diff --git a/CMakeLists.txt b/CMakeLists.txt
index a2aa26daaf18ee73e2da50894df9156ffc18a337..5d6ec22be922931b7c6a36923a017789d2cfa3cb 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -466,8 +466,8 @@ if(DOXYGEN_FOUND)
   if(DOXY-NOTFOUND)
     message(STATUS "Warning, doxypy seems to be missing on your system. You may not be able to properly generate the documentation.")
   endif()
-  configure_file(${CMAKE_SOURCE_DIR}/DoxyConf/hysop.doxyfile.in ${CMAKE_BINARY_DIR}/DoxyConf/hysop.doxyfile)
-  add_custom_target(doc COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/DoxyConf/hysop.doxyfile
+  configure_file(${CMAKE_SOURCE_DIR}/docs/config/hysop.doxyfile.in ${CMAKE_BINARY_DIR}/docs/config/hysop.doxyfile)
+  add_custom_target(doc COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/docs/config/hysop.doxyfile
   COMMENT "Generate hysop documentation using doxygen.")
 else()
   message(STATUS "Warning : cmake cannot find doxygen on your system. It means you will not be able to generate documentation for hysop.")
diff --git a/cmake/fortran_utils.cmake b/cmake/fortran_utils.cmake
index 8f56794452975c5e23ad0aed1de74d937fb21be4..79c56db9b7d9bd60d0d8a29c5724e4e43f4f4247 100644
--- a/cmake/fortran_utils.cmake
+++ b/cmake/fortran_utils.cmake
@@ -15,7 +15,7 @@
 # --> create f2hysop.pyf that will be used to generate hysop.f2hysop module.
 #
 function(write_main_pyf_file filename)
-  set(_file ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf.in)
+  set(_file ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf)
   file(WRITE ${_file}
 "!    -*- f90 -*-\n
 ! Generated file - Do not edit.\n
diff --git a/hysop/f2hysop.pyf.in b/hysop/f2hysop.pyf.in
deleted file mode 100755
index a11194e7df7e5f7f02bb55b202ff01bf3faa85e9..0000000000000000000000000000000000000000
--- a/hysop/f2hysop.pyf.in
+++ /dev/null
@@ -1,20 +0,0 @@
-!    -*- f90 -*-
-
-! Generated file - Do not edit.
-
-! Note: the context of this file is case sensitive.
-
-python module f2hysop ! in
-
-  interface
-      ! Example
-      include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'
-      ! precision
-      include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'
-      ! fftw
-      include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'
-      ! scales
-      include '@CMAKE_SOURCE_DIR@/hysop/f2py/scales2py.pyf'
-  end interface
-
-end python module f2hysop
\ No newline at end of file