entirely reworked cython wrapper

python/obitools3/obidms/_obidms.c

@@ -1 +0,0 @@
-#error Do not use this file, it is the result of a failed Cython compilation.

python/obitools3/obidms/_obidms.pxd

@@ -1,5 +1,8 @@
-from .capi.obidms   cimport OBIDMS_p
+#cython: language_level=3
-from .capi.obitypes cimport obiversion_t, OBIType_t
+
+from .capi.obidms       cimport OBIDMS_p
+from .capi.obidmscolumn cimport OBIDMS_column_p
+from .capi.obitypes     cimport obiversion_t, OBIType_t
 
 cdef class OBIDMS_column
             
@@ -19,3 +22,17 @@ cdef class OBIDMS:
                                     size_t nb_lines=*, 
                                     size_t nb_elements_per_line=*, 
                                     str elements_names=*)
+
+
+cdef class OBIDMS_column:
+
+    cdef OBIDMS_column_p pointer
+    cdef OBIDMS dms
+    cdef str data_type   # TODO keep as OBIType_t? both?
+    cdef str dms_name
+    cdef str column_name
+
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef list   get_elements_names(self)
+    cpdef str    get_data_type(self)
+    cpdef size_t get_nb_lines_used(self)

python/obitools3/obidms/_obidms.pyx

@@ -1,31 +1,44 @@
 #cython: language_level=3
 
-from obitools3.utils cimport bytes2str, str2bytes
-from obitools3.obidms.obidmscolumn._obidmscolumn cimport OBIDMS_column
 from pathlib import Path
 
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column
+from obitools3.utils cimport bytes2str, str2bytes
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obiversion_t   # TODO pourquoi je peux pas les declarer dans le pxd?
+
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport name_data_type
+from .capi.obidms cimport obi_dms
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_data_type_from_name
+from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_latest_version_from_name
+                                obi_column_get_latest_version_from_name, \
-# from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_column_get_line_count_from_name
+                                obi_column_get_line_count_from_name, \
-# 
+                                obi_column_get_nb_lines_used, \
-from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_writable         # TODO pourquoi pas cimport?
+                                obi_column_get_elements_names, \
-from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int cimport OBIDMS_column_int_read
+                                obi_create_column, \
-from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_writable
+                                obi_clone_column, \
-from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float cimport OBIDMS_column_float_read
+                                obi_open_column, \
-from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_writable
+                                obi_close_column
-from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool cimport OBIDMS_column_bool_read
+from .capi.obitypes cimport const_char_p, name_data_type
-from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_writable
+
-from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char cimport OBIDMS_column_char_read
+
-from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_writable
+from ._obidms cimport OBIDMS
-from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx cimport OBIDMS_column_idx_read
+from ._obidms cimport OBIDMS_column
+
+from ._obidmscolumn_int cimport OBIDMS_column_int, \
+                                OBIDMS_column_int_writable
+
+from ._obidmscolumn_float cimport OBIDMS_column_float, \
+                                  OBIDMS_column_float_writable
+
+from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
+                                 OBIDMS_column_bool_writable
+
+from ._obidmscolumn_char cimport OBIDMS_column_char, \
+                                 OBIDMS_column_char_writable
+
+from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
+                                OBIDMS_column_idx_writable
 
 
 cdef class OBIDMS :
     
-    def __init__(self, str dms_name) :       # TODO
+    def __init__(self, str dms_name) :
         
         # Declarations
         cdef bytes dms_name_b
@@ -61,7 +74,7 @@ cdef class OBIDMS :
                 column_name = entry.stem
                 column_name_b = str2bytes(column_name)
                 dms[column_name] = {}
-                data_type = bytes2str((name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
+                data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
                 latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
                 line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
                 dms[column_name]['data_type'] = data_type
@@ -71,18 +84,18 @@ cdef class OBIDMS :
 
         return dms
      
-    cpdef OBIDMS_column open_column(self,                   # TODO j'arrive pas a le passer en cpdef
+    cpdef OBIDMS_column open_column(self,
-                      str column_name,     # TODO
+                                    str column_name,
-                      bint create=False, 
+                                    bint create=False, 
-                      bint clone=False, bint clone_data=True,
+                                    bint clone=False, bint clone_data=True,
-                      obiversion_t version_number=-1, 
+                                    obiversion_t version_number=-1, 
-                      OBIType_t data_type=0,     # TODO 
+                                    OBIType_t data_type= <OBIType_t> 0,
-                      size_t nb_lines=0, 
+                                    size_t nb_lines=0, 
-                      size_t nb_elements_per_line=1, 
+                                    size_t nb_elements_per_line=1, 
-                      str elements_names=None):
+                                    str elements_names=None):
         
