Auto stash before merge of "feature-python_api-build_wheels" and...

Auto stash before merge of "feature-python_api-build_wheels" and "origin/feature-python_api-build_wheels"

.github/workflows/build_variants.yml

+name: Python libs
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+#  schedule:
+#    # Every day at 1am
+#    - cron: '0 1 * * *'
+
+jobs:
+
+  get_Latest:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[ci skip]')"
+
+    steps:
+    - name: Checkout ILL repo
+      run: |
+        git clone https://code.ill.fr/scientific-software/crysfml/ ./
+        git checkout feature-python_api-build_wheels
+        rm -rf ./.git ./Html
+    - uses: actions/upload-artifact@v2
+      with:
+        name: CrysFML_SRC
+        path: ${{ github.workspace }}
+        retention-days: 1
+
+
+  create-Linux:
+    runs-on: ubuntu-latest
+
+    needs: get_Latest
+
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        name: CrysFML_SRC
+
+    - name: Build manylinux wheels
+      run:  |
+        chmod +x ./Scripts/buildscript.sh
+        docker run -e PLAT=manylinux2010_x86_64 -v ${{ github.workspace }}:/io quay.io/pypa/manylinux2010_x86_64 /io/Scripts/buildscript.sh
+    - uses: actions/upload-artifact@v2
+      with:
+        name: CrysFML - Linux
+        path: ${{ github.workspace }}/dist/*.whl
+
+  create-OSX:
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.8']
+        os: [macos-10.15]
+        gcc_v: [ 10 ] # Version of GFortran we want to use.
+
+    runs-on: ${{ matrix.os }}
+
+    needs: get_Latest
+
+    steps:
+    - uses: actions/download-artifact@v2
+      with:
+        name: CrysFML_SRC
+
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.python-version}}
+
+    - name: Install cmake
+      run: pip3 install cmake delocate wheel
+
+    - name: Build CFML (OSX)
+      env:
+        FC: gfortran-${{ matrix.gcc_v }}
+        CC: gcc-${{ matrix.gcc_v }}
+      run: |
+        pip3 wheel ./ --no-deps -w ./old/
+        delocate-wheel -w dist -v ./old/*.whl
+    - uses: actions/upload-artifact@v2
+      with:
+        name: CrysFML - MacOS
+        path: ./dist/*.whl
+
+  create-Windows:
+    strategy:
+      max-parallel: 1
+      matrix:
+        python-version: [ '3.6', '3.7']
+        os: [ windows-latest ]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: true
+
+      - uses: msys2/setup-msys2@v2
+        with:
+          msystem: MSYS
+          install: cmake mingw-w64-x86_64-toolchain
+          update: true
+          path-type: inherit
+
+      - name: Build CFML
+        shell: msys2 {0}
+        id: build
+        run: python setup.py bdist_wheel
+        env:
+          MINGW_ARCH: MINGW64
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: CrysFML - Windows
+          path: ./dist/*.whl
+
+  Upload_Artifacts:
+    runs-on: ubuntu-latest
+    needs: [create-Linux, create-OSX]
+    steps:
+    - uses: actions/download-artifact@v2
+    - name: What is downloaded
+      run: |
+        ls -al
+    - name: Upload Artifacts GitHub releases
+      uses: ncipollo/release-action@v1
+      with:
+        draft: false
+        prerelease: true
+        allowUpdates: true
+        replacesArtifacts: true
+        token: ${{ secrets.GITHUB_TOKEN }}
+        artifacts: "./**/*.whl"
+        tag: "CurrentBuild"
+        body: "This is a build of the CFML libraries."

.gitignore

@@ -37,3 +37,12 @@
 
 # Directories
 Build
+
+.idea/
+build/
+
+CFML.egg-info/
+
+dist/
+
+*.whl

CMakeLists.txt

@@ -14,6 +14,7 @@ option(HEAP_ARRAYS "Put arrays in heap instead of stack (only for Windows ifort)
 option(PROG_EX "Build the Program Examples" ON)
 option(PYTHON_API "Build Python API" OFF)
 option(QPARALLEL "qparallel option for Ifort on Windows" ON)
+option(PYSETUP "Building from setup.py" OFF)
 
 if(DEFINED CMAKE_Fortran_COMPILER)
     set(CMAKE_Fortran_COMPILER ${CMAKE_Fortran_COMPILER} CACHE STRING "The Fortran compiler. One of 'ifort', 'g95' or 'gfortran'.")
@@ -52,16 +53,34 @@ message(STATUS "CrysFML installation path set to ${CRYSFML_PREFIX}")
 
