Cython API: compiling but not working

python/obitools3/commands/uniq.pyx

@@ -1,96 +0,0 @@
-from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
-from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection    # TODO cimport doesn't work
-
-from functools import reduce
-import time
-
-__title__="Grep view lines that match the given predicates"
-
-
-default_config = {   'inputview'    : None,
-                     'outputview'   : None
-                 }
-
-def addOptions(parser):
-
-    # TODO put this common group somewhere else but I don't know where
-    group=parser.add_argument_group('DMS and view options')
-
-    group.add_argument('--default-dms','-d', 
-                       action="store", dest="obi:defaultdms",
-                       metavar='<DMS NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the default DMS for reading and writing data.")
-
-    group.add_argument('--input-view','-i',
-                       action="store", dest="obi:inputview",
-                       metavar='<INPUT VIEW NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the input view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
-
-    group.add_argument('--output-view','-o',
-                       action="store", dest="obi:outputview",
-                       metavar='<OUTPUT VIEW NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the output view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
-
-
-    group=parser.add_argument_group('obi grep specific options')
-
-    group.add_argument('--predicate','-p',
-                       action="append", dest="grep:predicates",
-                       metavar='<PREDICATE>',
-                       default=None,
-                       type=str,
-                       help="Grep lines that match the given python expression on <line> or <sequence>.")
-
-    
-def run(config):
-    
-    # Open DMS
-    d = OBIDMS(config['obi']['defaultdms'])
-    
-    # Open input view 1
-    iview = d.open_view(config['obi']['inputview'])
-    
-    # Initialize the progress bar
-    pb = ProgressBar(len(iview), config, seconde=5)
-        
-    # Apply filter
-    selection = OBIView_line_selection(iview)
-    for i in range(len(iview)) :
-        pb(i)
-        line = iview[i]
-                
-        loc_env = {'sequence': line, 'line': line}      # TODO add taxonomy
-        
-        good = (reduce(lambda bint x, bint y: x and y,
-                (bool(eval(p, loc_env, line))
-                for p in config['grep']['predicates']), True))
-        
-        if good :
-            selection.append(i)
-         
-    # Create output view with the line selection
-    oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
-
-    #print("\n")
-    #print(repr(oview))
-
-    iview.close()
-    oview.close()
-    d.close()
-    
-    
-    
-
-    
-    
-    
-    
-