         # Declarations
-        cdef OBIDMS_column column         # TODO not sure object
+        cdef OBIDMS_column column
         cdef bytes column_name_b
         
         # Format the character string to send to C function
@@ -104,7 +117,7 @@ cdef class OBIDMS :
                                                     nb_lines, nb_elements_per_line, 
                                                     elements_names)
             else :
-                 column = OBIDMS_column_int_read(self, column_name, 
+                 column = OBIDMS_column_int(self, column_name, 
                                                  create, clone, clone_data, 
                                                  version_number, data_type, 
                                                  nb_lines, nb_elements_per_line, 
@@ -118,7 +131,7 @@ cdef class OBIDMS :
                                                       nb_lines, nb_elements_per_line, 
                                                       elements_names)
             else :
-                 column = OBIDMS_column_float_read(self, column_name, 
+                 column = OBIDMS_column_float(self, column_name, 
                                                    create, clone, clone_data, 
                                                    version_number, data_type, 
                                                    nb_lines, nb_elements_per_line, 
@@ -132,7 +145,7 @@ cdef class OBIDMS :
                                                      nb_lines, nb_elements_per_line, 
                                                      elements_names)
             else :
-                 column = OBIDMS_column_bool_read(self, column_name, 
+                 column = OBIDMS_column_bool(self, column_name, 
                                                   create, clone, clone_data, 
                                                   version_number, data_type, 
                                                   nb_lines, nb_elements_per_line, 
@@ -146,13 +159,125 @@ cdef class OBIDMS :
                                                      nb_lines, nb_elements_per_line, 
                                                      elements_names)
             else :
-                 column = OBIDMS_column_char_read(self, column_name, 
+                 column = OBIDMS_column_char(self, column_name, 
                                                   create, clone, clone_data, 
                                                   version_number, data_type, 
                                                   nb_lines, nb_elements_per_line, 
                                                   elements_names)
     
+#         elif data_type == 5 :
+#             if (create or clone) :
+#                 column = OBIDMS_column_idx_writable(self, column_name, 
+#                                                     create, clone, clone_data, 
+#                                                     version_number, data_type, 
+#                                                     nb_lines, nb_elements_per_line, 
+#                                                     elements_names)
+#             else :
+#                  column = OBIDMS_column_idx(self, column_name, 
+#                                             create, clone, clone_data, 
+#                                             version_number, data_type, 
+#                                             nb_lines, nb_elements_per_line, 
+#                                             elements_names)
+   
         else :
             raise Exception("Problem with the data type")
             