 # Include and library paths for Python. 
 # They must be set by the user.
-if(DEFINED PYTHON_LIBRARY_PATH)
-    set(PYTHON_LIBRARY_PATH ${PYTHON_LIBRARY_PATH} CACHE PATH "Python library path")
-else()
-    set(PYTHON_LIBRARY_PATH "" CACHE PATH "Python library path")
-endif()
-if(DEFINED PYTHON_INTERPRETER_PATH)
-    set(PYTHON_INTERPRETER_PATH ${PYTHON_INTERPRETER_PATH} CACHE PATH "Python interpreter path")
-else()
-    set(PYTHON_INTERPRETER_PATH "" CACHE PATH "Python interpreter path")
-endif()
+# if(DEFINED PYTHON_LIBRARY_PATH)
+#     set(PYTHON_LIBRARY_PATH ${PYTHON_LIBRARY_PATH} CACHE PATH "Python library path")
+# else()
+#     set(PYTHON_LIBRARY_PATH "" CACHE PATH "Python library path")
+# endif()
+# if(DEFINED PYTHON_INTERPRETER_PATH)
+#     set(PYTHON_INTERPRETER_PATH ${PYTHON_INTERPRETER_PATH} CACHE PATH "Python interpreter path")
+# else()
+#     set(PYTHON_INTERPRETER_PATH "" CACHE PATH "Python interpreter path")
+# endif()
+# Use CMake v3.12+ FindPython3 to find the system-compatible interpreter *and* libraries at once
+# This solves a potential issue on convoluted Windows build systems which have multiple
+# python interpreters, some of which do not have build-system compatibility (I'm looking at you, msys2 python)
+# In such a case FindPythonInterp might point to the wrong python interpreter and then further configuration
+# steps will fail to find any (or any compatible) libraries which match the interpreter.
+# find_package(Python3 COMPONENTS Interpreter Development)
+# # Since FindPython3 and FindPythonInterp set different variables, fake the FindPythonInterp result
+# # to prevent it running if called by, e.g., FindPybind11
+# if(Python3_FOUND)
+#   set(PYTHONINTERP_FOUND ON)
+#   set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+#   message(STATUS "USING PYTHON: " ${PYTHON_EXECUTABLE})
+# #   set(PYTHON_INTERPRETER_PATH ${Python3_EXECUTABLE})
+#   set(PYTHON_VERSION_STRING "${Python3_VERSION}")
+#   set(PYTHON_VERSION_MAJOR ${Python3_VERSION_MAJOR})
+#   set(PYTHON_VERSION_MINOR ${Python3_VERSION_MINOR})
+#   set(PYTHON_VERSION_PATCH ${Python3_VERSION_PATCH})
+# endif()
 
 # Include and library paths for HDF5.
 # They must be set by the user.

Program_Examples/ReadNeXuS/CMakeLists.txt

@@ -20,7 +20,7 @@ target_link_libraries(read_nexus crysfml)
 link_directories(${HDF5_LIBRARY_DIR})
 target_link_libraries(read_nexus ${HDF5_LIBRARIES})
 
-if(WIN32)
+if(WIN32 OR MSYS)
     get_filename_component(COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME_WE)
     if(COMPILER_NAME STREQUAL ifort)
 # Copy hdf5.dll hdf5_f90cstub.dll hdf5_fortran.dll

Python_API/Src/API_Atom_TypeDef.py

@@ -42,7 +42,7 @@ class Atom(CFML_api.FortranBindedClass):
         
     def __str__(self):
         xyz = self.xyz
-        return 'ATOM %s %s %s %s %s %s %s'%(self.label, self.chemical_symbol, str(xyz[0]), str(xyz[1]), str(xyz[2]), self.biso, self.site_multiplicity)
+        return 'ATOM %s %s %s %s %s %s %s %s %s'%(self.label, self.chemical_symbol, str(xyz[0]), str(xyz[1]), str(xyz[2]), str(self.biso), str(self.occ), str(self.moment), str(self.formal_charge))
     
     @property
     def label(self):
@@ -343,7 +343,12 @@ class AtomList(CFML_api.FortranBindedClass):
     """
     def __init__(self, string_array=None):
         CFML_api.FortranBindedClass.__init__(self)
+        self._mult = True
+        self._adp = True
         if string_array:
+            self._mult = False 
+            self._adp = False
+            
             dict = CFML_api.crysfml_api.atom_typedef_atomlist_from_CIF_string_array(string_array)
             self._set_fortran_address(dict["AtomList"])
               
