--- imach/CMakeLists.txt	2015/09/03 07:14:02	1.3
+++ imach/CMakeLists.txt	2019/05/09 15:04:48	1.20
@@ -6,11 +6,25 @@
 #      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 99r18)
 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 INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121) 2013-2016- Intel Software 2015-2018")
 #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}")
 
@@ -27,12 +41,23 @@ 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}.${IMACH_VERSION_MINOR} DESTINATION bin COMPONENT binaries )
 ADD_SUBDIRECTORY(html)
+ADD_SUBDIRECTORY(tests)
 ADD_SUBDIRECTORY(src)
 ADD_SUBDIRECTORY(distributions)
 #if (${WIN32})
@@ -65,11 +90,13 @@ 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 "${DOCDIR}")
+#not working install(FILES "imach.desktop" DESTINATION "${XDG_APPS_DIR}")
 #install(FILES "html" DESTINATION "${DOCDIR}")
 
+
 set(CPACK_PACKAGE_VERSION ${IMACH_VERSION})
-set(CPACK_PACKAGE_NAME "IMaCh")
-set(CPACK_PACKAGE_RELEASE 2)
+set(CPACK_PACKAGE_NAME "imach")
+set(CPACK_PACKAGE_RELEASE 1)
 set(CPACK_PACKAGE_CONTACT "Nicolas Brouard")
 set(CPACK_PACKAGE_VENDOR "INED")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "IMaCh Interpolated Markov Chain program")
@@ -159,6 +186,8 @@ ENABLE_TESTING()
 ADD_SUBDIRECTORY(html/doc)
 ADD_SUBDIRECTORY(html/doc/data)
 install(FILES "${PROJECT_SOURCE_DIR}/html/doc/mypar.imach" DESTINATION "html/doc/mypar.imach")
+ADD_TEST(testV2.imach  IMaCh-${IMACH_VERSION} tests/testV2.imach )
+ADD_TEST(testV1V2.imach  IMaCh-${IMACH_VERSION} tests/testV1V2.imach )
 ADD_TEST(mypar  IMaCh-${IMACH_VERSION} html/doc/mypar.imach )
 ADD_TEST(biaspar  IMaCh-${IMACH_VERSION} html/doc/biaspar.imach )
 #SET(FAB "po" CACHE STRING "Some user-specified option")
@@ -214,13 +243,29 @@ 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(UNIX)
+  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 ${CMAKE_BINARY_DIR}/html 
+      DESTINATION share/doc/${CMAKE_PROJECT_NAME})
+  else (DOXYGEN_FOUND)
+    message("Doxygen need to be installed to generate the doxygen documentation")
+  endif (DOXYGEN_FOUND)
+else (UNIX)
+  message("Doxygen only in UNIX doxygen documentation")
+endif (UNIX)
\ No newline at end of file