         return column
+
+
+
+cdef class OBIDMS_column :
+
+    # Should only be initialized through a subclass
+    def __init__(self, 
+                 OBIDMS dms, 
+                 str column_name,
+                 bint create, 
+                 bint clone, bint clone_data,
+                 obiversion_t version_number, 
+                 OBIType_t type,
+                 size_t nb_lines, 
+                 size_t nb_elements_per_line, 
+                 str elements_names):
+        
+        # Declarations
+        cdef bytes column_name_b
+        cdef bytes dms_name_b
+        cdef bytes elements_names_b
+        
+        # Fill structure
+        self.dms = dms
+        self.data_type = bytes2str(name_data_type(type))
+        self.column_name = column_name
+        
+        # Format the character strings to send them to C functions
+        column_name_b = str2bytes(column_name)
+        dms_name_b = str2bytes(self.dms.dms_name)
+        
+        # Create, clone or open column
+        if create :
+            if elements_names == None :  
+                elements_names_b = column_name_b
+            else :
+                elements_names_b = str2bytes(elements_names)
+            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
+        else :
+            if clone :
+                self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
+            else :
+                self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
+    
+    
+    def __iter__(self):
+    
+        # Declarations
+        cdef list elements_names
+        cdef str element_name
+        cdef bint multiple_elements
+        cdef object line               # TODO
+        cdef size_t lines_used
+        cdef size_t line_nb
+        
+        # Check if there are multiple elements per line anf if yes, get their names
+        elements_names = self.get_elements_names()
+        if len(elements_names) > 1 :
+            multiple_elements = True
+        else :
+            element_name = elements_names[0]
+        
+        # Yield each line
+        lines_used = obi_column_get_nb_lines_used(self.pointer)
+        for line_nb in xrange(lines_used):
+            if multiple_elements :
+                line = []
+                for element_name in elements_names :
+                    line.append(self.get_item(line_nb, element_name))
+            else :
+                line = self.get_item(line_nb, element_name)
+            yield line
+
+
+    def __setitem__(self, size_t line_nb, object value):
+        self.set_item(line_nb, "", value)
+
+        
+    def __getitem__(self, size_t line_nb):
+        return self.get_item(line_nb, "")
+
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        raise NotImplementedError
+    
+    cpdef list get_elements_names(self):
+        cdef bytes elements_names
+        elements_names = obi_column_get_elements_names(self.pointer)
+        return (bytes2str(elements_names)).split(';')
+
+             
+    cpdef str get_data_type(self):
+        return self.data_type
+
+    
+    cpdef size_t get_nb_lines_used(self):
+        return obi_column_get_nb_lines_used(self.pointer)
+        
+   

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -0,0 +1,16 @@
+../../../src/obidmscolumn_bool.c
+../../../src/obidmscolumn_bool.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c

python/obitools3/obidms/_obidmscolumn_bool.pxd

@@ -0,0 +1,17 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport obibool_t
+from .capi.obidmscolumn cimport OBIDMS_column_p
+                                                
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_bool(OBIDMS_column):
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
+    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
+    cpdef close(self)
+

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -0,0 +1,46 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obibool_with_elt_name, \
+                                obi_column_set_obibool_with_elt_name
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIBool_NA
+
+from obitools3.utils cimport str2bytes
+
+from cpython.bool cimport PyBool_FromLong
+
+
+cdef class OBIDMS_column_bool(OBIDMS_column):
+ 
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef obibool_t value
+        cdef object result
+        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+     
+    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
+        raise Exception("Column is read-only")
+     
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
+   
+    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
+        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0 :
+            raise Exception("Problem setting a value in a column")
+ 
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+     

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -0,0 +1,16 @@
+../../../src/obidmscolumn_char.c
+../../../src/obidmscolumn_char.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -0,0 +1,17 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport obichar_t
+from .capi.obidmscolumn cimport OBIDMS_column_p
+                                                
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_char(OBIDMS_column):
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
+    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
+    cpdef close(self)
+

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -0,0 +1,44 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obichar_with_elt_name, \
+                                obi_column_set_obichar_with_elt_name
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIChar_NA
+
+from obitools3.utils cimport str2bytes
+
+
+cdef class OBIDMS_column_char(OBIDMS_column) :
+ 
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef char value
+        cdef object result
+        value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIChar_NA :
+            result = None
+        else :
+            result = <bytes> value
+        return result
+
+    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
+        raise Exception("Column is read-only")
+ 
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+ 
+         
+cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
+ 
+    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
+        if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
+            raise Exception("Problem setting a value in a column")
+ 
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+      

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -0,0 +1,16 @@
+../../../src/obidmscolumn_float.c
+../../../src/obidmscolumn_float.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -0,0 +1,16 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport obifloat_t
+from .capi.obidmscolumn cimport OBIDMS_column_p
+                                                
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_float(OBIDMS_column):
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
+    cpdef close(self)
+    
+cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
+    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -0,0 +1,44 @@
+#cython: language_level=3
+
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obifloat_with_elt_name, \
+                                obi_column_set_obifloat_with_elt_name
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIFloat_NA
+
+from obitools3.utils cimport str2bytes
+
+
+cdef class OBIDMS_column_float(OBIDMS_column):
+
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef obifloat_t value
+        cdef object result
+        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIFloat_NA :
+            result = None
+        else :
+            result = <float> value
+        return result
+    
+    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
+        raise Exception("Column is read-only")
+
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                  
+
+cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
+
+    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
+        if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+ 