@@ -366,7 +371,7 @@ class AtomList(CFML_api.FortranBindedClass):
     @property
     def natoms(self):
         """
-        total number of atoms in the list
+        Total number of atoms in the list
         """
         return CFML_api.crysfml_api.atom_typedef_get_natoms(self.get_fortran_address())["natoms"]
     
@@ -374,3 +379,29 @@ class AtomList(CFML_api.FortranBindedClass):
         """ Print the list of atoms. """
         
         CFML_api.crysfml_api.atom_typedef_write_atom_list(self.get_fortran_address())
+
+
+    def set_mult_occ_cif(self,spg):
+        """
+        Update the multiplicity and modify the occupancy when reading from a CIF array,
+        in order to be in agreement with the definitions of Sfac in CrysFML
+        This needs to be run when the AtomList is initialised from a CIF-like stringarray
+        rather than from the class CIFFile
+        """
+        if (self._mult == False):
+            CFML_api.crysfml_api.atom_typedef_atomlist_reset_occ_cif(self.get_fortran_address(),spg.get_fortran_address())
+            self._mult = True
+        else:
+            print("Warning: multiplicity and occupancy have already been set")
+
+    def set_all_anisotropic_displacement_parameters_cif(self,cell):
+        """
+        Update all Atom fields for Us, Bs and betas
+        This needs to be run when the AtomList is initialised from a CIF-like stringarray
+        rather than from the class CIFFile
+        """
+        if (self._adp == False):
+            CFML_api.crysfml_api.atom_typedef_atomlist_set_all_adp_cif(self.get_fortran_address(),cell.get_fortran_address())
+            self._adp = True
+        else:
+            print("Warning: Anisotropic Displacement Parameters have already been set")

Python_API/Src/API_Crystal_Metrics.py

@@ -170,3 +170,72 @@ class Cell(CFML_api.FortranBindedClass):
         return CFML_api.crysfml_api.crystal_metrics_get_CartType(self.get_fortran_address())["CartType"]
 
 
+def k_to_cart_vector(code, vector, cell):
+    """ 
+    Convert a vector in crystal space to cartesian components
+    The value of code has been extended to use also the Busing-Levy
+    Cartesian system as reference also for direct and reciprocal space.
+    Codes:
+    The Cartesian frame is that defined by the setting of the Cell object
+    D: The components are given with respect to basis (a,b,c)
+    R: The components are given with respect to basis (a*,b*,c*)
+    BL: The components are given with respect to basis (a*,b*,c*) but
+    the Cartesian frame is that defined by Busing and Levy
+    BLD: The components are given with respect to basis (a,b,c) but
+    the Cartesian frame is that defined by Busing and Levy
+    ...
+    Parameters
+    ----------
+    code : str
+       Cartesian frame 
+    vector : np.array[dtype='float32', ndim=1]
+       kx,ky,kz coordinates 
+    cell : CMFL_api.crysfml_api.Cell
+
+    Returns:
+    np.array[dtype='float32', ndim=1] : coordinates in the chosen cartesian frame
+
+    """
+    return CFML_api.crysfml_api.crystal_metrics_cart_vector(code, vector, cell.get_fortran_address())["cart_vec"]
+
+def k_to_cart_unitary_vector(code, vector, cell):
+    """
+    Convert a vector in crystal space to unitary cartesian components
+    The value of code has been extended to use also the Busing-Levy
+    Cartesian system as reference also for direct and reciprocal space.
+    Codes:
+    The Cartesian frame is that defined by the setting of the Cell object
+    D: The components are given with respect to basis (a,b,c)
+    R: The components are given with respect to basis (a*,b*,c*)
+    BL: The components are given with respect to basis (a*,b*,c*) but
+    the Cartesian frame is that defined by Busing and Levy
+    BLD: The components are given with respect to basis (a,b,c) but
+    the Cartesian frame is that defined by Busing and Levy
+    ...
+    Parameters
+    ----------
+    code : str
+       Cartesian frame 
+    vector : np.array[dtype='float32', ndim=1]
+       kx,ky,kz coordinates 
+    cell : CMFL_api.crysfml_api.Cell
+
+    Returns:
+    np.array[dtype='float32', ndim=1] : coordinates in the chosen cartesian frame
+
+    """
+    return CFML_api.crysfml_api.crystal_metrics_cart_u_vector(code, vector, cell.get_fortran_address())["cart_vec"]
+
+def betas_from_biso(biso, cell):
+    """
+    Get Betas from Biso 
+    ...
+    Parameters
+    ----------
+    biso : float32
+    cell : CMFL_api.crysfml_api.Cell
+
+    Returns
+    np.array[dtype='float32', ndim=1] : betas[0:5] b11, b22, b33, b12, b13, b23
+    """
+    return CFML_api.crysfml_api.crystal_metrics_get_betas_from_biso(cell.get_fortran_address(),biso)["betas"]

