROJECT (imach)
 
 CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
 
@@ -27,36 +41,51 @@ CONFIGURE_FILE(
   "${PROJECT_SOURCE_DIR}/config.h.in"
   "${PROJECT_BINARY_DIR}/config.h"
 )
+# Examples for the documentation
 CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/mypar.imach.in" "html/doc/mypar.imach")
 CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/biaspar.imach.in" "html/doc/biaspar.imach")
 CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/data1.txt" "html/doc/data1.txt" COPYONLY)
 CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/data/mydata.txt" "html/doc/data/mydata.txt" COPYONLY)
+# Test files
+CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/data/data2.txt" "tests/data/data2.txt" COPYONLY)
+#CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/testV2.imach" "tests/testV2.imach" COPYONLY)
+#CONFIGURE_FILE("${PROJECT_SOURCE_DIR}/tests/testV1V2.imach" "tests/testV1V2.imach" COPYONLY)
+
 
 set (imach_SRCS ./src/imach.c)
 SET( CMAKE_VERBOSE_MAKEFILE on )
-ADD_EXECUTABLE ( IMaCh-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} ${imach_SRCS})
-INSTALL(TARGETS IMaCh-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} DESTINATION bin COMPONENT binaries )
+#SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ADD_EXECUTABLE (imach-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} ${imach_SRCS})
+INSTALL(TARGETS imach-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} DESTINATION bin COMPONENT binaries )
+#INSTALL(TARGETS imach DESTINATION bin COMPONENT binaries )
 ADD_SUBDIRECTORY(html)
 ADD_SUBDIRECTORY(tests)
-ADD_SUBDIRECTORY(src)
-ADD_SUBDIRECTORY(distributions)
+#ADD_SUBDIRECTORY(src) 
+#ADD_SUBDIRECTORY(distributions)
 #if (${WIN32})
 #if(APPLE)
 #  set(DOCDIR "${CMAKE_INSTALL_PREFIX}/${PROJECT_NAME}/doc")
 #endif()
 if(UNIX)
   #   set(CMAKE_CXX_COMPILER "gcc")
-  target_link_libraries(IMaCh-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} m)
+  target_link_libraries(imach-${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR} m)
   set(BINDIR "${CMAKE_INSTALL_PREFIX}/bin")
   set(DOCDIR "${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/doc")
-  set(MANDIR "${CMAKE_INSTALL_PREFIX}/share/man")
+  set(TESTDIR "${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/tests")
+  set(DATADIR "${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/tests/data")
+  set(MANDIR "${CMAKE_INSTALL_PREFIX}/share/man/man1")
   #set(EXAMPLE_CONF_DIR ${DOCDIR})
   set(XDG_APPS_DIR "${CMAKE_INSTALL_PREFIX}/share/applications")
   set(APPDATADIR "${CMAKE_INSTALL_PREFIX}/share/appdata")
   set(ICONDIR "${CMAKE_INSTALL_PREFIX}/share/icons")
+  install(FILES "distributions/gnulinux/imach.1" DESTINATION "${MANDIR}")
+  install(FILES "distributions/gnulinux/imach.png" DESTINATION "${ICONDIR}")
+  install(FILES "distributions/gnulinux/imach.desktop" DESTINATION "${XDG_APPS_DIR}")
 endif()
 if(MSVC)
   set(DOCDIR "${CMAKE_INSTALL_PREFIX}/${PROJECT_NAME}/doc")
+  set(TESTDIR "${CMAKE_INSTALL_PREFIX}/${PROJECT_NAME}/tests")
+  set(DATADIR "${CMAKE_INSTALL_PREFIX}/${PROJECT_NAME}/tests/data")
   set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} /MTd")
   set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} /MT")
   set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} /MTd")
@@ -70,26 +99,61 @@ install(FILES "html/doc/mypar.imach" DES
 install(FILES "html/doc/data/mydata.txt" DESTINATION "${DOCDIR}/data")
 install(FILES "html/doc/biaspar.imach" DESTINATION "${DOCDIR}")
 install(FILES "html/doc/data1.txt" DESTINATION "${DOCDIR}")
+install(FILES "src/README.txt" DESTINATION "${DOCDIR}")
+#install(FILES "tests/testV1V2.imach" DESTINATION "${TESTDIR}")
+install(FILES "tests/rtestV1V2.imach" DESTINATION "${TESTDIR}")
+install(FILES "tests/testV2.imach" DESTINATION "${TESTDIR}")
+install(FILES "tests/rtestV2.imach" DESTINATION "${TESTDIR}")
+install(FILES "tests/data/data2.txt" DESTINATION "${DATADIR}")
+#not working install(FILES "imach.desktop" DESTINATION "${XDG_APPS_DIR}")
 #install(FILES "html" DESTINATION "${DOCDIR}")
 