python/obitools3/obidms/_obidmscolumn_idx.cfiles

@@ -0,0 +1,16 @@
+../../../src/obidmscolumn_idx.c
+../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c

python/obitools3/obidms/_obidmscolumn_idx.pxd

@@ -0,0 +1,16 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport obiidx_t
+from .capi.obidmscolumn cimport OBIDMS_column_p
+                                                
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_idx(OBIDMS_column):
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
+    cpdef close(self)
+    
+cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
+    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_idx.pyx

@@ -0,0 +1,46 @@
+#cython: language_level=3
+
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obiidx_with_elt_name, \
+                                obi_column_set_obiidx_with_elt_name
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIIdx_NA
+
+from obitools3.utils cimport str2bytes
+
+from cpython.int cimport PyInt_FromSsize_t
+
+
+cdef class OBIDMS_column_idx(OBIDMS_column):
+
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef obiidx_t value
+        cdef object result
+        value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = PyInt_FromSsize_t(value)
+        return result
+    
+    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
+        raise Exception("Column is read-only")
+
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                  
+
+cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):     
+
+    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
+        if obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+ 

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -0,0 +1,16 @@
+../../../src/obidmscolumn_int.c
+../../../src/obidmscolumn_int.h
+../../../src/obidmscolumn.h
+../../../src/obidmscolumn.c
+../../../src/obidmscolumndir.h
+../../../src/obidmscolumndir.c
+../../../src/obidms.h
+../../../src/obidms.c
+../../../src/obierrno.h
+../../../src/obierrno.c
+../../../src/obilittlebigman.h
+../../../src/obilittlebigman.c
+../../../src/obitypes.h
+../../../src/obitypes.c
+../../../src/private_at_functions.h
+../../../src/private_at_functions.c

python/obitools3/obidms/_obidmscolumn_int.pxd

@@ -0,0 +1,16 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport obiint_t
+from .capi.obidmscolumn cimport OBIDMS_column_p
+                                                
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_int(OBIDMS_column):
+    cpdef object get_item(self, size_t line_nb, str element_name)
+    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
+    cpdef close(self)
+    
+cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
+    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -0,0 +1,48 @@
+#cython: language_level=3
+
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obiint_with_elt_name, \
+                                obi_column_set_obiint_with_elt_name
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIInt_NA
+
+from obitools3.utils cimport str2bytes
+
+from cpython.int cimport PyInt_FromLong
+
+from ._obidms cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_int(OBIDMS_column):
+
+    cpdef object get_item(self, size_t line_nb, str element_name):
+        cdef obiint_t value
+        cdef object result
+        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIInt_NA :
+            result = None
+        else :
+            result = PyInt_FromLong(value)
+        return result
+    
+    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
+        raise Exception("Column is read-only")
+
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                  
+
+cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
+
+    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
+        if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+ 

python/obitools3/obidms/capi/obidms.pxd

@@ -1,3 +1,7 @@
+#cython: language_level=3
+
+from .obitypes cimport const_char_p
+
 cdef extern from "obidms.h" nogil:
     struct OBIDMS_t:
         pass

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -1,19 +1,113 @@
+#cython: language_level=3
+
+from ..capi.obidms   cimport OBIDMS_p
+from ..capi.obitypes cimport const_char_p, \
+                             OBIType_t, \
+                             obiversion_t, \
+                             obiint_t, \
+                             obibool_t, \
+                             obichar_t, \
+                             obifloat_t, \
+                             obiidx_t
+
 cdef extern from "obidmscolumn.h" nogil:
     struct OBIDMS_column_t:
         pass
 