Python_API/Src/CMakeLists.txt

 #################################
 # Commad line arguments section
 #################################
-cmake_minimum_required(VERSION 3.1.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.13 FATAL_ERROR)
 
 #################################
 # Project section
@@ -29,39 +29,38 @@ set_source_files_properties(forpy_mod.f90 PROPERTIES COMPILE_FLAG "-cpp")
 # Dependencies section
 #################################
 # Add a dependency to crysfml_common to keep sure that the crysfml_common library will be built first.
+# See https://gitlab.kitware.com/cmake/cmake/-/issues/19226 for linking
 add_dependencies(${LIBRARY_NAME} crysfml_common)
 
-set(COMPATIBLE_VERSIONS 3.8 3.7 3.6 3.5)
-if (NOT PYTHON_INTERPRETER_PATH)
-  set(Python_ADDITIONAL_VERSIONS ${COMPATIBLE_VERSIONS})
-  find_package(PythonInterp REQUIRED)
-  set(PYTHON_INTERPRETER_PATH ${PYTHON_EXECUTABLE})
-  message(STATUS ${PYTHON_INTERPRETER_PATH})
-else()
-  message(STATUS "using Python interpreter provided with PYTHON_INTERPRETER_PATH variable: " ${PYTHON_INTERPRETER_PATH})
-endif()
-
-if (NOT PYTHON_LIBRARY_PATH)
-  set(Python_ADDITIONAL_VERSIONS ${COMPATIBLE_VERSIONS})
-  find_package(PythonLibs REQUIRED)
-  set(PYTHON_LIBRARY_PATH ${PYTHON_LIBRARY})
-  message(STATUS ${PYTHON_LIBRARY_PATH})
+if (NOT PYTHON_INTERPRETER_PATH OR NOT PYTHON_LIBRARY_PATH)
+  set(Python3_USE_STATIC_LIBS, TRUE)
+  find_package(Python3 COMPONENTS Interpreter Development)
+  set(PYTHON_INTERPRETER_PATH ${Python3_EXECUTABLE})
+  set(PYTHON_LIBRARY_PATH Python3::Python)
+  message(STATUS "Using Python interpreter found with PYTHON_INTERPRETER_PATH variable: " ${PYTHON_INTERPRETER_PATH})
+  message(STATUS "Linking Python extension with found PYTHON_LIBRARY_PATH variable: " ${PYTHON_LIBRARY_PATH})
 else()
+  message(STATUS "Using Python interpreter provided with PYTHON_INTERPRETER_PATH variable: " ${PYTHON_INTERPRETER_PATH})
   message(STATUS "Linking Python extension with provided PYTHON_LIBRARY_PATH variable: " ${PYTHON_LIBRARY_PATH})
 endif()
 
-if (UNIX)
-  add_library(Python3_LIB SHARED IMPORTED)
-  set_property(TARGET Python3_LIB PROPERTY IMPORTED_LOCATION ${PYTHON_LIBRARY_PATH})
-elseif(WIN32)
+
+
+
+if(WIN32 OR MSYS)
   add_library(Python3_LIB STATIC IMPORTED)
   set_property(TARGET Python3_LIB PROPERTY IMPORTED_LOCATION ${PYTHON_LIBRARY_PATH})
+  target_link_libraries(${LIBRARY_NAME} Python3_LIB)
 endif()
 
+# Set -Wl,-undefined,dynamic_lookup to OTHER_LDFLAGS
 # Set include and linking
 include_directories(${CRYSFML_COMMON_MODULE_DIRECTORY})
 target_link_libraries(${LIBRARY_NAME} crysfml_common)
-target_link_libraries(${LIBRARY_NAME} Python3_LIB)
+# Fix a problem on Mac OS X when building shared libraries
+if(APPLE)
+    set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -undefined dynamic_lookup")
+endif()
 