+
 set(CPACK_PACKAGE_VERSION ${IMACH_VERSION})
-set(CPACK_PACKAGE_NAME "IMaCh")
-set(CPACK_PACKAGE_RELEASE 2)
+set(CPACK_PACKAGE_NAME "imach")
+set(CPACK_PACKAGE_RELEASE 1)
 set(CPACK_PACKAGE_CONTACT "Nicolas Brouard")
 set(CPACK_PACKAGE_VENDOR "INED")
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "IMaCh Interpolated Markov Chain program")
 SET(CPACK_PACKAGE_VENDOR "IMaCh, INED")
-SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.txt")
+SET(CPACK_PACKAGE_LICENSE "GPLv2")
+#SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.txt")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/Copyright.txt")
 SET(CPACK_PACKAGE_VERSION_MAJOR "${IMACH_VERSION_MAJOR}")
 SET(CPACK_PACKAGE_VERSION_MINOR "${IMACH_VERSION_MINOR}")
 SET(CPACK_PACKAGE_VERSION_PATCH "${IMACH_VERSION_PATCH}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CMake ${CMake_VERSION_MAJOR}.${CMake_VERSION_MINOR}")
+#SET(CPACK_INSTALLED_DIRECTORIES "${PROJECT_SOURCE_DIR}" ".")
 #SET(CPACK_PACKAGE_EXECUTABLES "IMaCh" "IMaCh")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "IMaCh program estimates Health Expectancies from Cross-longitudinal surveys.")
+#SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.txt")
 SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/imach-desc.txt")
-#set(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
-set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_RELEASE}.${CMAKE_SYSTEM_PROCESSOR}")
+set(CPACK_RPM_PACKAGE_URL "http://euroreves.ined.fr/imach")
+IF(UNIX)
+  SET(CPACK_RPM_PACKAGE_LICENSE "GPL")
+  SET(CPACK_RPM_PACKAGE_GROUP "Applications/Sciences")
+  SET(CPACK_RPM_PACKAGE_REQUIRES "gnuplot >= 5.0, cmake >= 2.8")
+  SET(CPACK_GENERATOR "TXZ")
+  SET(CPACK_SOURCE_GENERATOR "TXZ")
+  SET(CPACK_SOURCE_TBZ2 "OFF")
+  SET(CPACK_SOURCE_TGZ "ON")
+  SET(CPACK_SOURCE_TOPLEVEL_TAG "Linux-src")
+  SET(CPACK_SOURCE_TXZ "ON")
+  SET(CPACK_SOURCE_TZ "ON")
+  SET(CPACK_SOURCE_ZIP "OFF")
+  #SET(CPACK_RPM_PREFIX "/usr/local")
+  # SET(CPACK_RPM_PACKAGE_PREFIX "/usr/local")
+   SET(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local")
+  # SET(CMAKE_INSTALL_PREFIX "/usr/local")
+  set(CPACK_RPM_PACKAGE_RELOCATABLE True)
+  # This a .spec Changelog not an Emacs ChangeLog that you get with C-x v a (vc-update-change-log)
+  # * Mon May 20 2019  Brouard Nicolas  <brouard@brouard.name>
+  # ${CMAKE_CURRENT_SOURCE_DIR}/specchangelog")
+  set(CPACK_RPM_CHANGELOG_FILE "${PROJECT_SOURCE_DIR}/src/Changelog")
+  SET(CPACK_BINARY_RPM "ON")
+  SET(CPACK_RPM_PACKAGE_SOURCES "ON")
+  set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_RELEASE}.${CMAKE_SYSTEM_PROCESSOR}")
+  SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_RELEASE}.src")
+ENDIF(UNIX)
 