     ctypedef OBIDMS_column_t* OBIDMS_column_p
 
-    OBIDMS_column_p obi_create_column(OBIDMS_p dms, const char* column_name, OBIType_t type, size_t nb_lines, size_t nb_elements_per_line, const char* elements_names)
+    OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
+                                      const_char_p column_name, 
+                                      OBIType_t type, 
+                                      size_t nb_lines, 
+                                      size_t nb_elements_per_line, 
+                                      const_char_p elements_names)
+    
     size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
-    const char* obi_column_get_elements_names(OBIDMS_column_p column)
+    
+    const_char_p obi_column_get_elements_names(OBIDMS_column_p column)
+    
     void obi_column_make_unwritable(OBIDMS_column_p column)
-    OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
+    
+    OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
+                                    const_char_p column_name, 
+                                    obiversion_t version_number)
+    
     OBIType_t obi_column_get_type(OBIDMS_column_p column)
+    
     int obi_close_column(OBIDMS_column_p column)
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
+    
-    OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bint clone_data)
+    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
+                                                 const_char_p column_name)
+    
+    OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
+                                     const_char_p column_name, 
+                                     obiversion_t version_number, 
+                                     bint clone_data)
+    
     int obi_truncate_and_close_column(OBIDMS_column_p column)
-    obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
+    
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
+    obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
-    size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name)
+                                                         const_char_p column_name)
+    
+    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
+                                                 const_char_p column_name)
+    
+    size_t obi_column_get_line_count_from_name(OBIDMS_p dms, 
+                                               const_char_p column_name)
+    
+    
+cdef extern from "obidmscolumn_int.h" nogil:
+    int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, 
+                                            size_t line_nb, 
+                                            const_char_p element_name, 
+                                            obiint_t value)
+    
+    obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, 
+                                                 size_t line_nb, 
+                                                 const_char_p element_name)
+
+cdef extern from "obidmscolumn_bool.h" nogil:
+
+    int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, 
+                                             size_t line_nb, 
+                                             const_char_p element_name, 
+                                             obibool_t value)
+    
+    obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, 
+                                                   size_t line_nb, 
+                                                   const_char_p element_name)
+
+cdef extern from "obidmscolumn_char.h" nogil:
+
+    int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, 
+                                             size_t line_nb, 
+                                             const_char_p element_name, 
+                                             obichar_t value)
+    
+    obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, 
+                                                   size_t line_nb, 
+                                                   const_char_p element_name)
+
+cdef extern from "obidmscolumn_float.h" nogil:
+
+    int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, 
+                                              size_t line_nb, 
+                                              const_char_p element_name, 
+                                              obifloat_t value)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
+                                                     size_t line_nb, 
+                                                     const_char_p element_name)
+
+cdef extern from "obidmscolumn_idx.h" nogil:
+
+    int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, 
+                                            size_t line_nb, 
+                                            const_char_p element_name, 
+                                            obiidx_t value)
+    
+    obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, 
+                                                 size_t line_nb, 
+                                                 const_char_p element_name)
+

python/obitools3/obidms/capi/obierrno.pxd

@@ -1,3 +1,5 @@
+#cython: language_level=3
+
+
 cdef extern from "obierrno.h" nogil:
     extern int obi_errno
-

python/obitools3/obidms/capi/obitypes.pxd

@@ -1,13 +1,18 @@
+#cython: language_level=3
+
+
 from libc.stdint cimport int32_t
 
 
 cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
+
 cdef extern from "obidmscolumn.h" nogil:
 
     ctypedef int32_t obiversion_t
 
+
 cdef extern from "obitypes.h" nogil:
 
     enum OBIType:       # TODO je sais pas si ça sert de declarer le contenu de l'enum
@@ -20,7 +25,6 @@ cdef extern from "obitypes.h" nogil:
     
     ctypedef OBIType OBIType_t
     
-
     enum OBIBool:
         pass
     
@@ -30,4 +34,10 @@ cdef extern from "obitypes.h" nogil:
     ctypedef char obichar_t  
     ctypedef size_t obiidx_t
 