 # Set library extension
 set_target_properties(${LIBRARY_NAME} PROPERTIES PREFIX "" OUTPUT_NAME ${LIBRARY_NAME})
@@ -69,7 +68,7 @@ set(LIBRARY_FILENAME "crysfml_api.so")
 if(APPLE)
     set_target_properties(${LIBRARY_NAME} PROPERTIES SUFFIX ".so")
     set(LIBRARY_FILENAME "crysfml_api.so")
-elseif(WIN32)
+elseif(WIN32 OR MSYS)
     set_target_properties(${LIBRARY_NAME} PROPERTIES SUFFIX ".pyd")
     set(LIBRARY_FILENAME "crysfml_api.pyd")
 endif()
@@ -112,42 +111,56 @@ endif (DOXYGEN_FOUND)
 #################################
 # Add tests
 add_test(NAME "Python_API_Tests" COMMAND ${PYTHON_INTERPRETER_PATH} -m unittest discover ${CMAKE_CURRENT_BINARY_DIR}/../Tests)
-add_custom_target(Python_Files ALL
+if(PYSETUP)
+    add_custom_target(Python_Files ALL
+        COMMAND
+        ${CMAKE_COMMAND} -E copy_directory
+        ${CMAKE_CURRENT_SOURCE_DIR}/../Tests
+        ${CMAKE_CURRENT_BINARY_DIR}/../Tests
+
+        COMMAND
+        ${CMAKE_COMMAND} -E copy_directory
+        ${CMAKE_CURRENT_SOURCE_DIR}
+        ${CMAKE_CURRENT_BINARY_DIR}/../Tests/CFML_api
+        )
+else()
+    add_custom_target(Python_Files ALL
         COMMAND
         ${CMAKE_COMMAND} -E copy_directory
         ${CMAKE_CURRENT_SOURCE_DIR}/../Tests
         ${CMAKE_CURRENT_BINARY_DIR}/../Tests
-        
+
         COMMAND
         ${CMAKE_COMMAND} -E copy_directory
         ${CMAKE_CURRENT_SOURCE_DIR}
         ${CMAKE_CURRENT_BINARY_DIR}/../Tests/CFML_api
-        
+
         COMMAND
         ${CMAKE_COMMAND} -E copy
         ${CMAKE_CURRENT_BINARY_DIR}/${LIBRARY_FILENAME}
-        ${CMAKE_CURRENT_BINARY_DIR}/../Tests/CFML_api
+        ${CMAKE_CURRENT_BINARY_DIR}/../Tests/CFML_api/${LIBRARY_FILENAME}
         )
-add_dependencies(Python_Files ${LIBRARY_NAME})
+endif()
 
+add_dependencies(Python_Files ${LIBRARY_NAME})
 
 #################################
 # Install section
 #################################
 # The rules for installing the library.
 install(DIRECTORY "" DESTINATION ${PYTHON_API_PREFIX}/CFML_api FILES_MATCHING PATTERN "*.py" PATTERN "Extensions" EXCLUDE)
-if(WIN32)
-install(TARGETS ${LIBRARY_NAME} RUNTIME DESTINATION ${PYTHON_API_PREFIX}/CFML_api)
+if(WIN32 OR MSYS)
+    install(TARGETS ${LIBRARY_NAME} RUNTIME DESTINATION ${PYTHON_API_PREFIX}/CFML_api)
 else()
-install(TARGETS ${LIBRARY_NAME} LIBRARY DESTINATION ${PYTHON_API_PREFIX}/CFML_api)
+    install(TARGETS ${LIBRARY_NAME} LIBRARY DESTINATION ${PYTHON_API_PREFIX}/CFML_api)
 endif()
 
 # Installing example files
 install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/../Examples" DESTINATION ${PYTHON_API_PREFIX} FILES_MATCHING PATTERN "*.py")
 install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/../Examples/Data" DESTINATION ${PYTHON_API_PREFIX}/Examples FILES_MATCHING PATTERN "*.cfl" PATTERN "*.cif")
-
-# Installing tests files
+#
+# # Installing tests files
 install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/../Tests" DESTINATION ${PYTHON_API_PREFIX} FILES_MATCHING PATTERN "*.py")
-
-# Installing documentation files
+#
+# # Installing documentation files
 install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doxygen/html" DESTINATION ${PYTHON_API_PREFIX}/Doc OPTIONAL)
\ No newline at end of file

Python_API/Src/Extensions/API_Atom_TypeDef.f90

@@ -4,6 +4,8 @@ module API_Atom_TypeDef
   use, intrinsic :: iso_c_binding
   use, intrinsic :: iso_fortran_env
 
