First version of the simplified setup.py script

python/obitools3/apps/temp.pxd

@@ -6,5 +6,3 @@ Created on 28 juillet 2017
 @author: coissac
 '''
 
-from obitools3.dms.dms cimport DMS
-from obitools3.utils cimport tobytes,tostr

python/obitools3/apps/temp.pyx

@@ -17,6 +17,9 @@ from obitools3.dms.dms import DMS
 from obitools3.apps.config import getConfiguration
 from obitools3.apps.config import logger
 
+from obitools3.dms.dms cimport DMS
+from obitools3.utils cimport tobytes,tostr
+
 cpdef get_temp_dir():
     """
     Returns a temporary directory object specific of this instance of obitools.

python/obitools3/dms/column/column.pxd

@@ -1,14 +1,21 @@
 #cython: language_level=3
 
+from obitools3.dms.capi.obitypes cimport index_t, \
+                                         name_data_type, \
+                                         obitype_t, \
+                                         obiversion_t, \
+                                         OBI_QUAL
 
-from ..capi.obitypes     cimport index_t, \
-                                 obitype_t
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_header_p, \
+                                 obi_close_column, \
+                                 obi_get_elements_names, \
+                                 obi_column_write_comments
                                  
-from ..capi.obidmscolumn cimport OBIDMS_column_p
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
                                                                  
-from ..view.view cimport View
+from obitools3.dms.view.view cimport View
  
-from ..object cimport OBIWrapper                          
+from obitools3.dms.object cimport OBIWrapper                          
 
  
 cdef dict __OBIDMS_COLUMN_CLASS__

python/obitools3/dms/column/column.pyx

@@ -3,27 +3,31 @@
 
 __OBIDMS_COLUMN_CLASS__ = {}
 
+from obitools3.dms.object cimport OBIWrapper                          
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
+from obitools3.dms.capi.obitypes cimport index_t, \
+                                         name_data_type, \
+                                         obitype_t, \
+                                         obiversion_t, \
+                                         OBI_QUAL
 
-from ..capi.obitypes cimport name_data_type, \
-                             obitype_t, \
-                             obiversion_t, \
-                             OBI_QUAL
-
-from ..capi.obidms cimport obi_import_column
-
-from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_header_p, \
                                  obi_close_column, \
                                  obi_get_elements_names, \
                                  obi_column_write_comments
+
+from obitools3.dms.capi.obidms cimport obi_import_column
+from obitools3.dms.view.view cimport View
+
                                      
-from ..capi.obiutils cimport obi_format_date
+from obitools3.dms.capi.obiutils cimport obi_format_date
  
-from ..capi.obiview cimport obi_view_add_column, \
+from obitools3.dms.capi.obiview cimport obi_view_add_column, \
                             obi_view_get_pointer_on_column_in_view, \
                             Obiview_p, \
                             NUC_SEQUENCE_COLUMN
 
-from ..object cimport OBIDeactivatedInstanceError
+from obitools3.dms.object cimport OBIDeactivatedInstanceError
 
 from obitools3.utils cimport tobytes, \
                              bytes2str, \

python/obitools3/dms/column/column_idx.pxd

@@ -1,10 +1,7 @@
 # #cython: language_level=3
  
 
-from ..capi.obitypes cimport index_t
-
-from .column cimport Column, \
-                      Column_multi_elts
+from obitools3.dms.capi.obitypes cimport index_t
 
 
 cdef class Column_idx(Column) :

python/obitools3/dms/column/column_idx.pyx

@@ -2,23 +2,26 @@
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
-from ..view.view cimport View
+from obitools3.dms.view.view cimport View
 
 from obitools3.utils cimport tobytes, \
                              obi_errno_to_exception
 
-from ..capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
+from obitools3.dms.capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
                              obi_get_index_with_elt_idx_and_col_p_in_view, \
                              obi_set_index_with_elt_name_and_col_p_in_view, \
                              obi_set_index_with_elt_idx_and_col_p_in_view, \
                              Obiview_p
 
-from ..capi.obidmscolumn cimport OBIDMS_column_p
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
 
-from ..capi.obitypes     cimport OBI_IDX, OBIIdx_NA, index_t
+from obitools3.dms.capi.obitypes     cimport OBI_IDX, OBIIdx_NA, index_t
 
 from cpython.long cimport PyLong_FromLongLong
 
+from obitools3.dms.column.column cimport Column, \
+                     Column_multi_elts
+
 
 # TODO overwrite other functions from Column and Column_multi_elts
 

python/obitools3/utils.pxd

@@ -1,4 +1,4 @@
-#cython: language_level=3
+# cython: language_level=3
 
 from obitools3.dms.capi.obitypes cimport obitype_t, index_t
 

python/obitools3/utils.pyx

@@ -1,4 +1,5 @@
-#cython: language_level=3
+# cython: language_level=3
+# distutils: include_dirs = src
 
 from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
                                          OBI_VOID, \