+    extern obiint_t   OBIInt_NA
+    extern obiidx_t   OBIIdx_NA
+    extern obifloat_t OBIFloat_NA
+    extern obichar_t  OBIChar_NA
+    extern obibool_t  OBIBool_NA
+
     char* name_data_type(int data_type)

python/obitools3/obidms/obidmscolumn/_obidmscolumn.pxd

@@ -1,20 +0,0 @@
-from obitools3.obidms.capi.obidms       cimport OBIDMS_p
-from obitools3.obidms.capi.obierrno     cimport obi_errno
-from obitools3.obidms.capi.obidmscolumn cimport OBIDMS_column_p
-
-
-cdef class OBIDMS
-
-
-cdef class OBIDMS_column:
-
-    cdef OBIDMS_column_p pointer
-    cdef OBIDMS dms
-    cdef str data_type   # TODO keep as OBIType_t? both?
-    cdef str dms_name
-    cdef str column_name
-
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef list   get_elements_names(self)
-    cpdef str    get_data_type(self)
-    cpdef size_t get_nb_lines_used(self)

python/obitools3/obidms/obidmscolumn/capidmscolumn.cfiles

@@ -1,16 +0,0 @@
-../../../../src/obidmscolumn_int.c
-../../../../src/obidmscolumn_int.h
-../../../../src/obidmscolumn.h
-../../../../src/obidmscolumn.c
-../../../../src/obidmscolumndir.h
-../../../../src/obidmscolumndir.c
-../../../../src/obidms.h
-../../../../src/obidms.c
-../../../../src/obierrno.h
-../../../../src/obierrno.c
-../../../../src/obilittlebigman.h
-../../../../src/obilittlebigman.c
-../../../../src/obitypes.h
-../../../../src/obitypes.c
-../../../../src/private_at_functions.h
-../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx

@@ -1,98 +0,0 @@
-#cython: language_level=3
-
-cdef class OBIDMS_column:
-
-    # Should only be initialized through a subclass
-    def __init__(self, 
-                 OBIDMS dms, 
-                 object column_name,    # TODO
-                 bint create, 
-                 bint clone, bint clone_data,
-                 obiversion_t version_number, 
-                 OBIType_t type,
-                 size_t nb_lines, 
-                 size_t nb_elements_per_line, 
-                 str elements_names):
-        
-        # Declarations
-        cpdef bytes column_name_b
-        cpdef bytes dms_name_b
-        cpdef bytes elements_names_b
-        
-        # Fill structure
-        self.dms = dms
-        self.data_type = (name_data_type(type)).decode('UTF-8')
-        self.column_name = column_name
-        
-        # Format the character strings to send them to C functions
-        column_name_b = column_name.encode(encoding='UTF-8')
-        dms_name_b = self.dms.dms_name.encode(encoding='UTF-8')
-        
-        # Create, clone or open column
-        if create :
-            if elements_names == None :  
-                elements_names_b = column_name_b
-            else :
-                elements_names_b = elements_names.encode(encoding='UTF-8')
-            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
-        else :
-            if clone :
-                self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
-            else :
-                self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
-    
-    
-    def __iter__(self):
-    
-        # Declarations
-        cpdef list elements_names
-        cpdef str element_name
-        cpdef bint multiple_elements
-        cpdef object line               # TODO
-        cdef size_t lines_used
-        cdef size_t line_nb
-        
-        # Check if there are multiple elements per line anf if yes, get their names
-        elements_names = self.get_elements_names()
-        if len(elements_names) > 1 :
-            multiple_elements = True
-        else :
-            element_name = elements_names[0]
-        
-        # Yield each line
-        lines_used = obi_column_get_nb_lines_used(self.pointer)
-        for line_nb in xrange(lines_used):
-            if multiple_elements :
-                line = []
-                for element_name in elements_names :
-                    line.append(self.get_item(line_nb, element_name))
-            else :
-                line = self.get_item(line_nb, element_name)
-            yield line
-
-
-    def __setitem__(self, size_t line_nb, object value):
-        self.set_item(line_nb, "", value)
-
-        
-    def __getitem__(self, size_t line_nb):
-        return self.get_item(line_nb, "")
-
-    cpdef object get_item(self, line_nb, element_name):
-        raise NotImplementedError
-
-    
-    cpdef get_elements_names(self):
-        cpdef bytes elements_names
-        elements_names = obi_column_get_elements_names(self.pointer)
-        return (elements_names.decode('UTF-8')).split(';')
-
-             
-    cpdef get_data_type(self):
-        return self.data_type
-
-    
-    cpdef get_nb_lines_used(self):
-        return obi_column_get_nb_lines_used(self.pointer)
-        
-   

python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.cfiles

@@ -1,16 +0,0 @@
-../../../../../src/obidmscolumn_bool.c
-../../../../../src/obidmscolumn_bool.h
-../../../../../src/obidmscolumn.h
-../../../../../src/obidmscolumn.c
-../../../../../src/obidmscolumndir.h
-../../../../../src/obidmscolumndir.c
-../../../../../src/obidms.h
-../../../../../src/obidms.c
-../../../../../src/obierrno.h
-../../../../../src/obierrno.c
-../../../../../src/obilittlebigman.h
-../../../../../src/obilittlebigman.c
-../../../../../src/obitypes.h
-../../../../../src/obitypes.c
-../../../../../src/private_at_functions.h
-../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pxd