+  use CFML_GlobalDeps, only : cp, eps
+
   use CFML_Atom_TypeDef, only: &
        Atom_List_type, &
        Atoms_Cell_type, &
@@ -13,9 +15,23 @@ module API_Atom_TypeDef
        Write_Atom_list, &
        Atom_type
 
+  Use CFML_Crystallographic_Symmetry, only: &
+       Get_Multip_Pos
+
+  use CFML_Crystal_Metrics, only: &
+       Convert_U_Betas, Convert_B_Betas
+
   use CFML_IO_Formats, only: &
        Read_Atom, Read_Cif_Atom
 
+  use API_Crystallographic_Symmetry, only: &
+       Space_Group_type_p, &
+       get_space_group_type_from_arg
+
+  use API_Crystal_Metrics, only: &
+       Crystal_Cell_type_p, &
+       get_cell_from_arg
+
   implicit none
 
   type Atom_type_p
@@ -178,6 +194,118 @@ contains
   end function atom_typedef_atomlist_from_CIF_string_array
 
 
+  !---- Modify occupation factors and set multiplicity of atoms
+  !---- in order to be in agreement with the definitions of Sfac in CrysFML
+  function atom_typedef_atomlist_reset_occ_cif(self_ptr, args_ptr) result(r) bind(c)
+        
+    type(c_ptr), value :: self_ptr
+    type(c_ptr), value :: args_ptr
+    type(c_ptr) :: r
+    type(tuple) :: args
+    type(dict) :: retval
+    integer :: num_args
+    integer :: ierror
+
+    type(Atom_List_Type_p) :: a_p
+    type(Space_Group_type_p) :: spg
+
+    real(kind=cp),dimension(6):: pos
+    integer :: i
+    
+    r = C_NULL_PTR   ! in case of an exception return C_NULL_PTR
+    ! use unsafe_cast_from_c_ptr to cast from c_ptr to tuple
+    call unsafe_cast_from_c_ptr(args, args_ptr)
+    ! Check if the arguments are OK
+    ierror = args%len(num_args)
+    ! we should also check ierror, but this example does not do complete error checking for simplicity
+    if (num_args /= 2) then
+       call raise_exception(TypeError, "update_occ_cif expects exactly 1 argument")
+       call args%destroy
+       return
+    endif
+    
+    ! Doing boring stuff
+    call get_atom_list_type_from_arg(args, a_p, 0)
+    call get_space_group_type_from_arg(args, spg, 1)
+
+    do i=1,a_p%p%natoms
+       pos(1:3)=a_p%p%atom(i)%x
+       a_p%p%atom(i)%Mult = Get_Multip_Pos(pos(1:3),SpG%p)
+       ! This step is needed for CIF file only as the convention is different!
+       a_p%p%atom(i)%Occ = a_p%p%atom(i)%Occ*real(a_p%p%atom(i)%Mult)/max(1.0,real(SpG%p%Multip))
+       if(a_p%p%atom(i)%occ < eps) a_p%p%atom(i)%occ=real(a_p%p%atom(i)%Mult)/max(1.0,real(SpG%p%Multip))
+    enddo
+
+    ierror = dict_create(retval)
+    r = retval%get_c_ptr()
+
+    call args%destroy
+    
+    
+  end function atom_typedef_atomlist_reset_occ_cif
+
+
+  function atom_typedef_atomlist_set_all_adp_cif(self_ptr, args_ptr) result(r) bind(c)
+        
+    type(c_ptr), value :: self_ptr
+    type(c_ptr), value :: args_ptr
+    type(c_ptr) :: r
+    type(tuple) :: args
+    type(dict) :: retval
+    integer :: num_args
+    integer :: ierror
+
+    type(Atom_List_Type_p) :: a_p
+    type(Crystal_Cell_type_p) :: cell
+
+    integer :: i
+    
+    r = C_NULL_PTR   ! in case of an exception return C_NULL_PTR
+    ! use unsafe_cast_from_c_ptr to cast from c_ptr to tuple
+    call unsafe_cast_from_c_ptr(args, args_ptr)
+    ! Check if the arguments are OK
+    ierror = args%len(num_args)
+    ! we should also check ierror, but this example does not do complete error checking for simplicity
+    if (num_args /= 2) then
+       call raise_exception(TypeError, "update_occ_cif expects exactly 1 argument")
+       call args%destroy
+       return
+