 IF(WIN32 AND NOT UNIX)
   # There is a bug in NSI that does not handle full unix paths properly. Make
@@ -147,7 +211,7 @@ INCLUDE(CPack)
 #   set(VERSION_PATCH "${BUILD_VERSION_PATCH}")
 # ENDIF()
 file( GLOB_RECURSE parameter_files RELATIVE
-"${CMAKE_CURRENT_SOURCE_DIR}/html/doc" "html/*.imach" )
+"${CMAKE_CURRENT_SOURCE_DIR}/html/doc" "html/*.imach" "tests/*.imach" )
 foreach( parameter_file ${parameter_files} )
   add_custom_command(
     OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${parameter_file}"
@@ -161,11 +225,13 @@ endforeach( parameter_file )
 
 #add_custom_target( CopyParameter ALL DEPENDS ${parameter_files_dest} )
 ENABLE_TESTING()
-ADD_SUBDIRECTORY(html/doc)
-ADD_SUBDIRECTORY(html/doc/data)
-install(FILES "${PROJECT_SOURCE_DIR}/html/doc/mypar.imach" DESTINATION "html/doc/mypar.imach")
-ADD_TEST(mypar  IMaCh-${IMACH_VERSION} html/doc/mypar.imach )
-ADD_TEST(biaspar  IMaCh-${IMACH_VERSION} html/doc/biaspar.imach )
+#ADD_SUBDIRECTORY(html/doc)
+#ADD_SUBDIRECTORY(html/doc/data)
+#install(FILES "${PROJECT_SOURCE_DIR}/html/doc/mypar.imach" DESTINATION "html/doc")
+ADD_TEST(testV2.imach  IMaCh-${IMACH_VERSION} tests/testV2.imach )
+ADD_TEST(testV1V2.imach  IMaCh-${IMACH_VERSION} tests/testV1V2.imach )
+ADD_TEST(mypar  IMaCh-${IMACH_VERSION} local/html/doc/ )
+ADD_TEST(biaspar  IMaCh-${IMACH_VERSION} local/html/doc/ )
 #SET(FAB "po" CACHE STRING "Some user-specified option")
 #set_target_properties(TARGET_NAME imach-${VERSION_MAJOR}.${VERSION_MINOR})
 #%comspec% /k ""C:\Program Files (x86)\Microsoft Visual Studio 12.0\Common7\Tools\VsDevCmd.bat""
@@ -219,13 +285,29 @@ ADD_TEST(biaspar  IMaCh-${IMACH_VERSION}
 #   endif()
 # endif()
 # Add a target to generate API documentation with Doxygen
-find_package(Doxygen)
-if(DOXYGEN_FOUND)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/latex/Doxyfile.in
-${CMAKE_CURRENT_BINARY_DIR}/latex/Doxyfile @ONLY)
-add_custom_target(doc
-${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/latex/Doxyfile
-WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/latex
-COMMENT "Generating IMaCh documentation with Doxygen" VERBATIM
-)
-endif()
\ No newline at end of file
+option(BUILD_DOC "Build documentation" ON)
+if(UNIXDODOXYGEN)
+  find_package(Doxygen)
+  if(DOXYGEN_FOUND)# set input and output files
+    #set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/../docs/Doxyfile.in) ~/Documents/imach/cvs/imach/latex/Doxyfile.in
+    set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/latex/Doxyfile.in)
+    set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+    
+    # request to configure the file
+    configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+    message("Doxygen build started")
+    
+    # note the option ALL which allows to build the docs together with the application
+    add_custom_target( doc_doxygen ALL
+      COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMENT "Generating API documentation with Doxygen in gnulinux/html/index.html"
+      VERBATIM )
+    install(DIRECTORY ${CMAKE_BINARY_DIR}/html 
+      DESTINATION local/share/doc/${CMAKE_PROJECT_NAME})
+  else (DOXYGEN_FOUND)
+    message("Doxygen need to be installed to generate the doxygen documentation")
+  endif (DOXYGEN_FOUND)
+  message("Doxygen only in UNIX doxygen documentation")
+endif (UNIXDODOXYGEN)
+