@@ -1,7 +0,0 @@
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
-
-
-cdef extern from "obidmscolumn_bool.h" nogil:
-
-    int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
-    obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pyx

@@ -1,35 +0,0 @@
-#cython: language_level=3
-
-from .capidmscolumn_bool cimport *
-
-
-cdef class OBIDMS_column_bool(OBIDMS_column) :
-
-    def get_item(self, line_nb, element_name):
-        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        return value
-    
-
-cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :     
-
-    def set_item(self, line_nb, element_name, value):
-        raise Exception('Column is read-only')
-    
-    def close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                        
-        
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool) :     
-  
-    def set_item(self, line_nb, element_name, value):
-        return obi_column_set_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
-
-    def close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                        
-    
-    

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.cfiles

@@ -1,16 +0,0 @@
-../../../../../src/obidmscolumn_char.c
-../../../../../src/obidmscolumn_char.h
-../../../../../src/obidmscolumn.h
-../../../../../src/obidmscolumn.c
-../../../../../src/obidmscolumndir.h
-../../../../../src/obidmscolumndir.c
-../../../../../src/obidms.h
-../../../../../src/obidms.c
-../../../../../src/obierrno.h
-../../../../../src/obierrno.c
-../../../../../src/obilittlebigman.h
-../../../../../src/obilittlebigman.c
-../../../../../src/obitypes.h
-../../../../../src/obitypes.c
-../../../../../src/private_at_functions.h
-../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pxd

@@ -1,7 +0,0 @@
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
-
-
-cdef extern from "obidmscolumn_char.h" nogil:
-
-    int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
-    obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx

@@ -1,33 +0,0 @@
-#cython: language_level=3
-
-from .capidmscolumn_char cimport *
-
-
-cdef class OBIDMS_column_char(OBIDMS_column) :
-
-    def get_item(self, line_nb, element_name):
-        cdef char value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        return <bytes> value
-
-
-cdef class OBIDMS_column_char_read(OBIDMS_column_char) :     
-
-    def set_item(self, line_nb, element_name, value):
-        raise Exception('Column is read-only')
-
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                        
-        
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
-
-    def set_item(self, line_nb, element_name, bytes value):
-        return obi_column_set_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value[0])
-
-    def close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-     

python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.cfiles

@@ -1,16 +0,0 @@
-../../../../../src/obidmscolumn_float.c
-../../../../../src/obidmscolumn_float.h
-../../../../../src/obidmscolumn.h
-../../../../../src/obidmscolumn.c
-../../../../../src/obidmscolumndir.h
-../../../../../src/obidmscolumndir.c
-../../../../../src/obidms.h
-../../../../../src/obidms.c
-../../../../../src/obierrno.h
-../../../../../src/obierrno.c
-../../../../../src/obilittlebigman.h
-../../../../../src/obilittlebigman.c
-../../../../../src/obitypes.h
-../../../../../src/obitypes.c
-../../../../../src/private_at_functions.h
-../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pxd

@@ -1,7 +0,0 @@
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
-
-
-cdef extern from "obidmscolumn_float.h" nogil:
-
-    int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
-    obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pyx

@@ -1,34 +0,0 @@
-#cython: language_level=3
-
-from .capidmscolumn_float cimport *
-
-
-cdef class OBIDMS_column_float(OBIDMS_column) :
-
-    def get_item(self, line_nb, element_name):
-        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        return value
-
-
-cdef class OBIDMS_column_float_read(OBIDMS_column_float) :     
-
-    def set_item(self, line_nb, element_name, value):
-        raise Exception('Column is read-only')
-
-    def close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                        
-        
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float) :     
-
-    def set_item(self, line_nb, element_name, value):
-        return obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
-
-    def close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-     
-    

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.cfiles

@@ -1,16 +0,0 @@
-../../../../../src/obidmscolumn_idx.c
-../../../../../src/obidmscolumn_idx.h
-../../../../../src/obidmscolumn.h
-../../../../../src/obidmscolumn.c
-../../../../../src/obidmscolumndir.h
-../../../../../src/obidmscolumndir.c
-../../../../../src/obidms.h
-../../../../../src/obidms.c
-../../../../../src/obierrno.h
-../../../../../src/obierrno.c
-../../../../../src/obilittlebigman.h
-../../../../../src/obilittlebigman.c
-../../../../../src/obitypes.h
-../../../../../src/obitypes.c
-../../../../../src/private_at_functions.h
-../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pxd

@@ -1,7 +0,0 @@
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
-
-
-cdef extern from "obidmscolumn_idx.h" nogil:
-
-    int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
-    obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx

@@ -1,33 +0,0 @@
-#cython: language_level=3
-
-from .capidmscolumn_idx cimport *
-
-
-cdef class OBIDMS_column_idx(OBIDMS_column) :
-    
-    def get_item(self, line_nb, element_name):
-        value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        return value
-
-    
-cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :     
-
-    def set_item(self, line_nb, element_name, value):
-        raise Exception('Column is read-only')
-
-    def close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                        
-        
-cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx) :     
-
-    def set_item(self, line_nb, element_name, value):
-        return obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
-
-    def close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-     

python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.cfiles

@@ -1,16 +0,0 @@
-../../../../../src/obidmscolumn_int.c
-../../../../../src/obidmscolumn_int.h
-../../../../../src/obidmscolumn.h
-../../../../../src/obidmscolumn.c
-../../../../../src/obidmscolumndir.h
-../../../../../src/obidmscolumndir.c
-../../../../../src/obidms.h
-../../../../../src/obidms.c
-../../../../../src/obierrno.h
-../../../../../src/obierrno.c
-../../../../../src/obilittlebigman.h
-../../../../../src/obilittlebigman.c
-../../../../../src/obitypes.h
-../../../../../src/obitypes.c
-../../../../../src/private_at_functions.h
-../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pxd

@@ -1,21 +0,0 @@
-from obitools3.obidms.capitypes cimport obiint_t
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column_p
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport OBIDMS_column
-
-cdef extern from "obidmscolumn_int.h" nogil:
-    int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
-    obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
-
-cdef class OBIDMS_column_int(OBIDMS_column):
-
-    #cpdef get_item(self, size_t line_nb, str element_name)
-    
-cdef class OBIDMS_column_int_read(OBIDMS_column_int):
-     
-#    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
-#    cpdef close(self)
-
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
-     
-#    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
-#    cpdef close(self)

python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pyx

@@ -1,37 +0,0 @@
-#cython: language_level=3
-
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_close_column
-from obitools3.obidms.obidmscolumn.capidmscolumn cimport obi_truncate_and_close_column
-from obitools3.obidms.capidms cimport obi_errno
-
-from cpython.int cimport PyInt_FromLong
-
-cdef class OBIDMS_column_int(OBIDMS_column) :
-
-    def object get_item(self, size_t line_nb, str element_name):
-        cdef obiint_t value
-        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        return PyInt_FromLong(value) 
-
-  
-cdef class OBIDMS_column_int_read(OBIDMS_column_int) :     
-
-    def set_item(self, size_t line_nb, str element_name, obiint_t value):
-        raise Exception('Column is read-only')
-
-    def close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                   
-        
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int) :     
-
-    def set_item(self, size_t line_nb, str element_name, obiint_t value):
-        return obi_column_set_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
-
-    def close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 

python/obitools3/utils.pxd

@@ -1,3 +1,5 @@
+#cython: language_level=3
+
 cdef bytes str2bytes(str string)
 
 cdef str bytes2str(bytes string)

python/obitools3/utils.pyx

@@ -1,3 +1,5 @@
+#cython: language_level=3
+
 cdef bytes str2bytes(str string):
     return string.encode('ascii')